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In order to identify the molecular basis for high‐affinity binding, the structure of free and Tip‐bound Lyn‐SH3 was determined by NMR spectroscopy. Tip forms additional contacts outside its classical proline‐rich recognition motif and, in particular, a strictly conserved leucine (L186) of the C‐terminally adjacent sequence stretch packs into a hydrophobic pocket on the Lyn surface. Although the existence of this pocket is no unique property of Lyn‐SH3, Lyn is the only Src family kinase that contains an additional aromatic residue (H41) in the n‐Src loop as part of this pocket. H41 covers L186 of Tip by forming tight hydrophobic contacts, and model calculations suggest that the increase in binding affinity compared with other SH3 domains can mainly be attributed to these additional interactions. 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alpha-amylases, Biochim Biophys Acta, 65, 200, 10.1016\u002F0006-3002(62)91039-9",{"doi":1353},"10.1016\u002F0006-3002(62)91039-9",{"id":24,"text":1355,"url":24,"identifiers":1356},"Luzzati, 1952, Traitement statistique des erreurs dans la détermination des structures cristallines, Acta Crystallogr, 5, 802, 10.1107\u002FS0365110X52002161",{"doi":1357},"10.1107\u002FS0365110X52002161",{"id":24,"text":1359,"url":24,"identifiers":1360},"MacGregor, 1988, α-Amylase structure and activity, J Protein Chem, 7, 399, 10.1007\u002FBF01024888",{"doi":1361},"10.1007\u002FBF01024888",{"id":24,"text":1363,"url":24,"identifiers":1364},"Minamiura, 1988, Handbook of amylases and related enzymes, 18",{},{"id":24,"text":1366,"url":24,"identifiers":1367},"Nakajima, 1986, Comparison of amino acid sequences of eleven different α-amylases, Appl Microbiol Biotechnol, 23, 355, 10.1007\u002FBF00257032",{"doi":1368},"10.1007\u002FBF00257032",{"id":24,"text":1370,"url":24,"identifiers":1371},"Nakamura, 1984, Sequences of cDNAs for human salivary and pancreatic α-amylases, Gene, 28, 263, 10.1016\u002F0378-1119(84)90265-8",{"doi":1372},"10.1016\u002F0378-1119(84)90265-8",{"id":24,"text":1374,"url":24,"identifiers":1375},"Nishide, 1986, Corrected sequences of cDNAs for human salivary and pancreatic α-amylases, Gene, 50, 371, 10.1016\u002F0378-1119(86)90341-0",{"doi":1376},"10.1016\u002F0378-1119(86)90341-0",{"id":24,"text":1378,"url":24,"identifiers":1379},"Pasero, 1986, Complete amino acid sequence and location of the five disulfide bridges in porcine pancreatic α-amylase, Biochim Biophys Acta, 869, 147, 10.1016\u002F0167-4838(86)90289-X",{"doi":1380},"10.1016\u002F0167-4838(86)90289-X",{"id":24,"text":1382,"url":24,"identifiers":1383},"Qian, 1994, The active center of a mammalian α-amylase. 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Aggregation of rhGCSF first involves the perturbation of its native structure to form a structurally expanded transition state, followed by assembly process to form an irreversible aggregate. The energy barriers of the two steps are reflected in the experimentally measured values of free energy of unfolding \u003Cjats:italic>(\u003C\u002Fjats:italic>Δ\u003Cjats:italic>G\u003Cjats:sub>unf\u003C\u002Fjats:sub>)\u003C\u002Fjats:italic> and osmotic second virial coefficient (\u003Cjats:italic>B\u003Cjats:sub>22\u003C\u002Fjats:sub>\u003C\u002Fjats:italic>), respectively. Under solution conditions where rhGCSF conformational stability dominates (i.e., large Δ\u003Cjats:italic>G\u003Cjats:sub>unf\u003C\u002Fjats:sub>\u003C\u002Fjats:italic> and negative \u003Cjats:italic>B\u003Cjats:sub>22\u003C\u002Fjats:sub>\u003C\u002Fjats:italic>), the first step is rate‐limiting, and increasing Δ\u003Cjats:italic>G\u003Cjats:sub>unf\u003C\u002Fjats:sub>\u003C\u002Fjats:italic> (e.g., by the addition of sucrose) decreases aggregation. In solutions where colloidal stability is high (i.e., large and positive \u003Cjats:italic>B\u003Cjats:sub>22\u003C\u002Fjats:sub>\u003C\u002Fjats:italic> values) the second step is rate‐limiting, and solution conditions (e.g., low pH and low ionic strength) that increase repulsive interactions between protein molecules are effective at reducing aggregation. rhGCSF aggregation is thus controlled by both conformational stability and colloidal stability, and depending on the solution conditions, either could be rate‐limiting.\u003C\u002Fjats:p>","\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>Chúng tôi đã nghiên cứu sự kết tụ không tự nhiên của yếu tố kích thích thuộc địa bạch cầu trung tính tái tổ hợp ở người (rhGCSF) trong các điều kiện dung dịch mà rhGCSF tự nhiên vừa ổn định về cấu hình so với trạng thái không gấp gọn vừa có nồng độ thấp hơn giới hạn hòa tan của nó. Quá trình kết tụ của rhGCSF đầu tiên liên quan đến việc ảnh hưởng đến cấu trúc tự nhiên của nó để hình thành một trạng thái chuyển tiếp mở rộng về mặt cấu trúc, sau đó là quá trình lắp ráp để hình thành một tập hợp không thể đảo ngược. Rào cản năng lượng của hai bước này được phản ánh trong các giá trị năng lượng tự do thực nghiệm của sự không gấp gọn \u003Cjats:italic>(\u003C\u002Fjats:italic>Δ\u003Cjats:italic>G\u003Cjats:sub>unf\u003C\u002Fjats:sub>\u003C\u002Fjats:italic>)\u003C\u002Fjats:italic> và hệ số virial thứ hai thẩm thấu (\u003Cjats:italic>B\u003Cjats:sub>22\u003C\u002Fjats:sub>\u003C\u002Fjats:italic>), tương ứng. Dưới các điều kiện dung dịch mà sự ổn định cấu hình của rhGCSF chiếm ưu thế (tức là, Δ\u003Cjats:italic>G\u003Cjats:sub>unf\u003C\u002Fjats:sub}\u003C\u002Fjats:italic> lớn và \u003Cjats:italic>B\u003Cjats:sub>22\u003C\u002Fjats:sub }\u003C\u002Fjats:italic> âm), bước đầu tiên là bước giới hạn tỷ lệ, và việc tăng cường Δ\u003Cjats:italic>G\u003Cjats:sub>unf\u003C\u002Fjats:sub>\u003C\u002Fjats:italic> (ví dụ, bằng cách thêm saccarozơ) làm giảm sự kết tụ. Trong các dung dịch mà sự ổn định keo cao (tức là, giá trị \u003Cjats:italic>B\u003Cjats:sub>22\u003C\u002Fjats:sub>\u003C\u002Fjats:italic> lớn và dương), bước thứ hai là bước giới hạn tỷ lệ, và các điều kiện dung dịch (ví dụ, pH thấp và độ dẫn điện thấp) làm tăng sự tương tác đẩy giữa các phân tử protein có hiệu quả trong việc giảm sự kết tụ. Sự kết tụ của rhGCSF do đó được kiểm soát bởi cả sự ổn định cấu hình và sự ổn định keo, và tùy thuộc vào các điều kiện dung dịch, một trong hai thứ có thể là bước giới hạn tỷ lệ.\u003C\u002Fjats:p>",{"EN":1448,"VI":1449},"Roles of conformational stability and colloidal stability in the aggregation of recombinant human granulocyte colony‐stimulating factor","Vai trò của sự ổn định cấu hình và sự ổn định keo trong quá trình kết tụ của yếu tố kích thích thuộc địa bạch cầu trung tính tái tổ hợp ở người",{"VOID":1451},"12717013",{"VOID":1453},"10.1110\u002Fps.0235703",[200],[1456],"VI","https:\u002F\u002Fonlinelibrary.wiley.com\u002Fdoi\u002F10.1110\u002Fps.0235703",[1459,1478,1495,1514,1529,1546],{"id":1460,"sortIndex":25,"researcher":24,"roles":1461,"affiliations":1462,"properties":1471,"displayName":1475,"givenName":24,"familyName":24},"385b285f-0965-4775-aa1e-8839989f80be",[],[1463],{"id":1464,"sortIndex":25,"affiliation":1465,"properties":24},"6b191c94-d03d-44c3-8267-7e19ca7318bb",{"id":1464,"createTime":24,"updateTime":24,"relativeEntities":1466,"slug":24,"properties":1467,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1470,"statistic":24},[],{"title":1468},{"EN":1469},"Department of Chemical Engineering, Center for Pharmaceutical Biotechnology, University of Colorado, Boulder, Colorado 80309-0242, USA",[],{"orcid":1472,"title":1474,"openalex":1476},{"VOID":1473},"https:\u002F\u002Forcid.org\u002F0000-0001-7448-9943",{"EN":1475},"Eva Y.",{"VOID":1477},"A5035188675",{"id":1479,"sortIndex":116,"researcher":24,"roles":1480,"affiliations":1481,"properties":1490,"displayName":1492,"givenName":24,"familyName":24},"4bf27cc2-4962-4876-ba19-0742f021e78f",[],[1482],{"id":1483,"sortIndex":25,"affiliation":1484,"properties":24},"e8ad6f9d-2a92-4c25-86fd-752e035598f8",{"id":1483,"createTime":24,"updateTime":24,"relativeEntities":1485,"slug":24,"properties":1486,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1489,"statistic":24},[],{"title":1487},{"VI":1488},"Amgen Inc., Amgen Center, Thousand Oaks, California 91320 USA",[],{"title":1491,"openalex":1493},{"EN":1492},"Sampathkumar Krishnan",{"VOID":1494},"A5002476539",{"id":1496,"sortIndex":114,"researcher":24,"roles":1497,"affiliations":1498,"properties":1507,"displayName":1511,"givenName":24,"familyName":24},"597e3de2-9b5f-4d2b-b5b8-704737cf2925",[],[1499],{"id":1500,"sortIndex":25,"affiliation":1501,"properties":24},"e4acd17f-6edb-40b0-ab62-c2179c9243d0",{"id":1500,"createTime":24,"updateTime":24,"relativeEntities":1502,"slug":24,"properties":1503,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":1506,"statistic":24},[],{"title":1504},{"EN":1505},"Amgen, Inc., Longmont, Colorado 80503, USA",[],{"orcid":1508,"title":1510,"openalex":1512},{"VOID":1509},"https:\u002F\u002Forcid.org\u002F0009-0001-5187-7844",{"EN":1511},"Brent S. 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S‐transferases (GSTs) are dimeric proteins that play an important role in cellular detoxification. Four GSTs from the mosquito \u003Cjats:italic>Anopheles dirus\u003C\u002Fjats:italic> species B (Ad), an important malaria vector in South East Asia, are produced by alternate splicing of a single transcription product and were previously shown to have detoxifying activity towards pesticides such as DDT. We have determined the crystal structures for two of these alternatively spliced proteins, AdGST1–3 (complexed with glutathione) and AdGST1–4 (apo form), at 1.75 and 2.45 Å resolution, respectively. These GST isozymes show differences from the related GST from the Australian sheep blowfly \u003Cjats:italic>Lucilia cuprina\u003C\u002Fjats:italic>; in particular, the presence of a C‐terminal helix forming part of the active site. This helix causes the active site of the \u003Cjats:italic>Anopheles\u003C\u002Fjats:italic> GSTs to be enclosed. The glutathione‐binding helix α2 and flanking residues are disordered in the AdGST1–4 (apo) structure, yet ordered in the AdGST1–3 (GSH‐bound) structure, suggesting that insect GSTs operate with an induced fit mechanism similar to that found in the plant phi‐ and human pi‐class GSTs. Despite the high overall sequence identities, the active site residues of AdGST1–4 and AdGST1–3 have different conformations.\u003C\u002Fjats:p>","\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>Glutathione S‐transferases (GSTs) là những protein dimmer có vai trò quan trọng trong việc giải độc tế bào. Bốn GST từ loài muỗi \u003Cjats:italic>Anopheles dirus\u003C\u002Fjats:italic> B (Ad), một vector sốt rét quan trọng ở Đông Nam Á, được sản xuất từ việc cắt tách phiên mã của một sản phẩm duy nhất và trước đây đã được chứng minh là có hoạt động giải độc đối với các loại thuốc trừ sâu như DDT. Chúng tôi đã xác định cấu trúc tinh thể của hai trong số các protein cắt tách này, AdGST1–3 (kết hợp với glutathione) và AdGST1–4 (dạng apo), với độ phân giải lần lượt là 1.75 và 2.45 Å. Các isozyme GST này cho thấy sự khác biệt so với GST liên quan từ ruồi cừu Úc \u003Cjats:italic>Lucilia cuprina\u003C\u002Fjats:italic>; đặc biệt, sự hiện diện của một α-helix C tận đóng vai trò là một phần của vị trí hoạt động. α-helix này khiến vị trí hoạt động của GST \u003Cjats:italic>Anopheles\u003C\u002Fjats:italic> bị bao kín. α-helix liên kết glutathione α2 và các dư lượng xung quanh có dạng không có trật tự trong cấu trúc AdGST1–4 (apo), nhưng có trật tự trong cấu trúc AdGST1–3 (liên kết với GSH), gợi ý rằng GST ở côn trùng hoạt động theo cơ chế phù hợp cảm ứng tương tự như cơ chế tìm thấy ở các GST phi- và pi- lớp ở thực vật và người. 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The folding patterns of the domains that bind flavin, NAD(P), and [2Fe‐2S] are very similar in the two systems. Alignment of the X‐ray structures of PDR and FNR substantiates the assignment of features that characterize a family of flavoprotein reductases whose members include cytochrome P‐450 reductase, sulfite and nitrate reductases, and nitric oxide synthase. Hallmarks of this subfamily of flavoproteins, here termed the FNR family, are an antiparallel \u003Cjats:italic>β\u003C\u002Fjats:italic>‐barrel that binds the flavin prosthetic group, and a characteristic variant of the classic pyridine nucleotide‐binding fold. Despite the similarities between FNR and PDR, attempts to model the structure of a dissociable FNR:ferredoxin complex by analogy with PDR reveal features that are at odds with chemical crosslinking studies (Zanetti, G., Morelli, D., Ronchi, S., Negri, A., Aliverti, A., & Curti, B., 1988, \u003Cjats:italic>Biochemistry 27\u003C\u002Fjats:italic>, 3753–3759).\u003C\u002Fjats:p>\u003Cjats:p>Differences in the binding sites for flavin and pyridine nucleotides determine the nucleotide specificities of FNR and PDR. The specificity of FNR for NADP\u003Cjats:sup>+\u003C\u002Fjats:sup> arises primarily from substitutions in FNR that favor interactions with the 2′ phosphate of NADP\u003Cjats:sup>+\u003C\u002Fjats:sup>. Variations in the conformation and sequences of the loop adjoining the flavin phosphate affect the selectivity for FAD versus FMN.\u003C\u002Fjats:p>\u003Cjats:p>The midpoint potentials for reduction of the flavin and [2Fe–2S] groups in PDR are higher than their counterparts in FNR and spinach ferredoxin, by about 120 mV and 260 mV, respectively. Comparisons of the structure of PDR with spinach FNR and with ferredoxin from \u003Cjats:italic>Anabaena 7120\u003C\u002Fjats:italic>, along with calculations of electrostatic potentials, suggest that local interactions, including hydrogen bonds, are the dominant contributors to these differences in potential.\u003C\u002Fjats:p>","\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>Cấu trúc của phthalate dioxygenase reductase (PDR), một flavoprotein đơn phân chứa sắt - lưu huỳnh, có chức năng cung cấp electron từ NADH đến phthalate dioxygenase, được so sánh với ferredoxin‐NADP\u003Cjats:sup>+\u003C\u002Fjats:sup> reductase (FNR) và ferredoxin, các protein có vai trò khử NADP\u003Cjats:sup>+\u003C\u002Fjats:sup> trong phản ứng cuối cùng của photosystem I. Các mô hình gập của các miền liên kết flavin, NAD(P) và [2Fe‐2S] là rất tương đồng trong hai hệ thống này. Sự căn chỉnh các cấu trúc X‐ray của PDR và FNR hỗ trợ việc xác định các đặc trưng đặc trưng cho một họ flavoprotein reductases mà các thành viên bao gồm cytochrome P‐450 reductase, sulfite và nitrate reductases, cùng với nitric oxide synthase. Những đặc điểm nổi bật của nhánh flavoprotein này, được gọi là họ FNR, là một thùng β song song ngược liên kết nhóm prosthetic flavin và một biến thể đặc trưng của kiểu gập nucleotide pyridine cổ điển. Mặc dù có sự tương đồng giữa FNR và PDR, những cố gắng để lập mô hình cấu trúc của phức hợp FNR:ferredoxin phân ly bằng cách so sánh với PDR lại chỉ ra những đặc điểm mâu thuẫn với các nghiên cứu về liên kết hóa học (Zanetti, G., Morelli, D., Ronchi, S., Negri, A., Aliverti, A., & Curti, B., 1988, \u003Cjats:italic>Biochemistry 27\u003C\u002Fjats:italic>, 3753–3759).\u003C\u002Fjats:p>\u003Cjats:p>Các khác biệt trong các vị trí liên kết flavin và nucleotide pyridine xác định tính đặc hiệu nucleotide của FNR và PDR. Tính đặc hiệu của FNR đối với NADP\u003Cjats:sup>+\u003C\u002Fjats:sup> chủ yếu do các thay thế trong FNR mà tạo điều kiện thuận lợi cho các tương tác với phosphate 2′ của NADP\u003Cjats:sup>+\u003C\u002Fjats:sup>. Các biến thể trong cấu hình và trình tự của vòng tiếp giáp với phosphate flavin ảnh hưởng đến sự chọn lọc cho FAD so với FMN.\u003C\u002Fjats:p>\u003Cjats:p>Các tiềm năng giữa cho sự khử flavin và [2Fe–2S] trong PDR cao hơn so với các đồng thể trong FNR và ferredoxin rau chân vịt, khoảng 120 mV và 260 mV, tương ứng. So sánh cấu trúc của PDR với FNR rau chân vịt và với ferredoxin từ \u003Cjats:italic>Anabaena 7120\u003C\u002Fjats:italic>, cùng với tính toán các tiềm năng tĩnh điện, gợi ý rằng các tương tác cục bộ, bao gồm cả liên kết hydro, là yếu tố đóng góp chủ yếu vào những khác biệt này trong tiềm năng.\u003C\u002Fjats:p>",{"EN":2166,"VI":2167},"Structural prototypes for an extended family of flavoprotein reductases: Comparison of phthalate dioxygenase reductase with ferredoxin reductase and ferredoxin","Các mẫu cấu trúc cho một họ mở rộng của flavoprotein reductase: So sánh phthalate dioxygenase reductase với ferredoxin reductase và ferredoxin",{"VOID":2169},"8298460",{"VOID":2171},"10.1002\u002Fpro.5560021212",[200],[1456],"https:\u002F\u002Fonlinelibrary.wiley.com\u002Fdoi\u002F10.1002\u002Fpro.5560021212",[2176,2193,2210,2227],{"id":2177,"sortIndex":25,"researcher":24,"roles":2178,"affiliations":2179,"properties":2188,"displayName":2190,"givenName":24,"familyName":24},"16f75389-1c4b-4dfe-99b6-a4b79eeaddc7",[],[2180],{"id":2181,"sortIndex":25,"affiliation":2182,"properties":24},"08f068b9-ab00-4f40-855e-22054e5c0621",{"id":2181,"createTime":24,"updateTime":24,"relativeEntities":2183,"slug":24,"properties":2184,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":2187,"statistic":24},[],{"title":2185},{"EN":2186},"Department of Biological Chemistry and Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109",[],{"title":2189,"openalex":2191},{"EN":2190},"Carl C. 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Chem., 265, 3513, 10.1016\u002FS0021-9258(19)39798-4",{"doi":2600},"10.1016\u002FS0021-9258(19)39798-4",{"id":24,"text":2602,"url":24,"identifiers":2603},"Swenson R.P., 1991, Flavins and Flavoproteins 1990, 415",{},{"id":24,"text":2605,"url":24,"identifiers":2606},"10.1016\u002F0378-1119(89)90299-0",{"doi":2605},{"id":24,"text":2608,"url":24,"identifiers":2609},"10.1107\u002FS0108767387099124",{"doi":2608},{"id":24,"text":2611,"url":24,"identifiers":2612},"10.1016\u002FS0022-2836(05)80330-4",{"doi":2611},{"id":24,"text":2614,"url":24,"identifiers":2615},"10.1016\u002F0005-2728(86)90254-9",{"doi":2614},{"id":24,"text":2617,"url":24,"identifiers":2618},"10.1073\u002Fpnas.87.22.8965",{"doi":2617},{"id":24,"text":2620,"url":24,"identifiers":2621},"10.1016\u002F0022-2836(86)90409-2",{"doi":2620},{"id":24,"text":2623,"url":24,"identifiers":2624},"10.1021\u002Fbi00410a035",{"doi":2623},{"id":2626,"createTime":2627,"updateTime":2628,"relativeEntities":2629,"slug":2630,"properties":2631,"entityType":196,"verifyStatus":197,"verifyTime":2627,"verifyNote":198,"languages":2649,"translateLanguages":2650,"viewCount":25,"primaryUrl":2651,"fullTextUrl":24,"authors":2652,"publicationType":243,"publisherRelationship":2691,"citationCount":2749,"citationInfo":2750,"publishDate":2753,"publishYear":2751,"citationAnalyzeStatus":23,"lastCitationAnalyze":24,"indexDatabases":2754,"openAccess":24,"references":2755,"isForceReanalyzing":526},"891a8545-c5ab-45e3-8d9d-4bb48c76b4d8","2025-01-26T23:46:44.493+00:00","2025-02-10T01:17:00.799+00:00",[],"Comprehensive-assessment-of-automatic-structural-alignment-against-a-manual-standard-the-scop-classification-of-proteins",{"mag":2632,"keywords":2634,"pmc":2635,"openalex":2637,"abstract":2639,"title":2642,"pm":2645,"doi":2647},{"VOID":2633},"2108138353",{"VI":1774},{"VOID":2636},"2143933",{"VOID":2638},"W2108138353",{"EN":2640,"VI":2641},"\u003Cjats:title>Abstract\u003C\u002Fjats:title>\u003Cjats:p>We apply a simple method for aligning protein sequences on the basis of a 3D structure, on a large scale, to the proteins in the scop classification of fold families. This allows us to assess, understand, and improve our automatic method against an objective, manually derived standard, a type of comprehensive evaluation that has not yet been possible for other structural alignment algorithms. Our basic approach directly matches the backbones of two structures, using repeated cycles of dynamic programming and least‐squares fitting to determine an alignment minimizing coordinate difference. Because of simplicity, our method can be readily modified to take into account additional features of protein structure such as the orientation of side chains or the location‐dependent cost of opening a gap. Our basic method, augmented by such modifications, can find reasonable alignments for all but 1.5% of the known structural similarities in scop, i.e., all but 32 of the 2,107 superfamily pairs. We discuss the specific protein structural features that make these 32 pairs so difficult to align and show how our procedure effectively partitions the relationships in scop into different categories, depending on what aspects of protein structure are involved (e.g., depending on whether or not consideration of side‐chain orientation is necessary for proper alignment). We also show how our pairwise alignment procedure can be extended to generate a multiple alignment for a group of related structures. We have compared these alignments in detail with corresponding manual ones culled from the literature. We find good agreement (to within 95% for the core regions), and detailed comparison highlights how particular protein structural features (such as certain strands) are problematical to align, giving somewhat ambiguous results. With these improvements and systematic tests, our procedure should be useful for the development of scop and the future classification of protein folds. Supplementary material is available at http:\u002F\u002Fbioinfo.mbb.yale.edu\u002Falign.\u003C\u002Fjats:p>","\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>Chúng tôi áp dụng một phương pháp đơn giản để căn chỉnh các trình tự protein dựa trên cấu trúc 3D, quy mô lớn, cho các protein trong phân loại scop của các gia đình gập. Điều này cho phép chúng tôi đánh giá, hiểu và cải thiện phương pháp tự động của mình so với một tiêu chuẩn thủ công được xây dựng một cách khách quan, một loại đánh giá toàn diện mà chưa có thể thực hiện cho các thuật toán căn chỉnh cấu trúc khác. Cách tiếp cận cơ bản của chúng tôi trực tiếp ghép nối khung xương của hai cấu trúc, sử dụng các chu trình lặp đi lặp lại của lập trình động và điều chỉnh bình phương nhỏ nhất để xác định một sự căn chỉnh giảm thiểu sự khác biệt tọa độ. Nhờ vào sự đơn giản, phương pháp của chúng tôi có thể dễ dàng điều chỉnh để xem xét các đặc điểm bổ sung của cấu trúc protein như định hướng của chuỗi bên hoặc chi phí mở một khoảng trống phụ thuộc vào vị trí. Phương pháp cơ bản của chúng tôi, được mở rộng bởi những điều chỉnh như vậy, có thể tìm thấy các sự căn chỉnh hợp lý cho tất cả ngoài 1,5% các tương đồng cấu trúc đã biết trong scop, tức là tất cả ngoài 32 trong số 2,107 cặp siêu gia đình. Chúng tôi thảo luận về các đặc điểm cấu trúc protein cụ thể làm cho 32 cặp này rất khó căn chỉnh và cho thấy cách quy trình của chúng tôi phân chia hiệu quả các mối quan hệ trong scop thành những loại khác nhau, tùy thuộc vào các khía cạnh của cấu trúc protein có liên quan (ví dụ, phụ thuộc vào việc liệu có cần cân nhắc đến định hướng chuỗi bên hay không để căn chỉnh chính xác). Chúng tôi cũng cho thấy cách quy trình căn chỉnh cặp của chúng tôi có thể được mở rộng để tạo ra một căn chỉnh đa chiều cho một nhóm các cấu trúc liên quan. Chúng tôi đã so sánh các căn chỉnh này một cách chi tiết với các căn chỉnh thủ công tương ứng lấy từ tài liệu. Chúng tôi thấy sự đồng thuận tốt (trong vòng 95% cho các vùng lõi), và so sánh chi tiết nổi bật cách những đặc điểm cấu trúc protein cụ thể (như một số sợi nhất định) gây khó khăn cho việc căn chỉnh, dẫn đến kết quả có phần không rõ ràng. Với những cải tiến và kiểm tra có hệ thống này, quy trình của chúng tôi sẽ hữu ích cho sự phát triển của scop và phân loại tương lai của các kiểu gập protein. Tài liệu bổ sung có sẵn tại http:\u002F\u002Fbioinfo.mbb.yale.edu\u002Falign.\u003C\u002Fjats:p>",{"EN":2643,"VI":2644},"Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins","Đánh giá toàn diện về căn chỉnh cấu trúc tự động so với tiêu chuẩn thủ công, phân loại protein 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Crystals of this rubredoxin grow in space group P2\u003Cjats:sub>1\u003C\u002Fjats:sub>2\u003Cjats:sub>1\u003C\u002Fjats:sub>2\u003Cjats:sub>1\u003C\u002Fjats:sub> with room temperature cell dimensions \u003Cjats:italic>a\u003C\u002Fjats:italic> = 34.6 å, \u003Cjats:italic>b\u003C\u002Fjats:italic> = 35.5 å, and \u003Cjats:italic>c\u003C\u002Fjats:italic> = 44.4 å. Initial phases were determined by the method of molecular replacement using the oxidized form of the rubredoxin from the mesophilic eubacterium, \u003Cjats:italic>Clostridium pasteurianum\u003C\u002Fjats:italic>, as a starting model. The oxidized and reduced models of \u003Cjats:italic>P. furiosus\u003C\u002Fjats:italic> rubredoxin each contain 414 nonhydrogen protein atoms comprising 53 residues. The model of the oxidized form contains 61 solvent H\u003Cjats:sub>2\u003C\u002Fjats:sub>O oxygen atoms and has been refined with X‐PLOR and TNT to a final \u003Cjats:italic>R\u003C\u002Fjats:italic> = 0.178 with root mean square (rms) deviations from ideality in bond distances and bond angles of 0.014 å and 2.06°, respectively. The model of the reduced form contains 37 solvent H\u003Cjats:sub>2\u003C\u002Fjats:sub>O oxygen atoms and has been refined to \u003Cjats:italic>R\u003C\u002Fjats:italic> = 0.193 with rms deviations from ideality in bond lengths of 0.012 å and in bond angles of 1.95°. The overall structure of \u003Cjats:italic>P. furiosus\u003C\u002Fjats:italic> rubredoxin is similar to the structures of mesophilic rubredoxins, with the exception of a more extensive hydrogen‐bonding network in the β‐sheet region and multiple electrostatic interactions (salt bridge, hydrogen bonds) of the Glu 14 side chain with groups on three other residues (the amino‐terminal nitrogen of Ala 1; the indole nitrogen of Trp 3; and the amide nitrogen group of Phe 29). The influence of these and other features upon the thermostability of the \u003Cjats:italic>P. furiosus\u003C\u002Fjats:italic> protein is discussed.\u003C\u002Fjats:p>","\u003Cjats:title>Tóm tắt\u003C\u002Fjats:title>\u003Cjats:p>Cấu trúc của các dạng oxi hóa và khử của rubredoxin từ vi khuẩn cổ đại \u003Cjats:italic>Pyrococcus furiosus\u003C\u002Fjats:italic>, một sinh vật phát triển tối ưu ở nhiệt độ 100 °C, đã được xác định bằng kỹ thuật tinh thể X‐ray với độ phân giải 1.8 Å. Các tinh thể rubredoxin này phát triển trong nhóm không gian P2\u003Cjats:sub>1\u003C\u002Fjats:sub>2\u003Cjats:sub>1\u003C\u002Fjats:sub>2\u003Cjats:sub>1\u003C\u002Fjats:sub> với kích thước tế bào ở nhiệt độ phòng \u003Cjats:italic>a\u003C\u002Fjats:italic> = 34.6 Å, \u003Cjats:italic>b\u003C\u002Fjats:italic> = 35.5 Å, và \u003Cjats:italic>c\u003C\u002Fjats:italic> = 44.4 Å. Các pha ban đầu được xác định bằng phương pháp thay thế phân tử, sử dụng dạng oxi hóa của rubredoxin từ vi khuẩn eubacterium có nhiệt độ tối ưu \u003Cjats:italic>Clostridium pasteurianum\u003C\u002Fjats:italic> làm mẫu khởi đầu. Các mô hình oxi hóa và khử của rubredoxin \u003Cjats:italic>P. furiosus\u003C\u002Fjats:italic> đều chứa 414 nguyên tử protein không chứa hydro, tương ứng với 53 dư lượng. Mô hình của dạng oxi hóa chứa 61 nguyên tử oxy nước H\u003Cjats:sub>2\u003C\u002Fjats:sub>O và đã được tinh chỉnh bằng X‐PLOR và TNT đến \u003Cjats:italic>R\u003C\u002Fjats:italic> = 0.178 với độ lệch trung bình căn bậc hai (rms) từ lý tưởng trong khoảng cách liên kết và góc liên kết là 0.014 Å và 2.06°, tương ứng. Mô hình của dạng khử chứa 37 nguyên tử oxy nước H\u003Cjats:sub>2\u003C\u002Fjats:sub>O và đã được tinh chỉnh đến \u003Cjats:italic>R\u003C\u002Fjats:italic> = 0.193 với độ lệch rms từ lý tưởng trong chiều dài liên kết là 0.012 Å và trong góc liên kết là 1.95°. Cấu trúc tổng thể của rubredoxin \u003Cjats:italic>P. furiosus\u003C\u002Fjats:italic> tương tự như cấu trúc của các rubredoxin sống trong điều kiện nhiệt độ trung bình, ngoại trừ một mạng lưới liên kết hydro rộng hơn trong vùng β-sheet và nhiều tương tác tĩnh điện (cầu muối, liên kết hydro) của chuỗi bên Glu 14 với các nhóm trên ba dư lượng khác (nitơ đầu amine của Ala 1; nitơ indole của Trp 3; và nhóm nitơ amide của Phe 29). Ảnh hưởng của những tính năng này và những yếu tố khác đối với sự ổn định nhiệt độ của protein \u003Cjats:italic>P. furiosus\u003C\u002Fjats:italic> cũng được thảo luận.\u003C\u002Fjats:p>",{"EN":3012,"VI":3013},"X‐ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium pyrococcus furiosus","Cấu trúc tinh thể X‐ray của các dạng oxi hóa và khử của rubredoxin từ vi khuẩn cổ đại nhiệt độ cao Pyrococcus furiosus",{"VOID":3015},"1303768",{"VOID":3017},"10.1002\u002Fpro.5560011111",[200],[1456],"https:\u002F\u002Fonlinelibrary.wiley.com\u002Fdoi\u002F10.1002\u002Fpro.5560011111",[3022,3039,3054,3071,3086,3103,3120],{"id":3023,"sortIndex":25,"researcher":24,"roles":3024,"affiliations":3025,"properties":3034,"displayName":3036,"givenName":24,"familyName":24},"ee5a135a-4e62-4af1-b8f8-3802a8e245b5",[],[3026],{"id":3027,"sortIndex":25,"affiliation":3028,"properties":24},"71fef125-9b58-4dc2-888c-babb7655dc6f",{"id":3027,"createTime":24,"updateTime":24,"relativeEntities":3029,"slug":24,"properties":3030,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":3033,"statistic":24},[],{"title":3031},{"VI":3032},"Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125",[],{"title":3035,"openalex":3037},{"EN":3036},"Michael W. 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This sequence was also found in the vanadium‐containing chloroperoxidase of \u003Cjats:italic>Curvularia inaequalis\u003C\u002Fjats:italic>. Several lines of evidence support this phosphatase motif identification. Crystal structure data on chloroperoxidase revealed that all three domains are in close proximity and several of the conserved residues are involved in the binding of the cofactor, vana‐date, a compound structurally similar to phosphate. Structure‐function analysis of the human glucose‐6‐phosphatase has shown that two of the conserved residues (the first domain arginine and the central domain histidine) are essential for enzyme activity. This conserved sequence motif was used to identify nine additional putative phosphatases from sequence databases, one of which has been determined to be a lipid phosphatase in yeast.\u003C\u002Fjats:p>","\u003Cjats:title>Tóm Tắt\u003C\u002Fjats:title>\u003Cjats:p>Chúng tôi đã xác định một động thái phosphatase mới, có thể bảo tồn, mô hình chuỗi KXXXXXXRP‐(X\u003Cjats:sub>12‐54\u003C\u002Fjats:sub>)‐PSGH‐(X\u003Cjats:sub>31‐54\u003C\u002Fjats:sub>))‐SRXXXXX HXXXD, được chia sẻ trong một số phosphatase lipid, phosphatase glucose‐6 của động vật có vú, và một tập hợp các phosphatase acid không chuyên biệt từ vi khuẩn. Chuỗi này cũng được tìm thấy trong chloroperoxidase chứa vanadi của \u003Cjats:italic>Curvularia inaequalis\u003C\u002Fjats:italic>. Nhiều bằng chứng hỗ trợ việc xác định mô hình phosphatase này. Dữ liệu cấu trúc tinh thể về chloroperoxidase cho thấy rằng cả ba miền đều ở gần nhau và một số dư lượng bảo tồn tham gia vào việc liên kết với cofactor, vanadate, một hợp chất có cấu trúc tương tự như phosphate. Phân tích cấu trúc-chức năng của phosphatase glucose‐6 ở người đã cho thấy rằng hai trong số các dư lượng bảo tồn (arginine miền đầu tiên và histidine miền trung tâm) là thiết yếu cho hoạt động của enzyme. Mô hình chuỗi bảo tồn này đã được sử dụng để xác định chín phosphatase tiềm năng bổ sung từ các cơ sở dữ liệu chuỗi, trong đó một trong số đó đã được xác định là một phosphatase lipid trong nấm men.\u003C\u002Fjats:p>",{"EN":3418,"VI":3419},"Identification of a novel phosphatase sequence motif","Khám Phá Một Động Thái Phosphatase Mới",{"VOID":3421},"9041652",{"VOID":3423},"10.1002\u002Fpro.5560060226",[200],[1456],"https:\u002F\u002Fonlinelibrary.wiley.com\u002Fdoi\u002F10.1002\u002Fpro.5560060226",[3428,3445],{"id":3429,"sortIndex":25,"researcher":24,"roles":3430,"affiliations":3431,"properties":3440,"displayName":3442,"givenName":24,"familyName":24},"e4774313-fcdb-4706-9e71-7d1d63e9ccf0",[],[3432],{"id":3433,"sortIndex":25,"affiliation":3434,"properties":24},"5d4d80bc-2c3f-45b5-ae96-548b8136726e",{"id":3433,"createTime":24,"updateTime":24,"relativeEntities":3435,"slug":24,"properties":3436,"entityType":24,"verifyStatus":24,"verifyTime":24,"verifyNote":24,"languages":24,"translateLanguages":24,"viewCount":24,"url":24,"parentIds":3439,"statistic":24},[],{"title":3437},{"EN":3438},"to: J. Stukey, Department of Biology, Hope College, P.O. 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