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Journal of Medicine and Pharmacy","Tạp chí Y Dược học Cần Thơ",{"EN":487,"VI":488},"\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">04\u002F10\u002F2015 Ministry of Information and Communications allowed Can Tho journal of medicine and pharmacy to operate (102 \u002FGP-BTTTT)\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">07\u002F16\u002F2015 Can Tho journal of medicine and pharmacy is internationally recognized: ISSN 2354-1210\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">In 2016, The journal has been included in the list of medical science journals by The State Council for professorship which is awarded a work score of 0-0.5 points for a published article.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Can Tho Journal of Medicine and Pharmacy welcome original works that haven’t been submitted or published in other medical journals. Posts must contain content related to one of the journal’s categories.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">The content published\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">The journal is divided into 3 categories:\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- Scientific research article: are valuable scientific works, which have been researched and accepted.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- Overview of medicine, biology and pharmacy: serving the objective of continuing training in the fields of medicine, biology and pharmacy; to systematize classical and modern knowledge.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- Update information on new knowledge about medicine, biology, pharmacy in the country and in the world.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Scope\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- Publication and introduction of scientific research in the fields:\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">+ Medicine (internal medicine, surgery, pediatrics, obstetrics and gynecology, odonto-stomatology, laboratory, oncology, traditional medicine, nursing).\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">+ Biology (genetics, biotechnology).\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">+ Pharmacology (pharmaceutics, drug quality analysis-control, synthetic pharmaceutical chemistry, biochemistry, pharmacognosy, botany, clinical pharmacy).\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- To enhance the quality of undergraduate, postgraduate education, scientifically researching and meet the necessary treatment in hospital.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- Introducing the updated domestic and oversea information about science technology to promote scientific research and exchanging technology in local, other universities.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">- Exchanging pharmaceutical and medical information for social health developing in the Mekong Delta and Vietnam.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">The object\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Postgraduate students, student of Can Tho University of Medicine and Pharmacy, scientists from schools, research institutes, hospitals, health centers, pharmaceutical companies of the Mekong Delta; other provinces and regions in Vietnam and other country.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Address\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Headquarters of Can Tho Journal of Medicine and Pharmacy, located Scientific Research and International Cooperation Office: 179 Nguyen Van Cu Street, An Khanh Ward, Ninh Kieu District, Can Tho City, Vietnam.\u003C\u002Fspan>\u003C\u002Fp>","\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Ngày 16\u002F7\u002F2015, Tạp chí Y Dược học Cần Thơ được cấp chỉ số quốc tế: ISSN 2354-1210.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Từ tháng 4\u002F2016, Tạp chí đã được Hội đồng Giáo sư ngành Y đưa vào danh sách các tạp chí khoa học Y học được tính điểm công trình 0-0,5 điểm cho một bài báo đăng.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Năm 2020 Tạp chí Y Dược học Cần Thơ đã được phê duyệt vào danh mục của các Hội đồng Giáo sư ngành Dược học được tính điểm công trình 0-0,5 điểm cho một bài báo đăng.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tạp chí Y Dược học Cần Thơ ra 12 số\u002Fnăm, 180-200 trang\u002Fsố.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Từ tháng 12\u002F2022 Tạp chí Y Dược học Cần Thơ là thành viên của hệ thống Crossref và từ tháng 01\u002F2023 tạp chí thực hiện bình duyệt online kín 2 chiều nhằm tăng tính minh bạch, tin cậy của các công trình nghiên cứu khoa học và đảm bảo tốt nhất chất lượng khoa học của bài viết.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tôn chỉ, mục đích và phạm vi của tạp chí\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tôn chỉ và mục đích hoạt động của tạp chí: xuất bản nhằm mục đích phổ biến kết quả từ các đề tài nghiên cứu khoa học; giao lưu trao đổi khoa học, chia sẻ kinh nghiệm, học tập, đồng thời cập nhật thông tin khoa học mới trong các lĩnh vực y, sinh, dược học trong và ngoài nước.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Phạm vi của tạp chí: Tạp chí xuất bản được chia thành 3 chuyên mục: (i) Bài báo nghiên cứu khoa học là kết quả công trình nghiên cứu khoa học có giá trị đã được triển khai nghiên cứu, (ii) Bài tổng quan y, sinh, dược học: phục vụ mục tiêu đào tạo liên tục trong lĩnh vực y, sinh, dược học; nhằm hệ thống hóa những kiến thức kinh điển và hiện đại; (iii) Thông tin cập nhật kiến thức mới về y, sinh, dược học trong nước và trên thế giới.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Chính sách truy cập mở\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tạp chí Y Dược học Cần Thơ áp dụng chính sách truy cập mở đối với các bài báo đã xuất bản đến với độc giả, nhằm mở rộng cơ hội tiếp cận các kết quả nghiên cứu chất lượng cao và tăng cường trao đổi kiến thức. Tạp chí đăng tải trực tuyến (miễn phí) toàn văn các bài báo được công bố trên website của Tạp chí (https:\u002F\u002Ftapchi.ctump.edu.vn).\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Đạo đức xuất bản\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tạp chí Y Dược học Cần Thơ cam kết tuân thủ đạo đức xuất bản phù hợp với các hướng dẫn và tiêu chuẩn của the Committee on Publication Ethics (COPE), tuân thủ các nguyên tắc của COPE’s Core Practices, Best Practices Guidelines for Journal Editors và Guidelines on Good Publication Practices.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Bản thảo bài báo chỉ được chấp nhận khi được tác giả chịu trách nhiệm chính cam kết các nội dung sau: Các nội dung của bản thảo chưa được đăng tải toàn bộ hoặc một phần ở các tạp chí khác; Tất cả các tác giả đều có đóng góp một cách đáng kể vào quá trình nghiên cứu hoặc chuẩn bị bản thảo và cùng chịu trách nhiệm về các nội dung của bản thảo; Tuân thủ các biện pháp đảm bảo đạo đức nghiên cứu (ví dụ thỏa thuận đồng ý tham gia nghiên cứu).\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Cam kết bảo mật\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tạp chí cam kết thực hiện và tuân thủ các quy định của luật và các văn bản hướng dẫn liên quan đến bảo mật thông tin cá nhân trên không gian mạng. Các thông tin mà người dùng (tác giả, độc giả, biên tập viên, người phản biện) nhập vào các biểu mẫu trên Hệ thống Quản lý xuất bản trực tuyến của tạp chí chỉ được sử dụng vào các mục đích đã được tuyên bố rõ ràng và sẽ không được cung cấp cho bất kỳ bên thứ ba nào khác, hay dùng vào bất kỳ mục đích nào khác.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Phí gửi bài\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Lệ phí gửi đăng bài: 1.000.000đ\u002Fbài báo\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Lệ phí gửi đăng nhanh: 1.500.000đ\u002Fbài báo\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Đối với tác giả là cán bộ viên chức thuộc Trường Đại học Y Dược Cần Thơ thì được hỗ trợ 50% lệ phí gửi đăng bài.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Đối với sinh viên thực hiện đề tài nghiên cứu khoa học cấp trường được hỗ trợ 100% lệ phí đăng bài ( Tác giả gửi đính kèm “ Quyết định về việc giao tổ chức thực hiện đề tài nghiên cứu khoa học cấp Trường của sinh viên”).\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Hình thức nộp lệ phí:\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">1. Tiền mặt:\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Nộp trực tiếp tại Phòng Tài chính - Kế toán, Trường Đại học Y Dược Cần Thơ, số 179 Nguyễn Văn Cừ, P. An Khánh, Q. Ninh Kiều, thành phố Cần Thơ.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">2. Chuyển khoản:\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tên Tài khoản: Trường ĐHYD Cần Thơ, Số TK: 0111000115668, tại ngân hàng Vietcombank chi nhánh Cần Thơ.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Thời gian: Áp dụng từ ngày 01\u002F02\u002F2023.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">* Phí gửi bài không được hoàn trả khi bài viết bị từ chối hoặc tác giả xin rút bài viết.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Quy trình phản biện bài báo\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tạp chí Y Dược học Cần Thơ thực hiện quy trình phản biện kín hai chiều nghiêm ngặt. Danh tính của những người phản biện không được tiết lộ cho các tác giả và ngược lại. Quy trình thẩm định bài báo đăng gồm các bước sau:\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tiếp nhận bản thảo\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Tác giả liên hệ gửi bản thảo đến Tạp chí qua hệ thống trực tuyến tại website: https:\u002F\u002Ftapchi.ctump.edu.vn. Hướng dẫn về cách đăng ký, gửi bài và chuẩn bị bản thảo được cung cấp trên website của Tạp chí.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Sàng lọc sơ bộ\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Sau khi Tòa soạn nhận được bài báo của tác giả, Ban Thư ký sẽ tiến hành kiểm tra sơ bộ bài báo (các yêu cầu về nội dung và hình thức). Những bài báo không đúng quy cách hoặc có nội dung không phù hợp hoặc vi phạm bản quyền sẽ bị từ chối (Ban Thư ký thông báo phản hồi đến tác giả trong vòng 1 tuần). Những bài báo đủ điều kiện, được Ban Thư ký tòa soạn chuyển đến Ban Biên tập có cùng chuyên môn với nội dung bài báo để đề xuất người phản biện. Thời gian kể từ khi Ban Biên tập nhận bài báo đến khi đề xuất người phản biện bài báo chậm nhất là 5 ngày.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Vòng phản biện\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">1. Ban Thư ký gửi bài và yêu cầu phản biện đến 02 phản biện độc lập.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">2. Các phản biện gởi nhận xét cho Ban Thư ký. Thời gian từ khi gửi bài cho phản biện đến khi nhận ý kiến của phản biện tối đa là 20 ngày.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Xử ký kết quả phản biện\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">1. Nếu ý kiến đồng ý cho đăng và không cần chỉnh sửa, Ban Thư ký tiếp tục đăng bài theo qui trình.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">2. Nếu ý kiến đồng ý đăng và cần chỉnh sửa, Ban Thư ký sẽ thông tin đến tác giả chỉnh sửa theo yêu cầu của người phản biện. Thời gian chỉnh sửa và gửi lại kéo dài không quá 2 tuần, từ khi tác giả bài báo nhận được thông tin (Quá trình này có thể lặp lại tối đa 2 lần\u002F1 bài báo). Khi có sự thống nhất, đồng ý của người phản biện; bài báo được tiếp tục đăng theo qui trình.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">3. Những bài báo có chất lượng không đạt yêu cầu, cả 2 phản biện không đồng ý cho đăng sẽ bị Tòa soạn từ chối đăng.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">Xuất bản\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">1. Ban Thư ký tổng hợp các bản thảo đã được tác giả hoàn thiện sau thẩm định trình Ban Biên tập xem xét, Tổng Biên tập phê duyệt, quyết định bài đăng theo các tiêu chí: sự phù hợp nội dung với tôn chỉ và mục đích, thể loại bài viết (ưu tiên các bài có bài có nghiên cứu chuyên sâu, hàm lượng khoa học cao), đóng góp mới bài báo, bài báo được ưu tiên đăng trong số gần nhất của Tạp chí theo thứ tự: tính thời sự, chất lượng bài báo và thời gian gửi bài.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">2. Ban Biên tập và Ban Thư ký biên tập bản thảo, chế bản, đọc rà soát lỗi. Thời gian hoàn thành từ 10-15 ngày.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">3. Ban Thư ký có trách nhiệm thông báo cho tác giả bài báo (bằng e-mail) về tình hình phê duyệt bài báo, thời gian, số kỳ, tập xuất bản bài báo theo qui định.\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>\u003Cp>\u003Cspan style=\"color: rgb(0, 0, 0);\">4. Danh sách bài báo theo số Tạp chí được in ấn và phát hành trong năm định kỳ được công bố chính thức trên website: https:\u002F\u002Ftapchi.ctump.edu.vn\u003C\u002Fspan>\u003C\u002Fp>\u003Cp>\u003Cbr>\u003C\u002Fp>",{"VOID":490},"wcQ1uqwAAAAJ","2023-05-30T08:17:21.868+00:00",[],[494],{"id":495,"createTime":28,"updateTime":28,"relativeEntities":496,"slug":28,"properties":497,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":507,"parentIds":508,"statistic":28},"6413896b-eca9-442b-a73f-182a58a0ce40",[],{"title":498,"address":501,"country":504,"abbreviation":505},{"EN":499,"VI":500},"Can Tho University of Medicine and Pharmacy","Trường Đại học Y Dược Cần Thơ",{"EN":502,"VI":503},"No 179, Nguyen Van Cu street, An Khanh ward, Ninh Kieu district, Can Tho city, Vietnam","Số 179, đường Nguyễn Văn Cừ, phường An Khánh, quận Ninh Kiều, thành phố Cần Thơ, Việt Nam",{"VOID":15},{"VOID":506},"ctump","http:\u002F\u002Fwww.ctump.edu.vn\u002F",[],[],"https:\u002F\u002Ftapchi.ctump.edu.vn\u002Findex.php\u002Fctump",{"impactFactor":32,"impactFactorByYear":512,"i10Index":32,"i10IndexLast5Year":32,"totalPublication":514,"totalPublicationByYear":515,"totalCitation":520,"totalCitationByYear":521,"totalCitationPerPublication":108,"totalCitationPerPublicationByYear":523,"hindexLast5Year":45,"hindex":45},{"2022":513,"2023":111,"2024":106},0.01,1556,{"2020":47,"2021":516,"2022":517,"2023":518,"2024":519,"2025":122},57,306,801,358,161,{"2021":146,"2022":280,"2023":522},99,{"2021":524,"2022":318,"2023":104},0.23,{"impactFactor":28,"impactFactorByYear":28,"i10Index":123,"i10IndexLast5Year":123,"totalPublication":526,"totalPublicationByYear":527,"totalCitation":526,"totalCitationByYear":528,"totalCitationPerPublication":40,"totalCitationPerPublicationByYear":531,"hindexLast5Year":49,"hindex":49},476,{"0":205,"2019":123,"2021":139,"2022":459,"2023":451,"2024":357,"2025":49,"2026":48},{"2021":42,"2022":123,"2023":161,"2024":529,"2025":360,"2026":530},136,83,{"2021":105,"2022":513,"2023":532,"2024":127,"2025":533,"2026":534},0.62,25.43,13.83,{"id":536,"createTime":537,"updateTime":382,"relativeEntities":538,"slug":539,"properties":540,"entityType":25,"verifyStatus":26,"verifyTime":28,"verifyNote":28,"languages":552,"translateLanguages":28,"viewCount":133,"subjectFields":553,"manageAffiliations":554,"indexDatabases":555,"url":556,"thumbnailPath":557,"statistic":558,"gsStatistic":594,"type":55,"analyzePriority":28},"6984a56a-db70-403b-9cc4-4013e1ceaffa","2023-05-09T06:47:40.346+00:00",[],"T%E1%BA%A1p%20ch%C3%AD%20Nghi%C3%AAn%20c%E1%BB%A9u%20n%C6%B0%E1%BB%9Bc%20ngo%C3%A0i",{"country":541,"issn":542,"title":544,"introduce":547,"gsId":550},{"VOID":15},{"VOID":543},"25252445",{"EN":545,"VI":546},"VNU Journal of Foreign Studies","Tạp chí Nghiên cứu nước ngoài",{"EN":548,"VI":549},"{\"ops\":[{\"insert\":\"\\n\\nThe \\n\"},{\"attributes\":{\"italic\":true},\"insert\":\"VNU Journal of Science\"},{\"insert\":\"\\n was established in 1985 for the publication of national and international research papers in all fields of natural sciences and technology, social sciences and humanities. 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issue: big data analyses in structural and functional genomics",{"VOID":928},"10.1007\u002Fs10969-016-9213-1","PUBLICATION","Auto Verify","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10969-016-9213-1",[933,949],{"id":934,"sortIndex":32,"researcher":28,"roles":935,"affiliations":937,"properties":946,"displayName":948,"givenName":28,"familyName":28},"e9f5701e-feaa-4b2c-a242-9b59b4958cd5",[936],"AUTHOR",[938],{"id":939,"sortIndex":32,"affiliation":940,"properties":28},"327c148e-518d-47d9-9116-2ee8962170b1",{"id":939,"createTime":28,"updateTime":28,"relativeEntities":941,"slug":28,"properties":942,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":945,"statistic":28},[],{"title":943},{"VI":944},"RIKEN Structural Biology Laboratory, Yokohama, Japan",[],{"title":947},{"VI":948},"Shigeyuki Yokoyama",{"id":950,"sortIndex":40,"researcher":28,"roles":951,"affiliations":952,"properties":979,"displayName":981,"givenName":28,"familyName":28},"7e96a4d3-149d-42a1-9e13-0e05a1dca2d9",[936],[953,961,970],{"id":954,"sortIndex":32,"affiliation":955,"properties":28},"715c5724-2021-4397-98d7-68a5174f12c1",{"id":954,"createTime":28,"updateTime":28,"relativeEntities":956,"slug":28,"properties":957,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":960,"statistic":28},[],{"title":958},{"VI":959},"Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan",[],{"id":962,"sortIndex":40,"affiliation":963,"properties":969},"57a5d7b0-c21e-47cf-b902-472276581f86",{"id":962,"createTime":28,"updateTime":28,"relativeEntities":964,"slug":28,"properties":965,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":968,"statistic":28},[],{"title":966},{"VI":967},"Center for Informational Biology, Ochanomizu University, Tokyo, Japan",[],{},{"id":971,"sortIndex":123,"affiliation":972,"properties":978},"710f1854-5245-4f1b-845b-686fb5415ce5",{"id":971,"createTime":28,"updateTime":28,"relativeEntities":973,"slug":28,"properties":974,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":977,"statistic":28},[],{"title":975},{"VI":976},"National Institute of Genetics, Shizuoka, Japan",[],{},{"title":980},{"VI":981},"Kei Yura","ARTICLE",{"url":931,"publisher":984,"properties":1004},{"id":868,"createTime":869,"updateTime":870,"relativeEntities":985,"slug":872,"properties":986,"entityType":25,"verifyStatus":880,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":32,"subjectFields":990,"manageAffiliations":991,"indexDatabases":992,"url":894,"thumbnailPath":28,"statistic":999,"gsStatistic":28,"type":55,"analyzePriority":28},[],{"issn":987,"title":988,"eissn":989},{"VOID":875},{"EN":877},{"VOID":879},[],[],[993],{"id":885,"indexDatabase":994,"url":891,"indexYears":892,"academicFieldIds":28,"indexDatabaseRanking":893},{"id":775,"createTime":28,"updateTime":28,"relativeEntities":995,"label":996,"description":997,"key":781,"publicationTags":998,"standard":28},[],{"EN":778,"VI":778},{"EN":778,"VI":780},[783],{"impactFactor":32,"impactFactorByYear":1000,"i10Index":128,"i10IndexLast5Year":32,"totalPublication":897,"totalPublicationByYear":1001,"totalCitation":899,"totalCitationByYear":1002,"totalCitationPerPublication":903,"totalCitationPerPublicationByYear":1003,"hindexLast5Year":323,"hindex":323},{"2012":423,"2013":40,"2014":110,"2015":108,"2016":116,"2017":524,"2018":108},{"2000":42,"2002":49,"2003":147,"2004":199,"2005":132,"2006":145,"2007":129,"2008":205,"2009":323,"2010":135,"2011":51,"2012":51,"2013":146,"2014":127,"2015":48,"2016":49,"2017":42},{"2004":564,"2005":901,"2007":564,"2008":47,"2009":324,"2010":161,"2011":902,"2012":134,"2013":128,"2014":323,"2015":134,"2016":45},{"2004":905,"2005":906,"2007":907,"2008":288,"2009":908,"2010":909,"2011":910,"2012":166,"2013":911,"2014":912,"2015":913,"2016":424},{"pages":1005,"volume":1007},{"VOID":1006},"67-67",{"VOID":1008},"17","2017-01-06",2017,[],false,{"id":1014,"createTime":1015,"updateTime":1016,"relativeEntities":1017,"slug":1018,"properties":1019,"entityType":929,"verifyStatus":26,"verifyTime":1016,"verifyNote":930,"languages":28,"translateLanguages":28,"viewCount":32,"primaryUrl":1028,"fullTextUrl":28,"authors":1029,"publicationType":982,"publisherRelationship":1073,"citationCount":28,"citationInfo":28,"publishDate":1099,"publishYear":1100,"citationAnalyzeStatus":880,"lastCitationAnalyze":28,"indexDatabases":1101,"openAccess":28,"references":28,"isForceReanalyzing":1012},"04116aaa-94fe-4614-b46a-3052ae9401b6","2024-01-17T05:03:52.613+00:00","2025-02-25T13:55:07.996+00:00",[],"Multi-domain-protein-families-and-domain-pairs-comparison-with-known-structures-and-a-random-model-of-domain-recombination",{"abstract":1020,"title":1022,"references":1024,"doi":1026},{"EN":1021},"There is a limited repertoire of domain families in nature that are duplicated and combined in different ways to form the set of proteins in a genome. Most proteins in both prokaryote and eukaryote genomes consist of two or more domains, and we show that the family size distribution of multi-domain protein families follows a power law like that of individual families. Most domain pairs occur in four to six different domain architectures: in isolation and in combinations with different partners. We showed previously that within the set of all pairwise domain combinations, most small and medium-sized families are observed in combination with one or two other families, while a few large families are very versatile and combine with many different partners. Though this may appear to be a stochastic pattern, in which large families have more combination partners by virtue of their size, we establish here that all the domain families with more than three members in genomes are duplicated more frequently than would be expected by chance considering their number of neighbouring domains. This duplication of domain pairs is statistically significant for between one and three quarters of all families with seven or more members. For the majority of pairwise domain combinations, there is no known three-dimensional structure of the two domains together, and we term these novel combinations. Novel domain combinations are interesting and important targets for structural elucidation, as the geometry and interaction between the domains will help understand the function and evolution of multi-domain proteins. Of particular interest are those combinations that occur in the largest number of multi-domain proteins, and several of these frequent novel combinations contain DNA-binding domains. Abbreviations: SCOP: Structural Classification of Proteins database, PDB: Protein DataBank, HMM: hidden Markov model",{"EN":1023},"Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination",{"VOID":1025},"Aloy, P. and Russell, R. B. (2002) Proc. Natl. Acad. Sci. USA., 99, 5896-5901.\nAloy P., Ciccarelli F. D., Leutwein C., Gavin A. C., Superti-Furga, G., Bork, P., Bottcher B. and Russell, R.B. (2002) EMBO Rep., 7, 628-635.\nApic, G., Gough, J. and Teichmann, S.A. (2001) J. Mol. Biol., 310, 311-325.\nBashton, M. and Chothia, C. (2002) J. Mol. Biol., 315, 927-939.\nBerman, H.M., Battistuz, T., Bhat, T.N., Bluhm, W.F., Bourne, P.E., Burkhardt, K., Feng, Z., Gilliland, G.L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J.D. and Zardecki, C. (2002) The protein data bank. Acta Crystallogr. D Biol. Crystallogr., 58, 899-907.\nBlevins, R.A. and Tulinsky, A. (1985) J. Biol. Chem., 260, 4264-4268.\nBlundell, T.L. and Mizuguchi, K. (2000) Prog. Biophys. Mol. Biol., 73, 289-295.\nBrenner, S.E. (2001) Nat. Rev. Genet., 2, 801-809.\nChothia, C. (1992) Nature, 357, 543-544.\nErdös, P. and Rényi, A. (1960) Magyar Tud. Akad. Mat. Kutato Int. Kozl. 5, 17-61.\nGeer, L.Y., Domrachev, M., Lipman D. J., Bryant, S. H. (2002) Genome Res., 12, 1619-1623\nGerstein, M. (1998a). Folding & Design, 3, 497-512.\nGerstein, M. (1998b) Proteins, 33, 518-534.\nGough, J., Karplus, K., Hughey, R. and Chothia, C. (2001) J. Mol. Biol., 313, 903-919.\nGough, J. and Chothia, C. (2002) Nucleic Acids Res., 30, 268-272.\nHegyi, H. and Gerstein, M. (2001) Genome Res., 11, 1632-40.\nJardine, O., Gough, J., Chothia, C. and Teichmann, S.A. (2002) Genome Res., 12, 916-929.\nKarplus, K., Barrett, C. and Hughey, R. (1998) Bioinformatics, 14, 846-56.\nKoonin, E. V., Wolf, Y. I., and Karev, P. (2002) Nature, 420, 218-223.\nLiu, J. and Rost, B. (2001) Protein Sci., 10, 1970-1979.\nLoConte, L., Brenner, S.E., Hubbard, T.J., Chothia, C. and Murzin, A.G. (2002) Nucleic Acids Res., 30, 264-7.\nKuznetsov, V.A., Pickalov, V.V., Senko, O.V. and Knott, G.D. (2002) J. Biol. Systems 10, 381-407.\nMurzin, A., Brenner, S. E., Hubbard, T. and Chothia, C. (1995) J. Mol. Biol., 247, 536-540.\nOrengo, C. A., Jones, D. T. and Thornton, J. M. (1994) Nature, 372, 631-634.\nPonting, C. P. and Russell, R. R. (2002) Annu. Rev. Biophys. Biomol. Struct., 31, 45-71.\nQian, J., Luscombe, N.M. and Gerstein, M. (2001) J. Mol. Biol., 313, 673-681.\nSigler, P. B., Jeffery, B.A., Matthews, B.W. and Blow, D. M. (1966) J. Mol. Biol., 15, 175-192.\nSpahn, C. M., Beckmann, R., Eswar, N., Penczek, P. A., Sali, A., Blobel, G. and Frank, J. (2002) Cell, 107, 373-386.\nTeichmann, S. A., Park, J. and Chothia, C. (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 14658-14663.\nTeichmann, S. A., Chothia, C. and Gerstein, M. (1999) Curr. Op. Struc. Biol., 9, 390-399.\nTeichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J. and Chothia, C. (2001) Trends Biotechnol., 19, 482-486.\nTeichmann, S. A., Rison, S. C., Thornton, J.M., Riley, M., Gough, J. and Chothia, C. (2001) J. Mol. Biol., 311, 693-708.\nWolf, Y. I., Grishin, N. V. and Koonin, E. V. (2000) J. Mol. Biol. 299, 897-905.\nWuchty, S. (2001) Mol. Biol. Evol. 18, 1715-1723.",{"VOID":1027},"10.1023\u002FA:1026113408773","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FA:1026113408773",[1030,1045,1060],{"id":1031,"sortIndex":32,"researcher":28,"roles":1032,"affiliations":1033,"properties":1042,"displayName":1044,"givenName":28,"familyName":28},"9f3074c9-7def-4bdc-997b-1bb4bea60ace",[936],[1034],{"id":1035,"sortIndex":32,"affiliation":1036,"properties":28},"28942e79-89b9-4e48-b062-8225944ac429",{"id":1035,"createTime":28,"updateTime":28,"relativeEntities":1037,"slug":28,"properties":1038,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1041,"statistic":28},[],{"title":1039},{"EN":1040},"MRC Laboratory of Molecular Biology, Cambridge, UK",[],{"title":1043},{"VI":1044},"Gordana Apic",{"id":1046,"sortIndex":40,"researcher":28,"roles":1047,"affiliations":1048,"properties":1057,"displayName":1059,"givenName":28,"familyName":28},"9483c3c7-b096-44b2-b34d-77e2b359d0be",[936],[1049],{"id":1050,"sortIndex":32,"affiliation":1051,"properties":28},"1c6b6a50-0a57-4bd8-893d-5ed14f9cafaa",{"id":1050,"createTime":28,"updateTime":28,"relativeEntities":1052,"slug":28,"properties":1053,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1056,"statistic":28},[],{"title":1054},{"VI":1055},"DKFZ (German Cancer Research Center), Heidelberg, Germany",[],{"title":1058},{"VI":1059},"Wolfgang Huber",{"id":1061,"sortIndex":123,"researcher":28,"roles":1062,"affiliations":1063,"properties":1070,"displayName":1072,"givenName":28,"familyName":28},"ef34292f-c4cf-4d0b-bdc1-7451305a9fe2",[936],[1064],{"id":1035,"sortIndex":32,"affiliation":1065,"properties":28},{"id":1035,"createTime":28,"updateTime":28,"relativeEntities":1066,"slug":28,"properties":1067,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1069,"statistic":28},[],{"title":1068},{"EN":1040},[],{"title":1071},{"VI":1072},"Sarah A. Teichmann",{"url":1028,"publisher":1074,"properties":1094},{"id":868,"createTime":869,"updateTime":870,"relativeEntities":1075,"slug":872,"properties":1076,"entityType":25,"verifyStatus":880,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":32,"subjectFields":1080,"manageAffiliations":1081,"indexDatabases":1082,"url":894,"thumbnailPath":28,"statistic":1089,"gsStatistic":28,"type":55,"analyzePriority":28},[],{"issn":1077,"title":1078,"eissn":1079},{"VOID":875},{"EN":877},{"VOID":879},[],[],[1083],{"id":885,"indexDatabase":1084,"url":891,"indexYears":892,"academicFieldIds":28,"indexDatabaseRanking":893},{"id":775,"createTime":28,"updateTime":28,"relativeEntities":1085,"label":1086,"description":1087,"key":781,"publicationTags":1088,"standard":28},[],{"EN":778,"VI":778},{"EN":778,"VI":780},[783],{"impactFactor":32,"impactFactorByYear":1090,"i10Index":128,"i10IndexLast5Year":32,"totalPublication":897,"totalPublicationByYear":1091,"totalCitation":899,"totalCitationByYear":1092,"totalCitationPerPublication":903,"totalCitationPerPublicationByYear":1093,"hindexLast5Year":323,"hindex":323},{"2012":423,"2013":40,"2014":110,"2015":108,"2016":116,"2017":524,"2018":108},{"2000":42,"2002":49,"2003":147,"2004":199,"2005":132,"2006":145,"2007":129,"2008":205,"2009":323,"2010":135,"2011":51,"2012":51,"2013":146,"2014":127,"2015":48,"2016":49,"2017":42},{"2004":564,"2005":901,"2007":564,"2008":47,"2009":324,"2010":161,"2011":902,"2012":134,"2013":128,"2014":323,"2015":134,"2016":45},{"2004":905,"2005":906,"2007":907,"2008":288,"2009":908,"2010":909,"2011":910,"2012":166,"2013":911,"2014":912,"2015":913,"2016":424},{"pages":1095,"volume":1097},{"VOID":1096},"67-78",{"VOID":1098},"4","2003-06-01",2003,[893],{"id":1103,"createTime":1104,"updateTime":1105,"relativeEntities":1106,"slug":1107,"properties":1108,"entityType":929,"verifyStatus":26,"verifyTime":1105,"verifyNote":930,"languages":28,"translateLanguages":28,"viewCount":32,"primaryUrl":1117,"fullTextUrl":28,"authors":1118,"publicationType":982,"publisherRelationship":1253,"citationCount":28,"citationInfo":28,"publishDate":1279,"publishYear":1280,"citationAnalyzeStatus":880,"lastCitationAnalyze":28,"indexDatabases":1281,"openAccess":28,"references":28,"isForceReanalyzing":1012},"048f2573-9cf1-4086-832f-c0a17d2c75eb","2023-12-25T08:04:28.127+00:00","2024-12-05T15:02:57.913+00:00",[],"Annotation-of-proteins-of-unknown-function-initial-enzyme-results",{"abstract":1109,"title":1111,"references":1113,"doi":1115},{"EN":1110},"Working with a combination of ProMOL (a plugin for PyMOL that searches a library of enzymatic motifs for local structural homologs), BLAST and Pfam (servers that identify global sequence homologs), and Dali (a server that identifies global structural homologs), we have begun the process of assigning functional annotations to the approximately 3,500 structures in the Protein Data Bank that are currently classified as having “unknown function”. Using a limited template library of 388 motifs, over 500 promising in silico matches have been identified by ProMOL, among which 65 exceptionally good matches have been identified. The characteristics of the exceptionally good matches are discussed.",{"EN":1112},"Annotation of proteins of unknown function: initial enzyme results",{"VOID":1114},"Bernstein FC, Koetzle TF, Williams GJB et al (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112:535–542\nBerman HM, Westbrook J, Feng Z et al (2000) The protein data bank. Nucleic Acids Res 28:235–242\nAltschul SF, Madden TL, Schäffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. doi:10.1093\u002Fnar\u002F25.17.3389\nFinn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–W37. doi:10.1093\u002Fnar\u002Fgkr367\nThe Uniprot Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res 36:D190–D195. doi:10.1093\u002Fnar\u002Fgkm895\nSonnhammer EL, Eddy SR, Durbin R (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28:405–420\nFinn RD, Miller BL, Clements J, Bateman A (2014) iPfam: a database of protein family and domain interactions found in the Protein Data Bank. Nucleic Acids Res 42:D364–D373. doi:10.1093\u002Fnar\u002Fgkt1210\nGifford LK, Carter LG, Gabanyi MJ et al (2012) The protein structure initiative structural biology knowledgebase technology portal: a structural biology web resource. J Struct Funct Genomics 13:57–62. doi:10.1007\u002Fs10969-012-9133-7\nHolm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545–W549. doi:10.1093\u002Fnar\u002Fgkq366\nFischer M, Zhang QC, Dey F et al (2011) MarkUs: a server to navigate sequence-structure-function space. Nucleic Acids Res 39:W357–W361. doi:10.1093\u002Fnar\u002Fgkr468\nHanson B, Westin C, Rosa M et al (2014) Estimation of protein function using template-based alignment of enzyme active sites. BMC Bioinformatics 15:87. doi:10.1186\u002F1471-2105-15-87\nDelano WL. The PyMOL molecular graphics system. Schrodinger, LLC., San Carlos, CA, USA\nPorter CT (2004) The catalytic site atlas: a resource of catalytic sites and residues identified in enzymes using structural data. Nucleic Acids Res 32:D129–D133. doi:10.1093\u002Fnar\u002Fgkh028\nBerman HM, Westbrook JD, Gabanyi MJ et al (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res 37:D365–D368. doi:10.1093\u002Fnar\u002Fgkn790\nTorrance JW, Bartlett GJ, Porter CT, Thornton JM (2005) Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. J Mol Biol 347:565–581. doi:10.1016\u002Fj.jmb.2005.01.044\nTrott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31:455–461. doi:10.1002\u002Fjcc.21334\nSeiler CY, Park JG, Sharma A et al (2014) DNASU plasmid and PSI:biology-materials repositories: resources to accelerate biological research. Nucleic Acids Res 42:D1253–D1260. doi:10.1093\u002Fnar\u002Fgkt1060\nCormier C, Park J, Fiacco M et al (2011) PSI:biology-materials repository: a biologist’s resource for protein expression plasmids. J Struct Funct Genomics 12:55–62. doi:10.1007\u002Fs10969-011-9100-8\nCormier C, Mohr S, Zuo D et al (2010) Protein structure initiative material repository: an open shared public resource of structural genomics plasmids for the biological community. Nucleic Acids Res 38:D743–D749. doi:10.1093\u002Fnar\u002Fgkp999\nVedadi M, Lew J, Artz J et al (2005) Genome-scale protein expression and structural biology of Plasmodium falciparum and related Apicomplexan organisms. Mol Biochem Parasitol 151:100–110. doi:10.1016\u002Fj.molbiopara.2006.10.011\nTan K, Rakowski E, Jedrzejczak R, Joachimiak A (2009) The crystal structure of a functionally unknown conserved protein from Enterococcus faecalis V583. doi: 10.2210\u002Fpdb3l1w\u002Fpdb\nMol CD, Kuo C-F, Thayer MM et al (1995) Structure and function of the multifunctional DNA-repair enzyme exonuclease III. Nature 374:381–386. doi:10.1038\u002F374381a0\nKuzin AP, Chen Y, Seetharaman J et al (2006) X-Ray structure of the hypothetical protein YXIM_BACsu from Bacillus subtilis. doi: 10.2210\u002Fpdb2o14\u002Fpdb\nHo YS, Sheffield PJ, Masuyama J et al (1999) Probing the substrate specificity of the intracellular brain platelet-activating factor acetylhydrolase. Protein Eng 12:693–700\nBurkhard P, Taylor P, Walkinshaw MD (2000) X-ray structures of small ligand-FKBP complexes provide an estimate for hydrophobic interaction energies. J Mol Biol 295:953–962. doi:10.1006\u002Fjmbi.1999.3411\nPatel S, Albert A, Blundell TL (2001) Hal2p: Ion selectivity and implications on inhibition mechanism. doi: 10.2210\u002Fpdb1k9z\u002Fpdb\nMursula AM, Hiltunen JK, Wierenga RK (2003) Structural studies on delta(3)-delta(2)-enoyl-CoA isomerase: the variable mode of assembly of the trimeric disks of the crotonase superfamily. FEBS Lett 557:81–87. doi:10.1016\u002FS0014-5793(03)01450-9\nJoint Center for Structural Genomics (JCSG) (2012) Crystal structure of a hypothetical protein (BACUNI_01323) from Bacteroides uniformis ATCC 8492 at 2.32 A resolution. doi: 10.2210\u002Fpdb4ghb\u002Fpdb\nSundaresan V, Yamaguchi M, Chartron J, Stout CD (2003) Conformational change in the NADP(H) binding domain of transhydrogenase defines four states. Biochemistry 42:12143–12153. doi:10.1021\u002Fbi035006q\nKim Y, Skarina T, Beasley S et al (2001) Crystal structure of Escherichia coli EC1530, a glyoxylate induced protein YgbM. Proteins 48:427–430. doi:10.1002\u002Fprot.10160\nSchmitt E, Mechulam Y, Fromant M et al (1997) Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase. EMBO J 16:4760–4769. doi:10.1093\u002Femboj\u002F16.15.4760\nInoue M, Kigawa T, Yokoyama S (2002) Solution structure of the cullin-3 homologue. doi: 10.2210\u002Fpdb1iuy\u002Fpdb\nVan Pouderoyen G, Snijder HJ, Benen JA, Dijkstra BW (2002) Structural insights into the processivity of endopolygalacturonase I from Aspergillus niger. FEBS Lett 554:462–466. doi:10.1016\u002FS0014-5793(03)01221-3\nChristen B, Hornemann S, Damberger FF, Wüthrich K (2009) Prion protein NMR structure from tammar wallaby (Macropus eugenii) shows that the beta2-alpha2 loop is modulated by long-range sequence effects. J Mol Biol 389:833–845. doi:10.1016\u002Fj.jmb.2009.04.040\nTeplyakov A, Obmolova G, Badet-Denisot MA et al (1997) Involvement of the C terminus in intramolecular nitrogen channeling in glucosamine 6-phosphate synthase: evidence from a 1.6 A crystal structure of the isomerase domain. Structure 6:1047–1055. doi:10.1016\u002FS0969-2126(98)00105-1\nZahn R, Liu A, Luhrs T et al (1999) NMR solution structure of the human prion protein. Proc Natl Acad Sci 97:145–null. doi: 10.1073\u002FPNAS.97.1.145\nGorman J, Shapiro L (2003) Structural Genomics target NYSGRC-T920 related to A\u002FB hydrolase fold. doi: 10.2210\u002Fpdb1r3d\u002Fpdb\nMin JR, Antoshenko T, Hong W et al (2005) Crystal structure of acetyltransferases domain of human testis-specific chromodomain protein Y 1. doi: 10.2210\u002Fpdb2fbm\u002Fpdb\nNocek B, Borovilos M, Clancy S, Joachimiak A (2006) Crystal structure of hypothetical protein MM_3350 from Methanosarcina mazei Go1. doi: 10.2210\u002Fpdb2i1s\u002Fpdb\nChang C, Chhor G, Cobb G, Joachimiak A (2009) Crystal structure of uncharacterized protein BP1543 from Bordetella pertussis Tohama I. doi: 10.2210\u002Fpdb3kk4\u002Fpdb\nVorobiev S, Scott L, Schauder C et al (2011) PDB ID: 3HFQ Crystal structure of the lp_2219 protein from Lactobacillus plantarum. doi:10.2210\u002Fpdb3hfq\u002Fpdb\nStone CB, Sugiman-Marangos SN, Junop MS, Mahony JB (2011) Crystal Structure of Cpn0803 from C. pneumoniae. doi: 10.2210\u002Fpdb3q9d\u002Fpdb\nJoint Center for Structural Genomics (JCSG) (2012) Crystal structure of a hypothetical protein (lpg1103) from Legionella pneumophila subsp. pneumophila str. Philadelphia 1 at 1.15 A resolution. doi: 10.2210\u002Fpdb4ezi\u002Fpdb\nJiang M, Chen X, Wu X-H et al (2009) Catalytic mechanism of SHCHC synthase in the menaquinone biosynthesis of Escherichia coli: identification and mutational analysis of the active site residues. Biochemistry 48:6921–6931. doi:10.1021\u002Fbi900897h\nHolden HM, Benning MM, Haller T, Gerlt JA (2001) The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters. Acc Chem Res 34:145–157. doi:10.1021\u002Far000053l\nKajander T, Merckel MC, Thompson A et al (2001) The structure of Neurospora crassa 3-carboxy-cis, cis-muconate lactonizing enzyme, a beta propeller cycloisomerase. Structure 10:483–492. doi:10.1016\u002FS0969-2126(02)00744-X\nSievers F, Wilm A, Dineen D et al (2011) Fast, scalable generation of high-quality protein multiple sequence alignments using clustal omega. Mol Syst Biol 7:539. doi:10.1038\u002Fmsb.2011.75\nGoujon M, McWilliam H, Li W et al (2010) A new bioinformatics analysis tools framework at EMBL–EBI. Nucleic Acids Res 38:W695–W699. doi:10.1093\u002Fnar\u002Fgkq313\nKleerebezem M, Boekhorst J, van Kranenburg R et al (2003) Complete genome sequence of Lactobacillus plantarum WCFS1. Proc Natl Acad Sci 100:1990–1995. doi:10.1073\u002Fpnas.0337704100\nThe Gene Ontology Consortium (2013) Gene ontology annotations and resources. Nucleic Acids Res 41:D530–D535. doi:10.1093\u002Fnar\u002Fgks1050\nHunter S, Jones P, Mitchell A et al (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res 40:D306–D312. doi:10.1093\u002Fnar\u002Fgkr948\nLima CD, Kniewel R, Solorzano V, Wu J (2003) Structure of a putative 7-bladed propeller isomerase. doi: 10.2210\u002Fpdb1ri6\u002Fpdb",{"VOID":1116},"10.1007\u002Fs10969-015-9194-5","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10969-015-9194-5",[1119,1134,1147,1160,1173,1186,1199,1212,1225,1240],{"id":1120,"sortIndex":32,"researcher":28,"roles":1121,"affiliations":1122,"properties":1131,"displayName":1133,"givenName":28,"familyName":28},"305364b1-60a9-48a1-b3a0-6a3cb5f7055d",[936],[1123],{"id":1124,"sortIndex":32,"affiliation":1125,"properties":28},"703234ac-a56d-4b8f-95b5-0d8f4bb00c1e",{"id":1124,"createTime":28,"updateTime":28,"relativeEntities":1126,"slug":28,"properties":1127,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1130,"statistic":28},[],{"title":1128},{"VI":1129},"College of Science, RIT, 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As a result, there is a growing need to obtain rapid structural information in a reliable form that is amenable to rational drug design. In this manner, NMR has been expanding and evolving its role in aiding the design process. A variety of NMR methodologies that cover a range of inherent resolution are described in the context of structure-based drug design in the era of structural genomics.",{"EN":1292},"Applications of NMR to structure-based drug design in structural genomics",{"VOID":1294},"Morris, P. E., Jr. and Omura, G. A. (2000) Curr. Pharm. Des. 6, 943–959.\nMaignan, S. and Mikol, V. (2001) Curr. Top. Med. Chem. 1, 161–174.\nCraik, D. J. and Scanlon, M. J. (2000) Annu. Rep. NMR Spectrosc 42, 115–174.\nColacino, J. M., Staschke, K. A. and Laver, W. G. (1999) Antiviral Chem. Chemother. 10, 155–185.\nGubernator, K. and Boehm, H. J. (1998) Methods Princ. Med. Chem 6, 15–36.\nKubinyi, H. (1998) Curr. Opin. Drug Discovery Dev. 1, 4–15.\nMihelich, E. D. and Schevitz, R.W. (1999) Biochim. Biophys. Acta 1441, 223–228.\nSintchak, M. D. and Nimmesgern, E. (2000) Immunopharmacology 47, 163–184.\nBlundell, T. L. (1996) Nature 384, Suppl.), 23–26.\nBabine, R. E. and Bender, S. L. (1997) Chem. Rev. 97, 1359–1472.\nBohacek, R. S., McMartin, C. and Guida, W. C. (1996) Med. Res. Rev. 16, 3–50.\nBurley, S. K. (2000) Nat. Struct. Biol. 7, 932–934.\nMontelione, G. T., Zheng, D., Huang, Y. J., Gunsalus, K. C. and Szyperski, T. (2000) Nat. Struct. Biol. 7, 982–985.\nPrestegard, J. H. (2001) Polym. Prepr. 42, 60.\nLamzin, V. S. and Perrakis, A. (2000) Nat. Struct. Biol. 7, 978–981.\nAbola, E., Kuhn, P., Earnest, T. and Stevens, R. C. (2000) Nat. Struct. Biol. 7, 973–977.\nArmstrong, J. W. (1999) Am. Biotechnol. Lab. 17, 26, 28.\nGonzalez, J. E. and Negulescu, P. A. (1998) Curr. Opin. Biotechnol. 9, 624–631.\nOldenburg, K. R. (1998) Annu. Rep. Med. Chem 33, 301–311.\nFernandes, P. B. (1998) Curr. Opin. Chem. Biol. 2, 597–603.\nKenny, B. A., Bushfield, M., Parry-Smith, D. J., Fogarty, S. and Treherne, J. M. (1998) Prog. Drug Res 51, 245–269.\nSilverman, L., Campbell, R. and Broach, J. R. (1998) Curr. Opin. Chem. Biol. 2, 397–403.\nOakley, A. J. and Wilce, M. C. J. (2000) Clin. Exp. Pharmacol. Physiol. 27, 145–151.\nRoberts, G. C. K. (2000) Drug Discovery Today 5, 230–240.\nShuker, S. B., Hajduk, P. J., Meadows, R. P. and Fesik, S. W. (1996) Science 274, 1531–1534.\nMoore, J. M. (1999) Biopolymers 51, 221–243.\nShapiro, M. J. and Wareing, J. R. (1999) Curr. Opin. Drug Discovery Dev. 2, 396–400.\nMoy, F. J., Haraki, K., Mobilio, D., Walker, G., Powers, R., Tabei, K., Tong, H. and Siegel, M. M. (2001) Anal. Chem. 73, 571–581.\nMoseley, H. N. B. and Montelione, G. T. (1999) Curr. Opin. Struct. Biol. 9, 635–642.\nPervushin, K. (2000) Q. Rev. Biophys. 33, 161–197.\nFowler, C. A., Tian, F., Al-Hashimi, H. M. and Prestegard, J. H. (2000) J. Mol. Biol. 304, 447–460.\nTjandra, N. and Bax, A. (1997) Science 278, 1111–4.\nFejzo, J., Lepre, C. A., Peng, J. W., Bemis, G. W., Ajay, Murcko, M. A. and Moore, J. M. (1999) Chem. Biol. 6, 755–769.\nDunayevskiy, Y. M., Lai, J.-J., Quinn, C., Talley, F. and Vouros, P. (1997) Rapid Commun. Mass Spectrom. 11, 1178–1184.\nSiegel, M. M., Tabei, K., Bebernitz, G. A. and Baum, E. Z. (1998) J. Mass Spectrom. 33, 264–273.\nSiegel, M. M. (2002) Curr. Topics Med. Chem. 2, 13–33.\nBlom, K. F., Larsen, B. S. and McEwen, C. N. (1999) J. Comb. Chem. 1, 82–90.\nPatapoff, T. W., Mrsny, R. J. and Lee, W. A. (1993) Anal. Biochem. 212, 71–8.\nSanchez, R., Pieper, U., Melo, F., Eswar, N., Marti-Renom, M. A., Madhusudhan, M. S., Mirkovic, N. and Sali, A. (2000) Nat. Struct. Biol. 7, 986–990.\nSkolnick, J. and Fetrow, J. S. (2000) Trends Biotechnol. 18, 34–39.\nSanchez, R. and Sali, A. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 13597–13602.\nSanchez, R. and Sali, A. (1999) J. Comput. Phys. 151, 388–401.\nChou, J. J., Li, S. and Bax, A. (2000) J. Biomol. NMR 18, 217–227.\nMeiler, J., Peti, W. and Griesinger, C. (2000) J. Biomol. NMR 17, 283–294.\nClore, G. M. and Gronenborn, A. M. (1991) Annu. Rev. Biophys. Biophys. Chem 20, 29–63.\nClore, G. M. and Gronenborn, A. M. (1989) Crit. Rev. Biochem. Mol. Biol. 24, 479–564.\nWishart, D. S. and Sykes, B. D. (1994) Meth. Enzymol 239, 363–92.\nKitchen, D., Hoffman, R. C., Moy, F. J. and Powers, R. (1998) Biochemistry 37, 10581–10588.\nMoy, F. J., Diblasio, E., Wilhelm, J. and Powers, R. (2001) J. Mol. Biol. 310, 219–230.\nClore, G. M. and Gronenborn, A. M. (1991) Science 252, 1390–9.\nLinge, J. P., O'Donoghue, S. I. and Nilges, M. (2001) Meth. Enzymol. 339, 71–90.\nGreenfield, N. J., Huang, Y. J., Palm, T., Swapna, G. V. T., Monleon, D., Montelione, G. T. and Hitchcock-DeGregori, S. E. (2001) J. Mol. Biol. 312, 833–847.\nXu, Y., Jablonsky, M. J., Jackson, P. L., Braun, W. and Krishna, N. R. (2001) J. Magn. Reson. 148, 35–46.\nXu, Y., Wu, J., Gorenstein, D. and Braun, W. (1999) J. Magn. Reson. 136, 76–85.\nBowers, P. M., Strauss, C. E. M. and Baker, D. (2000) J. Biomol. NMR 18, 311–318.\nRohl, C. A. and Baker, D. (2002) J. Am. Chem. Soc. 124, 2723–2729.\nGardner, K. H., Rosen, M. K. and Kay, L. E. (1997) Biochemistry 36, 1389–1401.\nClore, G. M., Starich, M. R., Bewley, C. A., Cai, M. and Kuszewski, J. (1999) J. Am. Chem. Soc. 121, 6513–6514.\nDelaglio, F., Kontaxis, G. and Bax, A. (2000) J. Am. Chem. Soc. 122, 2142–2143.\nAndrec, M., Du, P. and Levy, R. M. (2001) Journal of the American Chemical Society 123, 1222–1229.\nHus, J.-C., Marion, D. and Blackledge, M. (2001) J. Am. Chem. Soc. 123, 1541–1542.\nHuang, X., Moy, F. and Powers, R. (2000) Biochemistry 39, 13365–13375.\nMoy, F. J., Chanda, P. K., Chen, J. M., Cosmi, S., Edris, W., Skotnicki, J. S., Wilhelm, J. and Powers, R. (1999) Biochemistry 38, 7085–7096.\nChen, J. M., Nelson, F. C., Levin, J. I., Mobilio, D., Moy, F. J., Nilakantan, R., Zask, A. and Powers, R. (2000) J. Am. Chem. Soc. 122, 9648–9654.\nMoy, F. J., Chanda, P. K., Chen, J. M., Cosmi, S., Edris, W., Levin, J. I. and Powers, R. (2000) J. Mol. Biol. 302, 671–689.",{"VOID":1296},"10.1023\u002FA:1020445506369","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FA:1020445506369",[1299],{"id":1300,"sortIndex":32,"researcher":28,"roles":1301,"affiliations":1302,"properties":1311,"displayName":1313,"givenName":28,"familyName":28},"089f6390-800b-4396-b89e-803f22dd2f36",[936],[1303],{"id":1304,"sortIndex":32,"affiliation":1305,"properties":28},"a0077fcd-d134-4b8a-a619-ac90df78e060",{"id":1304,"createTime":28,"updateTime":28,"relativeEntities":1306,"slug":28,"properties":1307,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1310,"statistic":28},[],{"title":1308},{"VI":1309},"Department of Biological Chemistry, Wyeth Research, Cambridge, U.S.A",[],{"title":1312},{"VI":1313},"Robert Powers",{"url":1297,"publisher":1315,"properties":1335},{"id":868,"createTime":869,"updateTime":870,"relativeEntities":1316,"slug":872,"properties":1317,"entityType":25,"verifyStatus":880,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":32,"subjectFields":1321,"manageAffiliations":1322,"indexDatabases":1323,"url":894,"thumbnailPath":28,"statistic":1330,"gsStatistic":28,"type":55,"analyzePriority":28},[],{"issn":1318,"title":1319,"eissn":1320},{"VOID":875},{"EN":877},{"VOID":879},[],[],[1324],{"id":885,"indexDatabase":1325,"url":891,"indexYears":892,"academicFieldIds":28,"indexDatabaseRanking":893},{"id":775,"createTime":28,"updateTime":28,"relativeEntities":1326,"label":1327,"description":1328,"key":781,"publicationTags":1329,"standard":28},[],{"EN":778,"VI":778},{"EN":778,"VI":780},[783],{"impactFactor":32,"impactFactorByYear":1331,"i10Index":128,"i10IndexLast5Year":32,"totalPublication":897,"totalPublicationByYear":1332,"totalCitation":899,"totalCitationByYear":1333,"totalCitationPerPublication":903,"totalCitationPerPublicationByYear":1334,"hindexLast5Year":323,"hindex":323},{"2012":423,"2013":40,"2014":110,"2015":108,"2016":116,"2017":524,"2018":108},{"2000":42,"2002":49,"2003":147,"2004":199,"2005":132,"2006":145,"2007":129,"2008":205,"2009":323,"2010":135,"2011":51,"2012":51,"2013":146,"2014":127,"2015":48,"2016":49,"2017":42},{"2004":564,"2005":901,"2007":564,"2008":47,"2009":324,"2010":161,"2011":902,"2012":134,"2013":128,"2014":323,"2015":134,"2016":45},{"2004":905,"2005":906,"2007":907,"2008":288,"2009":908,"2010":909,"2011":910,"2012":166,"2013":911,"2014":912,"2015":913,"2016":424},{"pages":1336,"volume":1338},{"VOID":1337},"113-123",{"VOID":1339},"2","2002-06-01",2002,[893],{"id":1344,"createTime":1345,"updateTime":1346,"relativeEntities":1347,"slug":1348,"properties":1349,"entityType":929,"verifyStatus":26,"verifyTime":1346,"verifyNote":930,"languages":28,"translateLanguages":28,"viewCount":32,"primaryUrl":1358,"fullTextUrl":28,"authors":1359,"publicationType":982,"publisherRelationship":1440,"citationCount":28,"citationInfo":28,"publishDate":1466,"publishYear":1467,"citationAnalyzeStatus":880,"lastCitationAnalyze":28,"indexDatabases":1468,"openAccess":28,"references":28,"isForceReanalyzing":1012},"0978cc6b-e047-4708-873b-3f5aa83154a7","2024-02-07T21:42:07.314+00:00","2024-12-12T12:52:05.317+00:00",[],"Insights-into-the-biology-of-Escherichia-coli-through-structural-proteomics",{"abstract":1350,"title":1352,"references":1354,"doi":1356},{"EN":1351},"Escherichia coli has historically been an important organism for understanding a multitude of biological processes, and represents a model system as we attempt to simulate the workings of living cells. Many E. coli strains are also important human and animal pathogens for which new therapeutic strategies are required. For both reasons, a more complete and comprehensive understanding of the protein structure complement of E. coli is needed at the genome level. Here, we provide examples of insights into the mechanism and function of bacterial proteins that we have gained through the Bacterial Structural Genomics Initiative (BSGI), focused on medium-throughput structure determination of proteins from E. coli. We describe the structural characterization of several enzymes from the histidine biosynthetic pathway, the structures of three pseudouridine synthases, enzymes that synthesize one of the most abundant modified bases in RNA, as well as the combined use of protein structure and focused functional analysis to decipher functions for hypothetical proteins. Together, these results illustrate the power of structural genomics to contribute to a deeper biological understanding of bacterial processes.",{"EN":1353},"Insights into the biology of Escherichia coli through structural proteomics",{"VOID":1355},"Blattner FR, Plunkett G III, loch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode K, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) Science 277:1453–1462\nYamamoto Y, Aiba H, Baba T, Hayashi K, Inada T, Isono K, Itoh T, Kimura S, Kitagawa M, Makino K, Miki T, Mitsuhashi N, Mizobuchi K, Mori H, Nakade S, Nakamura Y, Nashimoto H, Oshima T, Oyama S, Saito N, Sampei G, Satoh Y, Sivasundaram S, Tagami H, Horiuchi T et al (1997) DNA Res 4:91–113\nHayashi K, Morooka N, Yamamoto Y, Fujlita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H and Horiuchi T (2006) Mol Systems Biol (doi: 10.1038\u002Fmsb4100049)\nRiley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett III G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006) Nucleic Acids Res 34:1–9\nKitagawa M, Ara T, Arifuzzaman M, Ioka-Nakamichi T, Inamoto E, Toyonaga H, Mori H (2005) DNA Res 12:291–299\nBaba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL and Mori H (2006) Mol Syst Biol (doi: 10.1038\u002Fmsb4100050)\nOishi Y, Yunomura S, Kawahashi Y, Doi N, Takashima H, Baba T, Mori H, Yanagawa H (2006) Proteomics 6:6433–6436\nArifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitaqawa M, Tomita M, Kanaya S, Wada C, Mori H (2006) Genome Res 16:686–691\nButland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005) Nature 433:531–537\nHuang C, Lin X, Wu L, Zhang D, Liu D, Wang S, Peng X (2006) J Proteome Res 5:3268–3276\nLasserre J-P, Beyne E, Pyndiah S, Lapaillerie D, Claveroi S, Bonneu M (2006) Electrophoresis 27:3306–3321\nStenberg F, Chovanec P, Maslen SL, Robinson CV, Ilag LL, von Heijne G, Daley DO (2005) J Biol Chem 280:34409–34419\nKang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR (2005) J Bacteriol 187:1135–1160\nLee PS, Lee KH (2005) Biotechnol Bioeng 84:801–814\nZaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006) Nature Methods 3:623–628\nCorbin RW, Paliy O, Yang F, Shabanowitz J, Platt M, Lyons CE, Root K, McAuliffe J, Jordan MI, Kustu S, Soupene E, Hunt DF (2003) Proc Natl Acad Sci USA 100:9232–9237\nJohansson C, Samskog J, Sundström L, Wadensten H, Björkesten L, Flensburg J (2006) Proteomics 6:4475–4485\nLopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005) Mol Cell Proteomics 4:1205–1209\nNobeli I, Ponstingl H, Krissinel EB, Thornton JM (2003) J Mol Biol 334:697–719\nIto M, Baba T, Mori H, Mori H (2005) Metabol Eng 7:318–327\nKang Y, Durfee T, Glasner JD, Qiu Y, Frisch D, Winterberg KM, Blattner FR (2004) J Bacteriol 186:4921–4930\nMolloy MP, Herbert BR, Slade MB, Rabilloud T, Nouwens AS, Williams KL, Gooley AA (2000) Eur J Biochem 267:2871–2881\nBrokx SJ, Ellison M, Locke T, Bottorff D, Frost L, Weiner JH (2004) J Bacteriol 186:3254–3258\nGonnet P, Rudd KE, Lisacek F (2004) Proteomics 4:1597–1613\nGerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D’Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási A-L, Oltvai ZN, Osterman AL (2003) J Bacteriol 185:5673–5684\nJoyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesley SA, Palsson BØ, Agarwalla S (2006) J Bacteriol 188:8259–8271\nFrankel G, Phillips AD, Rosenshine I, Dougan G, Kaper JB, Knutton S (1998) Mol Microbiol 30:911–921\nKaper JB, Nataro JP, Mobley HLT (2004) Nature Rev Microbiol 2:123–140\nFlores N, Xiao J, Berry A, Bolivar F, Valle F (1996) Nature Biotechnol 14:620–623\nArakawa K, Yamada Y, Shinoda K, Nakayama Y and Tomita M (2006) BMC Bioinformatics 7:168 (http:\u002F\u002Fwww.biomedcentral.com\u002F1471-2105\u002F7\u002F168)\nBaumbach J, Wittkop T, Rademacher K, Rahmann S, Brinkrolf K, Tauch A (2006) J Biotechnol 129:279–289\nHerrgård MJ, Fong SS, Palsson BØ (2006) PLOS Comput Biol 2:676–686\nIshii N, Robert M, Nakayama Y, Kanai A, Tomita M (2004) J Biotechnol 113:281–294\nKümmel A, Panke S, Heinemann M (2006) Mol Systems Biol (doi: 10.1038\u002Fmsb410004)\nReed JL, Palsson BØ (2004) Genome Res 14:797–1805\nSemsey S, Andersson AMC, Krishna S, Jensen MH, Masse E, Sneppen K (2006) Nucleic Acids Res 34:4960–4967\nSundararaj S, Guo A, Habibi-Nazhad B, Rouani M, Stothard P, Ellison M, Wishart DS (2004) Nucleic Acids Res 32:D293–D295\nWang Q, Chen X, Yang Y, Zhao X (2006) Appl Microbiol Biotechnol 73:887–894\nYura K, Yamaguchi A, Go M (2006) J Struct Funct Genomics (doi: 10.1007\u002Fs10969-006-9010-3)\nPerna NT, Plunkett G 3rd, Burland V, Mau B, Glasner JD, Rose DJ, Mayhew GF, Evans PS, Gregor J, Kirkpatrick HA, Pósfai G, Hackett J, Klink S, Boutin A, Shao Y, Miller L, Grotbeck EJ, Davis NW, Lim A, Dimalantal ET, Potamousis KD, Apodaca J, Anantharaman TS, Lin J, Yen G, Schwartz DC, Welch RA, Blattner FR (2001) Nature 409:529–533\nWelch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR , Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT , Mobley HL, Donnenberg MS, Blattner FR (2002) Proc Natl Acad Sci USA 99:17020–17024\nBerman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne, PE (2000) Nucleic Acids Res 28:235–242\nBrenner M, Ames, BN (1971) In: Vogel HJ (ed) Metabolic regulation. Academic Press, New York, pp 349–387\nWinkler ME (1996) Biosynthesis of histidne. In: Neidhardt FC (eds) Escherichia coli and Salmonella typhimurium: cellular and molecular biology, 2nd edn. American Society for Microbiology Press, Washington, D.C, pp 485–505\nAmes BN, Goldberger RF, Hartman PE, Martin RG, Roth JR (1967) In: Konigsberger VV, Bosch L (eds) Regulation of nucleic acid and protein biosynthesis. Elsevier Publishing Co., Amsterdam, pp 272–287\nBlasi F, Bruni, CB (1981) Curr Top Cell Regul 19:1–45\nMartin RG (1963) J Biol Chem 238:257–268\nSivaraman J, Myers RS, Boju L, Sulea T, Cygler M, Davisson VJ, Schrag JD (2005) Biochemistry 44:10071–10080\nD’Ordine RL, Klem TJ, Davisson VJ (1999) Biochemistry 38:1537–1546\nBrilli M, Fani R (2004) J Mol Evol 58:225–237\nHouston LL, Graham ME (1974) Arch Biochem Biophys 162:513–522\nAllen KN, Dunaway-Mariano D (2004) Trends Biochem Sci 29:495–503\nRangarajan ES, Proteau A, Wagner J, Hung MN, Matte A, Cygler M (2006) J Biol Chem 281:37930–37941\nCollet JF, Stroobant V, Pirard M, Delpierre G, Van Schaftingen E (1998) J Biol Chem 273:14107–14112\nLahiri SD, Zhang G, Dunaway-Mariano D, Allen KN (2003) Science 299:2067–2071\nCharette M, Gray MW (2000) IUBMB Life 49:341–351\nHamma T, Ferré-D’Amaré AR (2006) Chem Biol 13:1125–1135\nOfengand J, Bakin A, Wrzesinski J, Nurse K, Lane BG (1995) Biochem Cell Biol 73:915–924\nOfengand J (2002) FEBS Lett 514:17–25\nBakin A, Kowalak JA, McCloskey JA, Ofengand J (1994) Nucleic Acids Res 22:3681–3684\nOfengand J, Bakin A (1997) J Mol Biol 266:246–268\nTomita K, Ueda T, Watanabe K (1999) Nucleic Acids Res 27:1683–1689\nMeroueh M, Grohar PJ, Qiu J, SantaLucia J Jr, Scaringe SA, Chow CS (2000) Nucleic Acids Res 28:2075–2083\nAuerbach T, Bashan A, Yonath A (1997) Trends Biotechnol 22:570–576\nGustafsson C, Reid R, Greene PJ, Santi DV (1996) Nucl Acids Res 24:3756–3762\nKoonin EV (1996) Nucl Acids Res 24:2411–2415\nKaya Y, Ofengand J (2003) RNA 9:711–721\nRamamurthy V, Swann SL, Paulson JL, Spedaliere CJ, Mueller EG (1999) J Biol Chem 274:22225–22230\nGu X, Liu Y, Santi DV (1999) PNAS 96:14270–14275\nHuang L, Pookanjanatavip M, Gu X, Santi DV (1998) Biochemistry 37:344–351\nHoang C, Ferré-D’Amaré AR (2001) Cell 107:929–939\nMueller EG (2002) Nat Struct Biol 9:320–322\nSpedaliere CJ, Ginter JM, Johnston MV, Mueller EG (2004) J Am Chem Soc 126:12758–12759\nPhannachet K, Elias Y, Huang RH (2005) Biochemistry 44:15488–15494\nFoster PG, Huang L, Santi DV, Stroud RM (2000) Nat Struct Biol 7:23–27\nSivaraman J, Sauvé V, Larocque R, Stura EA, Schrag JD, Cygler M, Matte A (2002) Nat Struct Biol 9:353–358\nMizutani K, Machida Y, Unzai S, park S-Y, Tame JRH (2004) Biochemistry 43:4454–2263\nDel Campo M, Ofengand J, Malhotra A (2004) RNA 10:231–239\nSivaraman J, Iannuzzi P, Cygler M, Matte A (2004) J Mol Biol 335:87–101\nEricsson UB, Nordlund P, Hallberg BM (2004) FEBS Lett 565:59–64\nHoang C, Ferré-D’Amaré AR (2004) RNA 10:1026–1033\nKaya Y, Del Campo M, Ofengand J, Malhotra A (2004) J Biol Chem 279:18107–18110\nHoang C, Chen J, Vizthum CA, Kandel JM, Hamilton CS, Mueller EG, Ferre-D’Amare AR (2006) Mol Cell 17:535–545\nSunita S, Zhenxing H, Swaathi J, Cygler M, Matte A, Sivaraman J (2006) J Mol Biol 359:998–1009\nPan H, Ho JD, Stroud RM, Finer-Moore J (2007) J Mol Biol 367:1459–1470\nManival X, Charron C, Fourmann JB, Godard F, Charpentier B, Branlant C (2006) Nucl Acids Res 34:826–839\nMatte A, Louie GV, Sivaraman J, Cygler M, Burley SK (2005) Acta Cryst F61:350–354\nStaker BL, Korber P, Bardwell JC, Saper MA (2000) EMBO J. 19:749–757\nSankaranarayanan R, Dock-Bregeon AC, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D (1999) Cell 97:371–381\nWrzesinski J, Bakin A, Ofengand J, Lane BG (2000) IUBMB Life 50:33–37\nGutgsell NS, Del Campo M, Raychaudhuri S, Ofengand J (2001) RNA 7:990–998\nRaychaudhuri S, Conrad J, Hall BG, Ofengand J (1998) RNA 4:1407–1417\nOfengand J, Malhorta A, Remme J, Gutgsell NS, Del Campo M, Jean-Charles S et al (2001) Cold Spring Harbor Symp Quant Biol 66:147–159\nGutgsell NS, Deutscher MP, Ofengand J (2005) RNA 11:1141–1152\nDel Campo M, Kaya Y, Ofengand J (2001) RNA 7:1603–1615\nFerre-D’Amare AR (2003) Curr Opin Struct Biol 13:49–55\nPan H, Agarwalla S, Moustakas DT, Finer-Moore J, Stroud RM (2003) Proc Natl Acad Sci USA 100:12648–12653\nPhannachet K, Huang RH (2004) Nucleic Acids Res 32:1422–1429\nHur S, Stroud RM (2007) Mol Cell 26:189–203\nChaudhuri BN, Chan S, Perry LJ, Yeates TO (2004) J Biol Chem 279:24585–24591\nHoang C, Hamilton CS, Mueller EG, Ferré-D’Amaré AR (2005) Prot Sci 14:2201–2206\nAdams MA, Jia Z (2005) J Biol Chem 280:8358–8363\nSciara G, Kendrew SG, Miele AE, Marsh NG, Federici L, Malatesta F, Schimperna G, Savino C, Vallone B (2003) EMBO J 22:205–215\nChatterjee PK, Sternberg NL (1995) Proc Natl Acad Sci USA 92:8950–8954\nHayashi M, Hasegawa K, Oguni Y, Unemoto T (1990) Biochim Biophys Acta 1035:230–236\nWang G, Maier RJ (2004) Infect Immun 72:1391–1396\nAdams MA, Jia Z (2006) J Mol Biol 359:455–465\nLaw D, Kelly J (1995) Infect Immun 63:700–702\nStojiljkovic I, Hantke K (1992) EMBO J 11:4359–4367\nStojiljkovic I, Hantke K (1994) Mol Microbiol 13:719–732\nWyckoff EE, Duncan D, Torres AG, Mills M, Maase K, Payne SM (1998) Mol Microbiol 28:1139–1152\nSuits MD, Pal GP, Nakatsu K, Matte A, Cygler M, Jia Z (2005) Proc Natl Acad Sci USA 102:16955–16960\nPoulos TL (2005) Biochem Biophys Res Commun 338:337–345\nSuits MD, Jaffer N, Jia Z (2006) J Biol Chem 281:36776–36782",{"VOID":1357},"10.1007\u002Fs10969-007-9019-2","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10969-007-9019-2",[1360,1375,1390,1405,1418],{"id":1361,"sortIndex":32,"researcher":28,"roles":1362,"affiliations":1363,"properties":1372,"displayName":1374,"givenName":28,"familyName":28},"dfcfd306-2f76-4ee2-91d7-a4eaf5b2f7ee",[936],[1364],{"id":1365,"sortIndex":32,"affiliation":1366,"properties":28},"25bab94d-0d9e-4f7d-9003-fdb2b02e4a68",{"id":1365,"createTime":28,"updateTime":28,"relativeEntities":1367,"slug":28,"properties":1368,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1371,"statistic":28},[],{"title":1369},{"VI":1370},"Biotechnology Research Institute, National Research Council Canada, Montreal, Canada",[],{"title":1373},{"VI":1374},"Allan Matte",{"id":1376,"sortIndex":40,"researcher":28,"roles":1377,"affiliations":1378,"properties":1387,"displayName":1389,"givenName":28,"familyName":28},"2a13e61c-5069-4e72-9dc9-25e18eb9f77f",[936],[1379],{"id":1380,"sortIndex":32,"affiliation":1381,"properties":28},"ba787c28-ff9e-4240-ab4e-12b4ba4ca41e",{"id":1380,"createTime":28,"updateTime":28,"relativeEntities":1382,"slug":28,"properties":1383,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1386,"statistic":28},[],{"title":1384},{"VI":1385},"Department of Biochemistry, Queen's University, Kingston, Canada",[],{"title":1388},{"VI":1389},"Zongchao Jia",{"id":1391,"sortIndex":123,"researcher":28,"roles":1392,"affiliations":1393,"properties":1402,"displayName":1404,"givenName":28,"familyName":28},"b5575c2e-3f4b-4bd2-9e81-fd510999257d",[936],[1394],{"id":1395,"sortIndex":32,"affiliation":1396,"properties":28},"1823b41d-0f72-4315-8dc2-5fc3c627f7ba",{"id":1395,"createTime":28,"updateTime":28,"relativeEntities":1397,"slug":28,"properties":1398,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1401,"statistic":28},[],{"title":1399},{"VI":1400},"Department of Biological Sciences, National University of Singapore, Singapore, Singapore",[],{"title":1403},{"VI":1404},"S. Sunita",{"id":1406,"sortIndex":42,"researcher":28,"roles":1407,"affiliations":1408,"properties":1415,"displayName":1417,"givenName":28,"familyName":28},"cc43f83d-1c99-4e84-9916-da61eb5ae8f4",[936],[1409],{"id":1395,"sortIndex":32,"affiliation":1410,"properties":28},{"id":1395,"createTime":28,"updateTime":28,"relativeEntities":1411,"slug":28,"properties":1412,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1414,"statistic":28},[],{"title":1413},{"VI":1400},[],{"title":1416},{"VI":1417},"J. Sivaraman",{"id":1419,"sortIndex":45,"researcher":28,"roles":1420,"affiliations":1421,"properties":1437,"displayName":1439,"givenName":28,"familyName":28},"3217deac-21db-4e03-8125-855e6458d3fd",[936],[1422,1428],{"id":1365,"sortIndex":32,"affiliation":1423,"properties":28},{"id":1365,"createTime":28,"updateTime":28,"relativeEntities":1424,"slug":28,"properties":1425,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1427,"statistic":28},[],{"title":1426},{"VI":1370},[],{"id":1429,"sortIndex":40,"affiliation":1430,"properties":1436},"1808acda-c441-4740-a72a-41ddf3a67623",{"id":1429,"createTime":28,"updateTime":28,"relativeEntities":1431,"slug":28,"properties":1432,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1435,"statistic":28},[],{"title":1433},{"VI":1434},"Department of Biochemistry, McGill University, Montreal, Canada",[],{},{"title":1438},{"VI":1439},"Miroslaw Cygler",{"url":1358,"publisher":1441,"properties":1461},{"id":868,"createTime":869,"updateTime":870,"relativeEntities":1442,"slug":872,"properties":1443,"entityType":25,"verifyStatus":880,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":32,"subjectFields":1447,"manageAffiliations":1448,"indexDatabases":1449,"url":894,"thumbnailPath":28,"statistic":1456,"gsStatistic":28,"type":55,"analyzePriority":28},[],{"issn":1444,"title":1445,"eissn":1446},{"VOID":875},{"EN":877},{"VOID":879},[],[],[1450],{"id":885,"indexDatabase":1451,"url":891,"indexYears":892,"academicFieldIds":28,"indexDatabaseRanking":893},{"id":775,"createTime":28,"updateTime":28,"relativeEntities":1452,"label":1453,"description":1454,"key":781,"publicationTags":1455,"standard":28},[],{"EN":778,"VI":778},{"EN":778,"VI":780},[783],{"impactFactor":32,"impactFactorByYear":1457,"i10Index":128,"i10IndexLast5Year":32,"totalPublication":897,"totalPublicationByYear":1458,"totalCitation":899,"totalCitationByYear":1459,"totalCitationPerPublication":903,"totalCitationPerPublicationByYear":1460,"hindexLast5Year":323,"hindex":323},{"2012":423,"2013":40,"2014":110,"2015":108,"2016":116,"2017":524,"2018":108},{"2000":42,"2002":49,"2003":147,"2004":199,"2005":132,"2006":145,"2007":129,"2008":205,"2009":323,"2010":135,"2011":51,"2012":51,"2013":146,"2014":127,"2015":48,"2016":49,"2017":42},{"2004":564,"2005":901,"2007":564,"2008":47,"2009":324,"2010":161,"2011":902,"2012":134,"2013":128,"2014":323,"2015":134,"2016":45},{"2004":905,"2005":906,"2007":907,"2008":288,"2009":908,"2010":909,"2011":910,"2012":166,"2013":911,"2014":912,"2015":913,"2016":424},{"pages":1462,"volume":1464},{"VOID":1463},"45-55",{"VOID":1465},"8","2007-08-01",2007,[893],{"id":1470,"createTime":1471,"updateTime":1472,"relativeEntities":1473,"slug":1474,"properties":1475,"entityType":929,"verifyStatus":26,"verifyTime":1472,"verifyNote":930,"languages":28,"translateLanguages":28,"viewCount":32,"primaryUrl":1484,"fullTextUrl":28,"authors":1485,"publicationType":982,"publisherRelationship":1668,"citationCount":28,"citationInfo":28,"publishDate":1693,"publishYear":1280,"citationAnalyzeStatus":880,"lastCitationAnalyze":28,"indexDatabases":1694,"openAccess":28,"references":28,"isForceReanalyzing":1012},"09e6bd4a-ed94-4da8-b30a-4f1459859cb3","2024-01-10T09:47:26.858+00:00","2025-02-23T08:25:57.305+00:00",[],"A-SelB-EF-Tu-aIF2%CE%B3-like-protein-from-Methanosarcina-mazei-in-the-GTP-bound-form-binds-cysteinyl-tRNACys",{"abstract":1476,"title":1478,"references":1480,"doi":1482},{"EN":1477},"The putative translation elongation factor Mbar_A0971 from the methanogenic archaeon Methanosarcina barkeri was proposed to be the pyrrolysine-specific paralogue of EF-Tu (“EF-Pyl”). In the present study, the crystal structures of its homologue from Methanosarcina mazei (MM1309) were determined in the GMPPNP-bound, GDP-bound, and apo forms, by the single-wavelength anomalous dispersion phasing method. The three MM1309 structures are quite similar (r.m.s.d. \u003C 0.1 Å). The three domains, corresponding to domains 1, 2, and 3 of EF-Tu\u002FSelB\u002FaIF2γ, are packed against one another to form a closed architecture. The MM1309 structures resemble those of bacterial\u002Farchaeal SelB, bacterial EF-Tu in the GTP-bound form, and archaeal initiation factor aIF2γ, in this order. The GMPPNP and GDP molecules are visible in their co-crystal structures. Isothermal titration calorimetry measurements of MM1309·GTP·Mg2+, MM1309·GDP·Mg2+, and MM1309·GMPPNP·Mg2+ provided dissociation constants of 0.43, 26.2, and 222.2 μM, respectively. Therefore, the affinities of MM1309 for GTP and GDP are similar to those of SelB rather than those of EF-Tu. Furthermore, the switch I and II regions of MM1309 are involved in domain–domain interactions, rather than nucleotide binding. The putative binding pocket for the aminoacyl moiety on MM1309 is too small to accommodate the pyrrolysyl moiety, based on a comparison of the present MM1309 structures with that of the EF-Tu·GMPPNP·aminoacyl-tRNA ternary complex. A hydrolysis protection assay revealed that MM1309 binds cysteinyl (Cys)-tRNACys and protects the aminoacyl bond from non-enzymatic hydrolysis. Therefore, we propose that MM1309 functions as either a guardian protein that protects the Cys moiety from oxidation or an alternative translation factor for Cys-tRNACys.",{"EN":1479},"A SelB\u002FEF-Tu\u002FaIF2γ-like protein from Methanosarcina mazei in the GTP-bound form binds cysteinyl-tRNACys",{"VOID":1481},"Kaziro Y, Itoh H, Kozasa T, Nakafuku M, Satoh T (1991) Structure and function of signal-transducing GTP-binding proteins. Annu Rev Biochem 60:349–400\nWeijland A, Harmark K, Cool RH, Anborgh PH, Parmeggiani A (1992) Elongation factor Tu: a molecular switch in protein biosynthesis. Mol Microbiol 6:683–688\nSprinzl M (1994) Elongation factor Tu: a regulatory GTPase with an integrated effector. Trends Biochem Sci 19:245–250\nClark BF, Nyborg J (1997) The ternary complex of EF-Tu and its role in protein biosynthesis. Curr Opin Struct Biol 7:110–116\nRodnina MV, Wintermeyer W (2001) Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu Rev Biochem 70:415–435\nNilsson J, Nissen P (2005) Elongation factors on the ribosome. Curr Opin Struct Biol 15:349–354\nAsahara H, Uhlenbeck OC (2005) Predicting the binding affinities of misacylated tRNAs for Thermus thermophilus EF-Tu-GTP. Biochemistry 44:11254–11261\nRodnina MV, Fricke R, Wintermeyer W (1994) Transient conformational states of aminoacyl-tRNA during ribosome binding catalyzed by elongation factor Tu. Biochemistry 33:12267–12275\nOhta S, Nakanishi M, Tsuboi M, Arai K, Kaziro Y (1977) Structural fluctuation of the polypeptide-chain elongation factor Tu. A comparison of factors from Escherichia coli and Thermus thermophilus HB8. Eur J Biochem 78:599–608\nKjeldgaard M, Nissen P, Thirup S, Nyborg J (1993) The crystal structure of elongation factor EF-Tu from Thermus aquaticus in the GTP conformation. Structure 1:35–50\nBerchtold H, Reshetnikova L, Reiser CO, Schirmer NK, Sprinzl M, Hilgenfeld R (1993) Crystal structure of active elongation factor Tu reveals major domain rearrangements. Nature 365:126–132\nYatime L, Mechulam Y, Blanquet S, Schmitt E (2006) Structural switch of the gamma subunit in an archaeal aIF2 alpha gamma heterodimer. Structure 14:119–128\nSchmitt E, Panvert M, Lazennec-Schurdevin C, Coureux PD, Perez J, Thompson A, Mechulam Y (2012) Structure of the ternary initiation complex aIF2-GDPNP-methionylated initiator tRNA. Nat Struct Mol Biol 19:450–454\nStolboushkina E, Nikonov S, Zelinskaya N, Arkhipova V, Nikulin A, Garber M, Nikonov O (2013) Crystal structure of the archaeal translation initiation factor 2 in complex with a GTP analogue and Met-tRNAf(Met). J Mol Biol 425:989–998\nCommans S, Böck A (1999) Selenocysteine inserting tRNAs: an overview. FEMS Microbiol Rev 23:335–351\nThanbichler M, Böck A (2001) Functional analysis of prokaryotic SELB proteins. BioFactors 14:53–59\nLeibundgut M, Flick C, Thanbichler M, Böck A, Ban N (2005) Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J 24:11–22\nBerry MJ, Banu L, Harney JW, Larsen PR (1993) Functional characterization of the eukaryotic SECIS elements which direct selenocysteine insertion at UGA codons. EMBO J 12:3315–3322\nSuppmann S, Persson BC, Böck A (1999) Dynamics and efficiency in vivo of UGA-directed selenocysteine insertion at the ribosome. EMBO J 18:2284–2293\nCopeland PR, Driscoll DM (1999) Purification, redox sensitivity, and RNA binding properties of SECIS-binding protein 2, a protein involved in selenoprotein biosynthesis. J Biol Chem 274:25447–25454\nCopeland PR, Fletcher JE, Carlson BA, Hatfield DL, Driscoll DM (2000) A novel RNA binding protein, SBP2, is required for the translation of mammalian selenoprotein mRNAs. EMBO J 19:306–314\nSrinivasan G, James CM, Krzycki JA (2002) Pyrrolysine encoded by UAG in Archaea: charging of a UAG-decoding specialized tRNA. Science 296:1459–1462\nHao B, Gong W, Ferguson TK, James CM, Krzycki JA, Chan MK (2002) A new UAG-encoded residue in the structure of a methanogen methyltransferase. Science 296:1462–1466\nKrzycki JA (2005) The direct genetic encoding of pyrrolysine. Curr Opin Microbiol 8:706–712\nBlight SK, Larue RC, Mahapatra A, Longstaff DG, Chang E, Zhao G, Kang PT, Green-Church KB, Chan MK, Krzycki JA (2004) Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431:333–335\nPolycarpo C, Ambrogelly A, Berube A, Winbush SM, McCloskey JA, Crain PF, Wood JL, Söll D (2004) An aminoacyl-tRNA synthetase that specifically activates pyrrolysine. Proc Nat Acad Sci USA 101:12450–12454\nNamy O, Rousset JP, Napthine S, Brierley I (2004) Reprogrammed genetic decoding in cellular gene expression. Mol Cell 13:157–168\nIbba M, Söll D (2004) Aminoacyl-tRNAs: setting the limits of the genetic code. Genes Dev 18:731–738\nZhang Y, Baranov PV, Atkins JF, Gladyshev VN (2005) Pyrrolysine and selenocysteine use dissimilar decoding strategies. J Biol Chem 280:20740–20751\nLongstaff DG, Blight SK, Zhang L, Green-Church KB, Krzycki JA (2007) In vivo contextual requirements for UAG translation as pyrrolysine. Mol Microbiol 63:229–241\nNissen P, Kjeldgaard M, Thirup S, Polekhina G, Reshetnikova L, Clark BF, Nyborg J (1995) Crystal structure of the ternary complex of Phe-tRNAPhe, EF-Tu, and a GTP analog. Science 270:1464–1472\nAbel K, Yoder MD, Hilgenfeld R, Jurnak F (1996) An alpha to beta conformational switch in EF-Tu. Structure 4:1153–1159\nNissen P, Kjeldgaard M, Thirup S, Nyborg J (1999) The crystal structure of Cys-tRNACys-EF-Tu-GDPNP reveals general and specific features in the ternary complex and in tRNA. Structure 7:143–156\nMorikawa K, la Cour TF, Nyborg J, Rasmussen KM, Miller DL, Clark BF (1978) High resolution X-ray crystallographic analysis of a modified form of the elongation factor Tu: guanosine diphosphate complex. J Mol Biol 125:325–338\nPolekhina G, Thirup S, Kjeldgaard M, Nissen P, Lippmann C, Nyborg J (1996) Helix unwinding in the effector region of elongation factor EF-Tu-GDP. Structure 4:1141–1151\nSong H, Parsons MR, Rowsell S, Leonard G, Phillips SE (1999) Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05-Å resolution. J Mol Biol 285:1245–1256\nSchmitt E, Blanquet S, Mechulam Y (2002) The large subunit of initiation factor aIF2 is a close structural homologue of elongation factors. EMBO J 21:1821–1832\nRoll-Mecak A, Alone P, Cao C, Dever TE, Burley SK (2004) X-ray structure of translation initiation factor eIF2gamma: implications for tRNA and eIF2alpha binding. J Biol Chem 279:10634–10642\nSokabe M, Yao M, Sakai N, Toya S, Tanaka I (2006) Structure of archaeal translational initiation factor 2 betagamma-GDP reveals significant conformational change of the beta-subunit and switch 1 region. Proc Natl Acad Sci USA 103:13016–13021\nYatime L, Mechulam Y, Blanquet S, Schmitt E (2007) Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states. Proc Natl Acad Sci USA 104:18445–18450\nNikonov O, Stolboushkina E, Nikulin A, Hasenöhrl D, Bläsi U, Manstein DJ, Fedorov R, Garber M, Nikonov S (2007) New insights into the interactions of the translation initiation factor 2 from archaea with guanine nucleotides and initiator tRNA. J Mol Biol 373:328–336\nMilburn MV, Tong L, deVos AM, Brünger A, Yamaizumi Z, Nishimura S, Kim SH (1990) Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science 247:939–945\nSprang SR (1997) G protein mechanisms: insights from structural analysis. Annu Rev Biochem 66:639–678\nDeppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Baeumer S, Jacobi C, Brueggemann H, Lienard T, Christmann A, Boemecke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4:453–461\nAtkinson GC, Hauryliuk V, Tenson T (2011) An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea. BMC Evol Biol 11:22\nCollaborative Computational Project (1994) Number 4. Acta Crystallogr. D50:760–763\nDavis IW, Murray LW, Richardson JS, Richardson DC (2004) MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res 32:W615–W619\nHolm L, Kaariainen S, Rosenstrom P, Schenkel A (2008) Searching protein structure databases with DaliLite v. 3. Bioinformatics 24:2780–2781\nKobayashi K, Kikuno I, Kuroha K, Saito K, Ito K, Ishitani R, Inada T, Nureki O (2010) Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex. Proc Natl Acad Sci USA 107:17575–17579\nKobayashi K, Saito K, Ishitani R, Ito K, Nureki O (2012) Structural basis for translation termination by archaeal RF1 and GTP-bound EF1α complex. Nucleic Acids Res 40:9319–9328\nGrøftehauge MK, Therkelsen MØ, Taaning R, Skrydstrup T, Morth JP, Nissen P (2013) Identifying ligand-binding hot spots in proteins using brominated fragments. Acta Crystallogr F69:1060–1065\nParmeggiani A, Krab IM, Watanabe T, Nielsen RC, Dahlberg C, Nyborg J, Nissen P (2006) Enacyloxin IIa pinpoints a binding pocket of elongation factor Tu for development of novel antibiotics. J Biol Chem 281:2893–2900\nHolbrook SR, Kim SH (1989) Molecular model of the G protein alpha subunit based on the crystal structure of the HRAS protein. Proc Natl Acad Sci USA 86:1751–1755\nSaraste M, Sibbald PR, Wittinghofer A (1990) The P-loop-a common motif in ATP- and GTP-binding proteins. Trends Biochem Sci 15:430–434\nLeipe DD, Wolf YI, Koonin EV, Aravind L (2002) Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol 317:41–72\nDaviter T, Wieden HJ, Rodnina MV (2003) Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome. J Mol Biol 332:689–699\nLaalami S, Grentzmann G, Bremaud L, Cenatiempo Y (1996) Messenger RNA translation in prokaryotes: GTPase centers associated with translational factors. Biochimie 78:577–589\nMansilla F, Knudsen CR, Laurberg M, Clark BF (1997) Mutational analysis of Escherichia coli elongation factor Tu in search of a role for the N-terminal region. Protein Eng 10:927–934\nThanbichler M, Böck A, Goody RS (2000) Kinetics of the interaction of translation factor SelB from Escherichia coli with guanosine nucleotides and selenocysteine insertion sequence RNA. J Biol Chem 275:20458–20466\nArai N, Kaziro Y (1975) Mechanism of the ribosome-dependent uncoupled GTPase reaction catalyzed by polypeptide chain elongation factor G. J Biochem 77:439–447\nAgrawal RK, Penczek P, Grassucci RA, Frank J (1998) Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc Natl Acad Sci USA 95:6134–6138\nAgrawal RK, Heagle AB, Penczek P, Grassucci RA, Frank J (1999) EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. Nat Struct Biol 6:643–647\nStark H, Rodnina MV, Wieden HJ, van Heel M, Wintermeyer W (2000) Large-scale movement of elongation factor G and extensive conformational change of the ribosome during translocation. Cell 100:301–309\nValle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, Frank J (2003) Locking and unlocking of ribosomal motions. Cell 114:123–134\nHansson S, Singh R, Gudkov AT, Liljas A, Logan DT (2005) Crystal structure of a mutant elongation factor G trapped with a GTP analogue. FEBS Lett 579:4492–4497\nWilden B, Savelsbergh A, Rodnina MV, Wintermeyer W (2006) Role and timing of GTP binding and hydrolysis during EF-G-dependent tRNA translocation on the ribosome. Proc Natl Acad Sci USA 103:13670–13675\nConnell SR, Takemoto C, Wilson DN, Wang H, Murayama K, Terada T, Shirouzu M, Rost M, Schüler M, Giesebrecht J, Dabrowski M, Mielke T, Fucini P, Yokoyama S, Spahn CM (2007) Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol Cell 25:751–764\nHauryliuk V, Hansson S, Ehrenberg M (2008) Cofactor dependent conformational switching of GTPases. Biophys J 95:1704–1715\nNoble CG, Song H (2008) Structural studies of elongation and release factors. Cell Mol Life Sci 65:1335–1346\nFrolova L, Le Goff X, Zhouravleva G, Davydova E, Philippe M, Kisselev L (1996) Eukaryotic polypeptide chain release factor eRF3 is an eRF1- and ribosome-dependent guanosine triphosphatase. RNA 2:334–341\nKong C, Ito K, Walsh MA, Wada M, Liu Y, Kumar S, Barford D, Nakamura Y, Song H (2004) Crystal structure and functional analysis of the eukaryotic class II release factor eRF3 from S. pombe. Mol Cell 14:233–245\nHauryliuk V, Zavialov A, Kisselev L, Ehrenberg M (2006) Class-1 release factor eRF1 promotes GTP binding by class-2 release factor eRF3. Biochimie 88:747–757\ndes Georges A, Hashem Y, Unbehaun A, Grassucci RA, Taylor D, Hellen CU, Pestova TV, Frank J (2014) Structure of the mammalian ribosomal pre-termination complex associated with eRF1-eRF3-GDPNP. Nucleic Acids Res 42:3409–3418\nZavialov AV, Buckingham RH, Ehrenberg M (2001) A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3. Cell 107:115–124\nGao H, Zhou Z, Rawat U, Huang C, Bouakaz L, Wang C, Cheng Z, Liu Y, Zavialov A, Gursky R, Sanyal S, Ehrenberg M, Frank J, Song H (2007) RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129:929–941\nZhou J, Lancaster L, Trakhanov S, Noller HF (2012) Crystal structure of release factor RF3 trapped in the GTP state on a rotated conformation of the ribosome. RNA 18:230–240\nRoll-Mecak A, Cao C, Dever TE, Burley SK (2000) X-ray structures of the universal translation initiation factor IF2\u002FeIF5B: conformational changes on GDP and GTP binding. Cell 103:781–792\nRoll-Mecak A, Alone P, Cao C, Dever TE, Burley SK (2003) X-ray structure of translation initiation factor eIF2 gamma: implications for tRNA and eIF2alpha binding. J Biol Chem 279:10634–10642\nKuhle B, Ficner R (2014) eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining. EMBO J 33:1177–1191\nPaleskava A, Konevega AL, Rodnina MV (2012) Thermodynamics of the GTP-GDP-operated conformational switch of selenocysteine-specific translation factor SelB. J Biol Chem 287:27906–27912\nHauenstein SI, Perona JJ (2008) Redundant synthesis of cysteinyl-tRNACys in Methanosarcina mazei. J Biol Chem 283:22007–22017\nPingoud A, Urbanke C, Krauss G, Peters F, Maass G (1977) Ternary complex formation between elongation factor Tu, GTP and aminoacyl-tRNA: an equilibrium study. Eur J Biochem 78:403–409\nOtwinowski Z, Minor W (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol 276:307–326\nWeeks CM, Miller R (1999) Optimizing Shake-and-Bake for proteins. Acta Crystallogr. D55:492–500\nTerwilliger TC (2003) SOLVE and RESOLVE: automated structure solution and density modification. Methods Enzymol 374:22–37\nCohen SX, Ben Jelloul M, Long F, Vagin A, Knipscheer P, Lebbink J, Sixma TK, Lamzin VS, Murshudov GN, Perrakis A (2008) ARP\u002FwARP and molecular replacement: the next generation. Acta Crystallogr D64:49–60\nJones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A47:110–119\nEmsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D60:2126–2132\nBrünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Simulated-annealing real-space refinement as a tool in model building. Acta Crystallogr D54:905–921\nMurshudov GN, Skubák P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D67:355–367\nAdams PD, Afonine PV, Bunkóczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung L-W, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D66:213–221\nKrissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D60:2256–2268\nYanagisawa T, Ishii R, Fukunaga R, Kobayashi T, Sakamoto K, Yokoyama S (2008) Crystallographic studies on multiple conformational states of active-site loops in pyrrolysyl-tRNA synthetase. J Mol Biol 378:634–652\nThompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680\nGouet P, Courcelle E, Stuart DI, Metoz F (1999) ESPript: analysis of multiple sequence alignments in PostScript. 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the effort to produce proteins coded by diverse genomes, structural genomics projects often must express genes containing codons that are rare in the production strain. To address this problem, genes expressing tRNAs corresponding to those codons are typically coexpressed from a second plasmid in the host strain, or from genes incorporated into production plasmids. Here we describe the modification of a series of LIC pMCSG vectors currently used in the high-throughput (HTP) production of proteins to include crucial tRNA genes covering rare codons for Arg (AGG\u002FAGA) and Ile (AUA). We also present variants of these new vectors that allow analysis of ligand binding or co-expression of multiple proteins introduced through two independent LIC steps. Additionally, to accommodate the cloning of multiple large proteins, the size of the plasmids was reduced by approximately one kilobase through the removal of non-essential DNA from the base vector. Production of proteins from core vectors of this series validated the desired enhanced capabilities: higher yields of proteins expressed from genes with rare codons occurred in most cases, biotinylated derivatives enabled detailed automated ligand binding analysis, and multiple proteins introduced by dual LIC cloning were expressed successfully and in near balanced stoichiometry, allowing tandem purification of interacting proteins.",{"EN":1748},"New LIC vectors for production of proteins from genes containing rare codons",{"VOID":1750},"Fox BG, Goulding C, Malkowski MG, Stewart L, Deacon A (2008) Nat Methods 5:129–132\nElsliger MA, Deacon AM, Godzik A, Lesley SA, Wooley J, Wuthrich K, Wilson IA (2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66:1137–1142\nGraslund S, Nordlund P, Weigelt J, Hallberg BM, Bray J, Gileadi O, Knapp S, Oppermann U, Arrowsmith C, Hui R, Ming J, dhe-Paganon S, Park HW, Savchenko A, Yee A, Edwards A, Vincentelli R, Cambillau C, Kim R, Kim SH, Rao Z, Shi Y, Terwilliger TC, Kim CY, Hung LW, Waldo GS, Peleg Y, Albeck S, Unger T, Dym O, Prilusky J, Sussman JL, Stevens RC, Lesley SA, Wilson IA, Joachimiak A, Collart F, Dementieva I, Donnelly MI, Eschenfeldt WH, Kim Y, Stols L, Wu R, Zhou M, Burley SK, Emtage JS, Sauder JM, Thompson D, Bain K, Luz J, Gheyi T, Zhang F, Atwell S, Almo SC, Bonanno JB, Fiser A, Swaminathan S, Studier FW, Chance MR, Sali A, Acton TB, Xiao R, Zhao L, Ma LC, Hunt JF, Tong L, Cunningham K, Inouye M, Anderson S, Janjua H, Shastry R, Ho CK, Wang D, Wang H, Jiang M, Montelione GT, Stuart DI, Owens RJ, Daenke S, Schutz A, Heinemann U, Yokoyama S, Bussow K, Gunsalus KC (2008) Nat Methods 5:135–146\nPeti W, Page R, Moy K, O’Neil-Johnson M, Wilson IA, Stevens RC, Wuthrich K (2005) J Struct Funct Genomics 6:259–267\nPrice WN 2nd, Handelman SK, Everett JK, Tong SN, Bracic A, Luff JD, Naumov V, Acton T, Manor P, Xiao R, Rost B, Montelione GT, Hunt JF (2011) Microb Inform Exp 1:6\nXiao R, Anderson S, Aramini J, Belote R, Buchwald WA, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang YJ, Janjua H, Jiang M, Kornhaber GJ, Lee DY, Locke JY, Ma LC, Maglaqui M, Mao L, Mitra S, Patel D, Rossi P, Sahdev S, Sharma S, Shastry R, Swapna GV, Tong SN, Wang D, Wang H, Zhao L, Montelione GT, Acton TB (2010) J Struct Biol 172:21–33\nKerrigan JJ, Xie Q, Ames RS, Lu Q (2011) Protein Expr Purif 75:1–14\nPerrakis A, Romier C (2008) Methods Mol Biol 426:247–256\nScheich C, Kummel D, Soumailakakis D, Heinemann U, Bussow K (2007) Nucleic Acids Res 35:e43\nStols L, Zhou M, Eschenfeldt WH, Millard CS, Abdullah J, Collart FR, Kim Y, Donnelly MI (2007) Protein Expr Purif 53:396–403\nTolia NH, Joshua-Tor L (2006) Nat Methods 3:55–64\nEschenfeldt WH, Maltseva N, Stols L, Donnelly MI, Gu M, Nocek B, Tan K, Kim Y, Joachimiak A (2010) J Struct Funct Genomics 11:31–39\nEschenfeldt WH, Stols L, Millard CS, Joachimiak A, Donnelly MI (2009) Methods Mol Biol 498:105–115\nHassell AM, An G, Bledsoe RK, Bynum JM, Carter HL 3rd, Deng SJ, Gampe RT, Grisard TE, Madauss KP, Nolte RT, Rocque WJ, Wang L, Weaver KL, Williams SP, Wisely GB, Xu R, Shewchuk LM (2007) Acta Crystallogr D Biol Crystallogr 63:72–79\nKim Y, Babnigg G, Jedrzejczak R, Eschenfeldt WH, Li H, Maltseva N, Hatzos-Skintges C, Gu M, Makowska-Grzyska M, Wu R, An H, Chhor G, Joachimiak A (2011) Methods 55:12–28\nMakowska-Grzyska M, Kim Y, Wu R, Wilton R, Gollapalli DR, Wang XK, Zhang R, Jedrzejczak R, Mack JC, Maltseva N, Mulligan R, Binkowski TA, Gornicki P, Kuhn ML, Anderson WF, Hedstrom L, Joachimiak A (2012) Biochemistry 51:6148–6163\nVedadi M, Niesen FH, Allali-Hassani A, Fedorov OY, Finerty PJ Jr, Wasney GA, Yeung R, Arrowsmith C, Ball LJ, Berglund H, Hui R, Marsden BD, Nordlund P, Sundstrom M, Weigelt J, Edwards AM (2006) Proc Natl Acad Sci USA 103:15835–15840\nMorris DP, Roush ED, Thompson JW, Moseley MA, Murphy JW, McMurry JL (2010) Biochemistry 49:6386–6393\nRothbard JB, Zhao X, Sharpe O, Strohman MJ, Kurnellas M, Mellins ED, Robinson WH, Steinman L (2011) J Immunol 186:4263–4268\nStols L, Gu M, Dieckman L, Raffen R, Collart FR, Donnelly MI (2002) Protein Expr Purif 25:8–15\nGodiska R, Mead D, Dhodda V, Wu C, Hochstein R, Karsi A, Usdin K, Entezam A, Ravin N (2010) Nucleic Acids Res 38:e88\nDel Tito BJ Jr, Ward JM, Hodgson J, Gershater CJ, Edwards H, Wysocki LA, Watson FA, Sathe G, Kane JF (1995) J Bacteriol 177:7086–7091\nGarcia OL, Gonzalez B, Menendez A, Sosa AE, Fernandez JR, Santana H, Meneses N (1996) Ann N Y Acad Sci 782:79–86\nActon TB, Gunsalus KC, Xiao R, Ma LC, Aramini J, Baran MC, Chiang YW, Climent T, Cooper B, Denissova NG, Douglas SM, Everett JK, Ho CK, Macapagal D, Rajan PK, Shastry R, Shih LY, Swapna GV, Wilson M, Wu M, Gerstein M, Inouye M, Hunt JF, Montelione GT (2005) Methods Enzymol 394:210–243\nKay BK, Thai S, Volgina VV (2009) Methods Mol Biol 498:185–196\nScholle MD, Collart FR, Kay BK (2004) Protein Expr Purif 37:243–252\nCooper MA (2006) Drug Discov Today 11:1061–1067\nSchmitt H-M, Brecht A, Piehler J, Gauglitz G (1997) Biosens Bioelectron 12:809–816\nGarcia GM, Mar PK, Mullin DA, Walker JR, Prather NE (1986) Cell 45:453–459\nSelzer G, Som T, Itoh T, Tomizawa J (1983) Cell 32:119–129\nBeckett D, Kovaleva E, Schatz PJ (1999) Protein Sci 8:921–929\nBirnboim HC, Doly J (1979) Nucleic Acids Res 7:1513–1523\nKim Y, Dementieva I, Zhou M, Wu R, Lezondra L, Quartey P, Joachimiak G, Korolev O, Li H, Joachimiak A (2004) J Struct Funct Genomics 5:111–118\nKapust RB, Tozser J, Fox JD, Anderson DE, Cherry S, Copeland TD, Waugh DS (2001) Protein Eng 14:993–1000\nNallamsetty S, Kapust RB, Tozser J, Cherry S, Tropea JE, Copeland TD, Waugh DS (2004) Prot Expr Purif 38:108–115\nDonnelly MI, Zhou M, Millard CS, Clancy S, Stols L, Eschenfeldt WH, Collart FR, Joachimiak A (2006) Prot Expr Purif 47:446–454\nBurlingham BT, Widlanski TS (2003) J Chem Education 80:214–218\nKane JF (1995) Curr Opin Biotechnol 6:494–500\nRosenberg AH, Goldman E, Dunn JJ, Studier FW, Zubay G (1993) J Bacteriol 175:716–722\nSpanjaard RA, Chen K, Walker JR, van Duin J (1990) Nucleic Acids Res 18:5031–5036\nNovy R, Drott D, Yaeger K, Mierendorf R (2001) Innovations 12:1\nLee SF, Li YJ, Halperin SA (2009) Microbiology 155:3581–3588\nBrown TA (2010) Gene cloning and DNA analysis: an introduction. Wiley, New York\nLee JY, Janes BK, Passalacqua KD, Pfleger BF, Bergman NH, Liu H, Hakansson K, Somu RV, Aldrich CC, Cendrowski S, Hanna PC, Sherman DH (2007) J Bacteriol 189:1698–1710\nHotta K, Kim CY, Fox DT, Koppisch AT (2010) Microbiology 156:1918–1925\nMiethke M, Marahiel MA (2007) Microbiol Mol Biol Rev 71:413–451",{"VOID":1752},"10.1007\u002Fs10969-013-9163-9","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10969-013-9163-9",[1755,1770,1785,1798,1811,1824],{"id":1756,"sortIndex":32,"researcher":28,"roles":1757,"affiliations":1758,"properties":1767,"displayName":1769,"givenName":28,"familyName":28},"b5a44a36-39e1-45f5-a95d-50e989eb7d5a",[936],[1759],{"id":1760,"sortIndex":32,"affiliation":1761,"properties":28},"ac2c67d9-3446-4123-8fe1-fe6651fb8f21",{"id":1760,"createTime":28,"updateTime":28,"relativeEntities":1762,"slug":28,"properties":1763,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1766,"statistic":28},[],{"title":1764},{"VI":1765},"Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, USA",[],{"title":1768},{"VI":1769},"William H. Eschenfeldt",{"id":1771,"sortIndex":40,"researcher":28,"roles":1772,"affiliations":1773,"properties":1782,"displayName":1784,"givenName":28,"familyName":28},"83adacf5-8cfa-4d1d-8325-717096621bfc",[936],[1774],{"id":1775,"sortIndex":32,"affiliation":1776,"properties":28},"864e37b5-1543-4d68-9d23-4b6fb0080c16",{"id":1775,"createTime":28,"updateTime":28,"relativeEntities":1777,"slug":28,"properties":1778,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1781,"statistic":28},[],{"title":1779},{"VI":1780},"Center for Structural Genomics of Infectious Diseases, Computational Institute, University of Chicago, Chicago, USA",[],{"title":1783},{"VI":1784},"Magdalena Makowska-Grzyska",{"id":1786,"sortIndex":123,"researcher":28,"roles":1787,"affiliations":1788,"properties":1795,"displayName":1797,"givenName":28,"familyName":28},"46096e1b-5713-4139-a7cc-dd23ada2af9c",[936],[1789],{"id":1760,"sortIndex":32,"affiliation":1790,"properties":28},{"id":1760,"createTime":28,"updateTime":28,"relativeEntities":1791,"slug":28,"properties":1792,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1794,"statistic":28},[],{"title":1793},{"VI":1765},[],{"title":1796},{"VI":1797},"Lucy Stols",{"id":1799,"sortIndex":42,"researcher":28,"roles":1800,"affiliations":1801,"properties":1808,"displayName":1810,"givenName":28,"familyName":28},"49780461-8184-40ed-81d5-64461c73048c",[936],[1802],{"id":1760,"sortIndex":32,"affiliation":1803,"properties":28},{"id":1760,"createTime":28,"updateTime":28,"relativeEntities":1804,"slug":28,"properties":1805,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1807,"statistic":28},[],{"title":1806},{"VI":1765},[],{"title":1809},{"VI":1810},"Mark I. Donnelly",{"id":1812,"sortIndex":45,"researcher":28,"roles":1813,"affiliations":1814,"properties":1821,"displayName":1823,"givenName":28,"familyName":28},"57340da2-1fad-4eb1-aeeb-70b6fd1d3145",[936],[1815],{"id":1760,"sortIndex":32,"affiliation":1816,"properties":28},{"id":1760,"createTime":28,"updateTime":28,"relativeEntities":1817,"slug":28,"properties":1818,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1820,"statistic":28},[],{"title":1819},{"VI":1765},[],{"title":1822},{"VI":1823},"Robert Jedrzejczak",{"id":1825,"sortIndex":46,"researcher":28,"roles":1826,"affiliations":1827,"properties":1841,"displayName":1843,"givenName":28,"familyName":28},"7ca809c4-7352-481d-b64f-445c9942ef82",[936],[1828,1834],{"id":1760,"sortIndex":32,"affiliation":1829,"properties":28},{"id":1760,"createTime":28,"updateTime":28,"relativeEntities":1830,"slug":28,"properties":1831,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1833,"statistic":28},[],{"title":1832},{"VI":1765},[],{"id":1775,"sortIndex":40,"affiliation":1835,"properties":1840},{"id":1775,"createTime":28,"updateTime":28,"relativeEntities":1836,"slug":28,"properties":1837,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1839,"statistic":28},[],{"title":1838},{"VI":1780},[],{},{"title":1842},{"VI":1843},"Andrzej Joachimiak",{"url":1753,"publisher":1845,"properties":1865},{"id":868,"createTime":869,"updateTime":870,"relativeEntities":1846,"slug":872,"properties":1847,"entityType":25,"verifyStatus":880,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":32,"subjectFields":1851,"manageAffiliations":1852,"indexDatabases":1853,"url":894,"thumbnailPath":28,"statistic":1860,"gsStatistic":28,"type":55,"analyzePriority":28},[],{"issn":1848,"title":1849,"eissn":1850},{"VOID":875},{"EN":877},{"VOID":879},[],[],[1854],{"id":885,"indexDatabase":1855,"url":891,"indexYears":892,"academicFieldIds":28,"indexDatabaseRanking":893},{"id":775,"createTime":28,"updateTime":28,"relativeEntities":1856,"label":1857,"description":1858,"key":781,"publicationTags":1859,"standard":28},[],{"EN":778,"VI":778},{"EN":778,"VI":780},[783],{"impactFactor":32,"impactFactorByYear":1861,"i10Index":128,"i10IndexLast5Year":32,"totalPublication":897,"totalPublicationByYear":1862,"totalCitation":899,"totalCitationByYear":1863,"totalCitationPerPublication":903,"totalCitationPerPublicationByYear":1864,"hindexLast5Year":323,"hindex":323},{"2012":423,"2013":40,"2014":110,"2015":108,"2016":116,"2017":524,"2018":108},{"2000":42,"2002":49,"2003":147,"2004":199,"2005":132,"2006":145,"2007":129,"2008":205,"2009":323,"2010":135,"2011":51,"2012":51,"2013":146,"2014":127,"2015":48,"2016":49,"2017":42},{"2004":564,"2005":901,"2007":564,"2008":47,"2009":324,"2010":161,"2011":902,"2012":134,"2013":128,"2014":323,"2015":134,"2016":45},{"2004":905,"2005":906,"2007":907,"2008":288,"2009":908,"2010":909,"2011":910,"2012":166,"2013":911,"2014":912,"2015":913,"2016":424},{"pages":1866,"volume":1868},{"VOID":1867},"135-144",{"VOID":1869},"14","2013-09-22",2013,[893],{"id":1874,"createTime":1875,"updateTime":1876,"relativeEntities":1877,"slug":1878,"properties":1879,"entityType":929,"verifyStatus":26,"verifyTime":1876,"verifyNote":930,"languages":28,"translateLanguages":28,"viewCount":32,"primaryUrl":1888,"fullTextUrl":28,"authors":1889,"publicationType":982,"publisherRelationship":1957,"citationCount":28,"citationInfo":28,"publishDate":1982,"publishYear":1983,"citationAnalyzeStatus":880,"lastCitationAnalyze":28,"indexDatabases":1984,"openAccess":28,"references":28,"isForceReanalyzing":1012},"0da93cd1-0f16-4613-97c0-e00e001389b6","2023-12-27T11:25:04.932+00:00","2025-01-08T14:10:48.178+00:00",[],"His-tag-effect-on-solubility-of-human-proteins-produced-in-Escherichia-coli-a-comparison-between-four-expression-vectors",{"abstract":1880,"title":1882,"references":1884,"doi":1886},{"EN":1881},"We have compared four different vectors for expression of proteins with N- or C-terminal hexahistidine (His6) tags in Escherichia coli by testing these on 20 human proteins. We looked at total recombinant protein production levels per gram dry cell weight, solubility of the target proteins, and yield of soluble and total protein when purified by immobilized metal ion affinity purification. It was found that, in general, both N- and C-terminal His6 tags have a noticeable negative effect on protein solubility, but the effect is target protein specific. A solubilizing fusion tag was able to partly counteract this negative effect. Most target proteins could be purified under denaturing conditions and about half of the proteins could be purified under physiological conditions. The highest protein production levels and yield of purified protein were obtained from a construct with a C-terminal His tag. We also observe a large variation in cell growth rate, which we determined to be partly caused by the expression vectors and partly by the targets. This variation was found to be independent of the production level, solubility and tertiary structure content of the target proteins. \n                abbreviations:\n               BSA – bovine serum albumin; DBD – DNA binding domain; DCW – dry cell weight; EDTA – ethylenediaminetetraacetic acid; GFP – green fluorescent protein; IMAC – immobilized metal ion affinity chromatography; IPTG – isopropyl-β-d-thiogalactopyranoside; LB – Luria-Bertani; MES – 2-(N-morpholino) ethane sulfonic acid; OD – optical density; ORF – open reading frame; PCR – polymerase chain reaction; SDS-PAGE – sodium dodecyl sulfate polyacrylamide gel electrophoresis.",{"EN":1883},"His tag effect on solubility of human proteins produced in Escherichia coli: a comparison between four expression vectors",{"VOID":1885},"Andrews, D., Rattenbury, J., Anand, V., Mattatall, N.R. and Hill, B.C. (2004) Protein Expr. Purif. 33, 57–65.\nBell, C.E. and Lewis, M. (2000) Nat. Struct. Biol. 7, 209–214.\nBradford, M.M. (1976) Anal. Biochem. 72, 248–254.\nBraun, P., Hu, Y., Shen, B., Halleck, A., Koudinya, M., Harlow, E. and LaBaer, J. (2002) Proc. Natl. Acad. Sci. USA 99, 2654–2659.\nBusso, D., Kim, R. and Kim, S.-H. (2003) J. Biochem. Biophys. Methods 55, 233–240.\nFriedman, A.M., Fischmann, T.O. and Steitz, T.A. (1995) Science 268, 1721–1727.\nFu, D. And Maloney P.C. (1997) J. Biol. Chem. 272, 2129–2135.\nHammarström, M., Hellgren, N., van den Berg, S., Berglund, H. and Härd, T. (2002) Protein Sci. 11, 313–321.\nHamosh, A., Scott., A.F., Amberger, J., Valle, D. and McKusick, V.A. (2000) Hum. Mutat. 15, 57–61.\nHansson, H., Okoh, M.P., Smith, C.I.E., Vihinen, M. and Härd, T. (2001) FEBS Lett. 489, 67–70.\nHuth, J.R., Bewley, C.A., Jackson, B.M., Hinnebusch, A.G., Clore, G.M. and Gronenborn, A.M. (1997) Protein Sci. 6, 2359–2364.\nKapust, R.B. and Waugh, D.S. (1999) Protein Sci. 8, 1668–1674.\nKohli, B.M. and Ostermeier, C. (2003) Protein Expr. Purif. 28, 362–367.\nMohanty, A.K. and Wiener, M.C. (2004) Protein Expr. Purif. 33, 311–325.\nNeri, D., Billeter, M. and Wüthrich, K. (1992) J. Mol. Biol. 223, 743–767.\nNilsson, B., Moks, T., Jansson, B., Abrahmsén, L., Elmblad, A., Holmgren, E., Henrichson, C., Jones, A.T. and Uhlén, M. (1987) Protein Eng. 1, 107–113.\nOxenoid, K., Kim, H.J., Jacob, J., Sönnichsen, F.D. and Sanders, C.R. (2004) J. Am. Chem. Soc. 126, 5048–5049.\nPryor, K.D. and Leiting, B. (1997) Protein Expr. Purif. 10, 309–319.\nRoutzahn, K.M. and Waugh, D.S. (2002) J. Struct. Funct. Genomics 2, 83–92.\nShih, Y.-P., Kung, W.-M., Chen, J.-C., Yeh, C.-H., Wang, A.H.-J. and Wang, T.-F. (2002) Protein Sci. 11, 1724–1719.\nStaunton, D., Owen, J. and Campbell, I. (2003) Acc. Chem. Res. 36, 207–214.\nTabor, S. and Richardson, C.C. (1985) Proc. Natl. Acad. Sci. USA 82, 2074–1078.\nThaw, P., Baxter, N. J., Hounslow, A. M., Price, C., Waltho, J. P. and Craven, C. J. (2001) Nat. Struct. Biol. 8, 701–704.\nWoestenenk, E.A., Hammarström, M., Härd, T. and Berglund, H. (2003) Anal. Biochem. 318, 71–79.\nYee, A., Pardee, K., Christendat, D., Savchenko, A., Edwards, A.M. and Arrowsmith, C. (2003) Acc. Chem. Res. 36, 183–189.\nZhang, G., Gurtu, V. and Kain, S.R. (1996) Biochem. Biophys. Res. Commun. 227, 707–711.",{"VOID":1887},"10.1023\u002FB:jsfg.0000031965.37625.0e","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FB:jsfg.0000031965.37625.0e",[1890,1905,1918,1931,1944],{"id":1891,"sortIndex":32,"researcher":28,"roles":1892,"affiliations":1893,"properties":1902,"displayName":1904,"givenName":28,"familyName":28},"8ba9543c-d278-48e8-82a9-4c9fd9956ea1",[936],[1894],{"id":1895,"sortIndex":32,"affiliation":1896,"properties":28},"aaf4bf5c-54dd-4969-a261-91c52459e69c",{"id":1895,"createTime":28,"updateTime":28,"relativeEntities":1897,"slug":28,"properties":1898,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1901,"statistic":28},[],{"title":1899},{"VI":1900},"Department of Biotechnology, Royal Insitute of Technology (KTH), AlbaNova University Center, Stockholm, Sweden",[],{"title":1903},{"VI":1904},"Esmeralda A. Woestenenk",{"id":1906,"sortIndex":40,"researcher":28,"roles":1907,"affiliations":1908,"properties":1915,"displayName":1917,"givenName":28,"familyName":28},"9991a7f1-543b-4b0b-b591-2dfcff2e8871",[936],[1909],{"id":1895,"sortIndex":32,"affiliation":1910,"properties":28},{"id":1895,"createTime":28,"updateTime":28,"relativeEntities":1911,"slug":28,"properties":1912,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1914,"statistic":28},[],{"title":1913},{"VI":1900},[],{"title":1916},{"VI":1917},"Martin Hammarström",{"id":1919,"sortIndex":123,"researcher":28,"roles":1920,"affiliations":1921,"properties":1928,"displayName":1930,"givenName":28,"familyName":28},"fb2b5676-fe42-4ee1-aa6d-2f8b7ff1d951",[936],[1922],{"id":1895,"sortIndex":32,"affiliation":1923,"properties":28},{"id":1895,"createTime":28,"updateTime":28,"relativeEntities":1924,"slug":28,"properties":1925,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1927,"statistic":28},[],{"title":1926},{"VI":1900},[],{"title":1929},{"VI":1930},"Susanne van den Berg",{"id":1932,"sortIndex":42,"researcher":28,"roles":1933,"affiliations":1934,"properties":1941,"displayName":1943,"givenName":28,"familyName":28},"2095bfce-b67f-40d3-a4b7-0f6b4187efe7",[936],[1935],{"id":1895,"sortIndex":32,"affiliation":1936,"properties":28},{"id":1895,"createTime":28,"updateTime":28,"relativeEntities":1937,"slug":28,"properties":1938,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1940,"statistic":28},[],{"title":1939},{"VI":1900},[],{"title":1942},{"VI":1943},"Torleif Härd",{"id":1945,"sortIndex":45,"researcher":28,"roles":1946,"affiliations":1947,"properties":1954,"displayName":1956,"givenName":28,"familyName":28},"5b7099aa-789c-4d9e-affc-83e597120c63",[936],[1948],{"id":1895,"sortIndex":32,"affiliation":1949,"properties":28},{"id":1895,"createTime":28,"updateTime":28,"relativeEntities":1950,"slug":28,"properties":1951,"entityType":28,"verifyStatus":28,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":28,"url":28,"parentIds":1953,"statistic":28},[],{"title":1952},{"VI":1900},[],{"title":1955},{"VI":1956},"Helena Berglund",{"url":1888,"publisher":1958,"properties":1978},{"id":868,"createTime":869,"updateTime":870,"relativeEntities":1959,"slug":872,"properties":1960,"entityType":25,"verifyStatus":880,"verifyTime":28,"verifyNote":28,"languages":28,"translateLanguages":28,"viewCount":32,"subjectFields":1964,"manageAffiliations":1965,"indexDatabases":1966,"url":894,"thumbnailPath":28,"statistic":1973,"gsStatistic":28,"type":55,"analyzePriority":28},[],{"issn":1961,"title":1962,"eissn":1963},{"VOID":875},{"EN":877},{"VOID":879},[],[],[1967],{"id":885,"indexDatabase":1968,"url":891,"indexYears":892,"academicFieldIds":28,"indexDatabaseRanking":893},{"id":775,"createTime":28,"updateTime":28,"relativeEntities":1969,"label":1970,"description":1971,"key":781,"publicationTags":1972,"standard":28},[],{"EN":778,"VI":778},{"EN":778,"VI":780},[783],{"impactFactor":32,"impactFactorByYear":1974,"i10Index":128,"i10IndexLast5Year":32,"totalPublication":897,"totalPublicationByYear":1975,"totalCitation":899,"totalCitationByYear":1976,"totalCitationPerPublication":903,"totalCitationPerPublicationByYear":1977,"hindexLast5Year":323,"hindex":323},{"2012":423,"2013":40,"2014":110,"2015":108,"2016":116,"2017":524,"2018":108},{"2000":42,"2002":49,"2003":147,"2004":199,"2005":132,"2006":145,"2007":129,"2008":205,"2009":323,"2010":135,"2011":51,"2012":51,"2013":146,"2014":127,"2015":48,"2016":49,"2017":42},{"2004":564,"2005":901,"2007":564,"2008":47,"2009":324,"2010":161,"2011":902,"2012":134,"2013":128,"2014":323,"2015":134,"2016":45},{"2004":905,"2005":906,"2007":907,"2008":288,"2009":908,"2010":909,"2011":910,"2012":166,"2013":911,"2014":912,"2015":913,"2016":424},{"pages":1979,"volume":1981},{"VOID":1980},"217-229",{"VOID":1734},"2004-09-01",2004,[893],{"id":1986,"createTime":1987,"updateTime":1988,"relativeEntities":1989,"slug":1990,"properties":1991,"entityType":929,"verifyStatus":26,"verifyTime":1988,"verifyNote":930,"languages":28,"translateLanguages":28,"viewCount":32,"primaryUrl":2000,"fullTextUrl":28,"authors":2001,"publicationType":982,"publisherRelationship":2126,"citationCount":28,"citationInfo":28,"publishDate":2152,"publishYear":2153,"citationAnalyzeStatus":880,"lastCitationAnalyze":28,"indexDatabases":2154,"openAccess":28,"references":28,"isForceReanalyzing":1012},"0f376898-544c-4f6a-a8cc-b579504a4938","2024-01-08T23:06:11.960+00:00","2025-02-06T09:07:46.949+00:00",[],"Distance-matrix-based-approach-to-protein-structure-prediction",{"abstract":1992,"title":1994,"references":1996,"doi":1998},{"EN":1993},"Much structural information is encoded in the internal distances; a distance matrix-based approach can be used to predict protein structure and dynamics, and for structural refinement. Our approach is based on the square distance matrix D = [r\n                        \n                  ij\n                  2\n                ] containing all square distances between residues in proteins. This distance matrix contains more information than the contact matrix C, that has elements of either 0 or 1 depending on whether the distance r\n                        ij is greater or less than a cutoff value r\n                        cutoff. We have performed spectral decomposition of the distance matrices \n                  \n                    \n                  \n                  $$ {\\mathbf{D}} = \\sum {\\lambda_{k} {\\mathbf{v}}_{k} {\\mathbf{v}}_{k}^{T} } $$\n                , in terms of eigenvalues \n                  \n                    \n                  \n                  $$ \\lambda_{k} $$\n                 and the corresponding eigenvectors \n                  \n                    \n                  \n                  $$ {\\mathbf{v}}_{k} $$\n                 and found that it contains at most five nonzero terms. A dominant eigenvector is proportional to r\n                        2—the square distance of points from the center of mass, with the next three being the principal components of the system of points. By predicting r\n                        2 from the sequence we can approximate a distance matrix of a protein with an expected RMSD value of about 7.3 Å, and by combining it with the prediction of the first principal component we can improve this approximation to 4.0 Å. We can also explain the role of hydrophobic interactions for the protein structure, because r is highly correlated with the hydrophobic profile of the sequence. Moreover, r is highly correlated with several sequence profiles which are useful in protein structure prediction, such as contact number, the residue-wise contact order (RWCO) or mean square fluctuations (i.e. crystallographic temperature factors). We have also shown that the next three components are related to spatial directionality of the secondary structure elements, and they may be also predicted from the sequence, improving overall structure prediction. We have also shown that the large number of available HIV-1 protease structures provides a remarkable sampling of conformations, which can be viewed as direct structural information about the dynamics. After structure matching, we apply principal component analysis (PCA) to obtain the important apparent motions for both bound and unbound structures. There are significant similarities between the first few key motions and the first few low-frequency normal modes calculated from a static representative structure with an elastic network model (ENM) that is based on the contact matrix C (related to D), strongly suggesting that the variations among the observed structures and the corresponding conformational changes are facilitated by the low-frequency, global motions intrinsic to the structure. Similarities are also found when the approach is applied to an NMR ensemble, as well as to atomic molecular dynamics (MD) trajectories. Thus, a sufficiently large number of experimental structures can directly provide important information about protein dynamics, but ENM can also provide a similar sampling of conformations. Finally, we use distance constraints from databases of known protein structures for structure refinement. We use the distributions of distances of various types in known protein structures to obtain the most probable ranges or the mean-force potentials for the distances. We then impose these constraints on structures to be refined or include the mean-force potentials directly in the energy minimization so that more plausible structural models can be built. This approach has been successfully used by us in 2006 in the CASPR structure refinement (\n                  http:\u002F\u002Fpredictioncenter.org\u002FcaspR\n                  \n                ).",{"EN":1995},"Distance matrix-based approach to protein structure prediction",{"VOID":1997},"Pokarowski P, Kloczkowski A, Jernigan RL, Kothari NS, Pokarowska M, Kolinski A (2005) Inferring ideal amino acid interaction forms from statistical protein contact potentials. Proteins: Struct Funct Bioinform 59:49–57. doi:10.1002\u002Fprot.20380\nKawashima S, Kanehisa M (2000) AAindex: amino acid index database. Nucleic Acids Res 28:374. doi:10.1093\u002Fnar\u002F28.1.374\nKawashima S, Pokarowski P, Pokarowska M, Kolinski A, Katayama T, Kanehisa M (2008) AAindex: amino acid index database, progress report 2008. Nucleic Acids Res 36:D202–D205. doi:10.1093\u002Fnar\u002Fgkm998\nPokarowski P, Kloczkowski A, Nowakowski S, Pokarowska M, Jernigan RL, Kolinski A (2007) Ideal amino acid exchange forms for approximating substitution matrices. Proteins: Struct Funct Bioinform 69:379–393. doi:10.1002\u002Fprot.21509\nBastolla U, Porto M, Roman HE, Vendruscolo M (2005) Principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins: Struct Funct Bioinform 58:22–30. doi:10.1002\u002Fprot.20240\nChoi IG, Kwon J, Kim SH (2004) Local feature frequency profile: a method to measure structural similarity in proteins. Proc Natl Acad Sci USA 101:3797–3802. doi:10.1073\u002Fpnas.0308656100\nDomingues FS, Rahnenfuhrer J, Lengauer T (2007) Conformational analysis of alternative protein structures. Bioinformatics 23:3131–3138. doi:10.1093\u002Fbioinformatics\u002Fbtm499\nGodzik A, Skolnick J, Kolinski A (1993) Regularities in interaction patterns of globular-proteins. Protein Eng 6:801–810. doi:10.1093\u002Fprotein\u002F6.8.801\nHeger A, Lappe M, Holm L (2004) Accurate detection of very sparse sequence motifs. J Comput Biol 11:843–857. doi:10.1089\u002Fcmb.2004.11.843\nHolm L, Park J (2000) DaliLite workbench for protein structure comparison. Bioinformatics 16:566–567. doi:10.1093\u002Fbioinformatics\u002F16.6.566\nHuang YM, Bystroff C (2006) Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions. Bioinformatics 22:413–422. doi:10.1093\u002Fbioinformatics\u002Fbti828\nJaroszewski L, Li WZ, Godzik A (2002) In search for more accurate alignments in the twilight zone. Protein Sci 11:1702–1713. doi:10.1110\u002Fps.4820102\nKolodny R, Linial N (2004) Approximate protein structural alignment in polynomial time. Proc Natl Acad Sci USA 101:12201–12206. doi:10.1073\u002Fpnas.0404383101\nMooney SD, Liang MHP, DeConde R, Altman RB (2005) Structural characterization of proteins using residue environments. Proteins: Struct Funct Bioinform 61:741–747. doi:10.1002\u002Fprot.20661\nPazos F, Valencia A (2008) Protein co-evolution, co-adaptation and interactions. EMBO J 27:2648–2655. doi:10.1038\u002Femboj.2008.189\nRodionov MA, Galaktionov SG (1992) Analysis of the 3-dimensional structure of proteins in terms of residue contact matrices. 1. The contact criterion. Mol Biol 26:773–776\nSato T, Yamanishi Y, Kanehisa M, Toh H (2005) The inference of protein–protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21:3482–3489. doi:10.1093\u002Fbioinformatics\u002Fbti564\nSato T, Yamanishi Y, Horimoto K, Kanehisa M, Toh H (2006) Partial correlation coefficient between distance matrices as a new indicator of protein–protein interactions. Bioinformatics 22:2488–2492. doi:10.1093\u002Fbioinformatics\u002Fbtl419\nSchneider TR (2000) Objective comparison of protein structures: error-scaled difference distance matrices. Acta Crystallogr D Biol Crystallogr 56:714–721. doi:10.1107\u002FS0907444900003723\nSnyder DA, Montelione GT (2005) Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. Proteins: Struct Funct Bioinform 59:673–686. doi:10.1002\u002Fprot.20402\nSnyder DA, Bhattacharya A, Huang YPJ, Montelione GT (2005) Assessing precision and accuracy of protein structures derived from NMR data. Proteins: Struct Funct Bioinform 59:655–661. doi:10.1002\u002Fprot.20499\nSzustakowski JD, Weng ZP (2000) Protein structure alignment using a genetic algorithm. Proteins-Structure Funct Genet 38:428–440. doi:10.1002\u002F(SICI)1097-0134(20000301)38:4\u003C428::AID-PROT8>3.0.CO;2-N\nYe JP, Janardan R (2004) Approximate multiple protein structure alignment using the sum-of-pairs distance. J Comput Biol 11:986–1000. doi:10.1089\u002Fcmb.2004.11.986\nZhou XB, Chou J, Wong STC (2006) Protein structure similarity from principle component correlation analysis. BMC Bioinformatics 7:40 (10pp)\nFlory PJ (1976) Statistical thermodynamics of random networks. Proc R Soc Lond A: Math Phys Eng Sci 351:351–380\nKloczkowski A, Mark JE, Erman B (1989) Chain dimensions and fluctuations in random elastomeric networks 1 phantom Gaussian networks in the undeformed state. Macromolecules 22:1423–1432. doi:10.1021\u002Fma00193a070\nBahar I, Atilgan AR, Erman B (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 2:173–181. doi:10.1016\u002FS1359-0278(97)00024-2\nHaliloglu T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins. Phys Rev Lett 79:3090–3093. doi:10.1103\u002FPhysRevLett.79.3090\nTirion MM (1996) Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 77:1905–1908. doi:10.1103\u002FPhysRevLett.77.1905\nKundu S, Melton JS, Sorensen DC, Phillips GN (2002) Dynamics of proteins in crystals: comparison of experiment with simple models. Biophys J 83:723–732. doi:10.1016\u002FS0006-3495(02)75203-X\nSen TZ, Feng YP, Garcia JV, Kloczkowski A, Jernigan RL (2006) The extent of cooperativity of protein motions observed with elastic network models is similar for atomic and coarser-grained models. J Chem Theory Comput 2:696–704. doi:10.1021\u002Fct600060d\nAtilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys J 80:505–515. doi:10.1016\u002FS0006-3495(01)76033-X\nKeskin O, Bahar I, Flatow D, Covell DG, Jernigan RL (2002) Molecular mechanisms of chaperonin GroEL-GroES function. Biochemistry 41:491–501. doi:10.1021\u002Fbi011393x\nKeskin O, Durell SR, Bahar I, Jernigan RL, Covell DG (2002) Relating molecular flexibility to function: a case study of tubulin. Biophys J 83:663–680. doi:10.1016\u002FS0006-3495(02)75199-0\nNavizet I, Lavery R, Jernigan RL (2004) Myosin flexibility: structural domains and collective vibrations. Proteins-Structure Funct Genet 54:384–393. doi:10.1002\u002Fprot.10476\nWang YM, Rader AJ, Bahar I, Jernigan RL (2004) Global ribosome motions revealed with elastic network model. J Struct Biol 147:302–314. doi:10.1016\u002Fj.jsb.2004.01.005\nWang YM, Jernigan RL (2005) Comparison of tRNA motions in the free and ribosomal bound structures. Biophys J 89:3399–3409. doi:10.1529\u002Fbiophysj.105.064840\nYan A, Wang Y, Kloczkowski A, Jernigan RL (2008) Effects of protein subunits removal on the computed motions of partial 30S structures of the ribosome. J Chem Theory Comput 4:1757–1767\nCrippen GM, Havel TF (1978) Stable calculation of coordinates from distance information. Acta Crystallogr A 34:282–284. doi:10.1107\u002FS0567739478000522\nHavel TF, Crippen GM, Kuntz ID (1979) Effects of distance constraints on macromolecular conformation. 2. Simulation of experimental results and theoretical predictions. Biopolymers 18:73–81. doi:10.1002\u002Fbip.1979.360180108\nHavel TF, Kuntz ID, Crippen GM (1983) The combinatorial distance geometry method for the calculation of molecular-conformation. 1. A new approach to an old problem. J Theor Biol 104:359–381. doi:10.1016\u002F0022-5193(83)90112-1\nHavel TF, Crippen GM, Kuntz ID, Blaney JM (1983) The combinatorial distance geometry method for the calculation of molecular-conformation. 2. Sample problems and computational statistics. J Theor Biol 104:383–400. doi:10.1016\u002F0022-5193(83)90113-3\nHavel TF, Kuntz ID, Crippen GM (1983) The theory and practice of distance geometry. Bull Math Biol 45:665–720\nPetsko GA, Frauenfelder H (1980) Crystallographic approaches to the dynamics of ligand-binding to myoglobin. Fed Proc 39:1648\nHalle B (2002) Flexibility and packing in proteins. Proc Natl Acad Sci USA 99:1274–1279. doi:10.1073\u002Fpnas.032522499\nChen P, Wang B, Wong HS, Huang DS (2007) Prediction of protein B-factors using multi-class bounded SVM. Protein Pept Lett 14:185–190. doi:10.2174\u002F092986607779816078\nYang L, Song G, Carriquiry A, Jernigan RL (2008) Close correspondence between the motions from principal component analysis of multiple HIV-1 protease structures and elastic network modes. Structure 16:321–330. doi:10.1016\u002Fj.str.2007.12.011\nSippl MJ (1990) Calculation of conformational ensembles from potentials of mean force—an approach to the knowledge-based prediction of local structures in globular-proteins. J Mol Biol 213:859–883\nSippl MJ (1992) Detection of native-like models for amino-acid-sequences of unknown 3-dimensional structure in a data-base of known protein conformations. Proteins 13:258–271\nSippl MJ (1993) Recognition of errors in 3-dimensional structures of proteins. Proteins-Structure Funct Genet 17:355–362. doi:10.1002\u002Fprot.340170404\nSippl MJ (1995) Knowledge-based potentials for proteins. Curr Opin Struct Biol 5:229–235\nSippl MJ, Scheraga HA (1986) Cayley-Menger coordinates. Proc Natl Acad Sci USA 83:2283–2287. doi:10.1073\u002Fpnas.83.8.2283\nSippl MJ, Scheraga HA (1985) Solution of the embedding problem and decomposition of symmetric-matrices. Proc Natl Acad Sci USA 82:2197–2201. doi:10.1073\u002Fpnas.82.8.2197\nMelo F, Feytmans E (1997) Novel knowledge-based mean force potential at atomic level. J Mol Biol 267:207–222. doi:10.1006\u002Fjmbi.1996.0868\nMelo F, Feytmans E (1998) Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 277:1141–1152. doi:10.1006\u002Fjmbi.1998.1665\nGarbuzynskiy SO, Melnik BS, Lobanov MY, Finkelstein AV, Galzitskaya OV (2005) Comparison of X-ray and NMR structures: is there a systematic difference in residue contacts between X-ray and NMR-resolved protein structures? Proteins: Struct Funct Bioinform 60:139–147. doi:10.1002\u002Fprot.20491\nWu D, Cui F, Jernigan R, Wu ZJ (2007) PIDD: database for protein inter-atomic distance distributions. Nucleic Acids Res 35:D202–D207. doi:10.1093\u002Fnar\u002Fgkl802\nUlrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Wenger RK, Yao HY, Markley JL (2008) BioMagResBank. Nucleic Acids Res 36:D402–D408. doi:10.1093\u002Fnar\u002Fgkm957\nBrunger AT, Adams PD, Clore GM, Delano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921. doi:10.1107\u002FS0907444998003254\nBrunger AT (2007) Version 1.2 of the crystallography and NMR system. Nat Protoc 2:2728–2733. doi:10.1038\u002Fnprot.2007.406\nWu D, Jernigan R, Wu ZJ (2007) Refinement of NMR-determined protein structures with database derived mean-force potentials. Proteins: Struct Funct Bioinform 68:232–242. doi:10.1002\u002Fprot.21358\nBrooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) Charmm—a program for macromolecular energy, minimization, and dynamics calculations. 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