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membrane proteins present unparalleled challenges for structural genomics programs. Samples from this class of proteins are not only difficult to produce in quantities sufficient for analysis by X-ray diffraction or NMR, but their hydrophobic properties add extra dimension to their purification and subsequent crystallization. New systems that seek to tackle the production problems are in development. In our laboratory, one such strategy exploits the unique physiology of the Rhodobacter species of photosynthetic bacteria where we have designed an overexpression system that coordinates the heterologous production of targeted hydrophobic proteins with nascent, unfilled membranes that can be used to harbor them. In this study, we describe the means by which purification of recombinant membrane proteins produced in such a fashion can be purified efficiently from Rhodobacter membranes using relatively higher-throughput, semi-automated methods. These protocols utilize a state-of-the-art FPLCTM system for affinity chromatography, followed by gel filtration or ion exchange chromatography to enhance purity for crystallization attempts. The Rhodobacter expression system coupled with the semi-automation of purification steps represents an advance towards the development of a strategy for obtaining structures for membrane proteins at a more rapid pace.",{"EN":460},"Towards higher-throughput membrane protein production for structural genomics initiatives",{"VOID":462},"[\"647393643816862345\"]",{"VOID":464},"Frishman, D. and Mewes, H.W. (1997) Nat. Struct. Biol. 4, 626–628.\nEssen, L.-O. (2002) Gene Funct. Dis. 3, 39–48.\nDrew, D., Froderberg, L., Baars, L. and de Gier, J.-W.L. (2003) Biochim. Biophys. Acta 1610, 3–10.\nBerman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res. 28, 235–242.\nArechaga, I., Miroux, B., Karrasch, S., Huijbregts, R., de Kruijff, B., Runswick, M.J. and Walker, J.E. (2000) FEBS Lett. 482, 215–219.\nMiroux, B. and Walker, J.E. (1996) J. Mol. Biol. 260, 289–298.\nKiefer, H., Maier, K. and Vogel, R. (1999) Biochem. Soc. Trans. 27, 908–912.\nGrisshammer, R. and Tate, C. (1995) Quart. Rev. Biophys. 28, 315–422.\nPalczewski, K., Kumasaka, T., Hori, T., Behnke, C.A., Motoshima, H., Fox, B.A., Le Trong, I., Teller, D.C., Okada, T., Stenkamp, R.E., Yamamoto, M. and Miyano, M. (2000) Science 289, 739–745.\nDrews, G. and Golecki, J.R. (1995) In Anoxygenic Photosynthetic Bacteria (Eds, Blankenship, R.E., Madigan, M.T. and Bauer, C.E.), Kluwer, Dordrecht, The Netherlands, pp. 231–257.\nKirmaier, C., Laible, P.D., Czarnecki, K., Hata, A.N., Hanson, D.K., Bocian, D.F. and Holten, D. (2002) J. Phys. Chem. B 106, 1799–1808.\nPokkuluri, P.R., Laible, P.D., Deng, Y.L., Wong, T.N., Hanson, D. K. and Schiffer, M. (2002) Biochemistry 41, 5998–6007.\nScott, H.N., Laible, P.D. and Hanson, D.K. (2003) Plasmid 50, 74–79.",{"VOID":466},"10.1023\u002FB:JSFG.0000029201.33710.46","2024-05-15T02:32:29.254+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FB:JSFG.0000029201.33710.46",[470,485,498,513],{"id":471,"sortIndex":21,"researcher":20,"roles":472,"affiliations":473,"properties":482,"displayName":484,"givenName":20,"familyName":20},"8cc5623f-2cc3-43de-9e7e-4b0a0abc439f",[121],[474],{"id":475,"sortIndex":21,"affiliation":476,"properties":20},"8984c395-4465-492f-8730-fff07fafe939",{"id":475,"createTime":20,"updateTime":20,"relativeEntities":477,"slug":20,"properties":478,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":481,"statistic":20},[],{"title":479},{"VI":480},"Biosciences Division, Argonne National Laboratory, Argonne, USA",[],{"title":483},{"VI":484},"Philip D. 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Scott",{"id":499,"sortIndex":160,"researcher":20,"roles":500,"affiliations":501,"properties":510,"displayName":512,"givenName":20,"familyName":20},"ea6c1bbf-ca10-40f6-af5a-dbd13f92a26e",[121],[502],{"id":503,"sortIndex":21,"affiliation":504,"properties":20},"3cf1100e-24aa-4dbc-a262-69e9aa8bb688",{"id":503,"createTime":20,"updateTime":20,"relativeEntities":505,"slug":20,"properties":506,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":509,"statistic":20},[],{"title":507},{"VI":508},"Amersham Biosciences Corporation, 800 Centennial Avenue, Piscataway, USA",[],{"title":511},{"VI":512},"Lynda Henry",{"id":514,"sortIndex":52,"researcher":20,"roles":515,"affiliations":516,"properties":523,"displayName":525,"givenName":20,"familyName":20},"30f3e04c-a33e-4617-a0b6-dc8de838a103",[121],[517],{"id":475,"sortIndex":21,"affiliation":518,"properties":20},{"id":475,"createTime":20,"updateTime":20,"relativeEntities":519,"slug":20,"properties":520,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":522,"statistic":20},[],{"title":521},{"VI":480},[],{"title":524},{"VI":525},"Deborah K. Hanson",{"url":468,"publisher":527,"properties":547},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":528,"slug":10,"properties":529,"entityType":18,"verifyStatus":19,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":21,"subjectFields":533,"manageAffiliations":534,"indexDatabases":535,"url":40,"thumbnailPath":20,"statistic":542,"gsStatistic":20,"type":90,"analyzePriority":20},[],{"issn":530,"title":531,"eissn":532},{"VOID":13},{"EN":15},{"VOID":17},[],[],[536],{"id":26,"indexDatabase":537,"url":37,"indexYears":38,"academicFieldIds":20,"indexDatabaseRanking":39},{"id":28,"createTime":20,"updateTime":20,"relativeEntities":538,"label":539,"description":540,"key":34,"publicationTags":541,"standard":20},[],{"EN":31,"VI":31},{"EN":31,"VI":33},[36],{"impactFactor":21,"impactFactorByYear":543,"i10Index":49,"i10IndexLast5Year":21,"totalPublication":50,"totalPublicationByYear":544,"totalCitation":66,"totalCitationByYear":545,"totalCitationPerPublication":76,"totalCitationPerPublicationByYear":546,"hindexLast5Year":60,"hindex":60},{"2012":43,"2013":44,"2014":45,"2015":46,"2016":47,"2017":48,"2018":46},{"2000":52,"2002":53,"2003":54,"2004":55,"2005":56,"2006":57,"2007":58,"2008":59,"2009":60,"2010":61,"2011":62,"2012":62,"2013":63,"2014":64,"2015":65,"2016":53,"2017":52},{"2004":68,"2005":69,"2007":68,"2008":70,"2009":71,"2010":72,"2011":73,"2012":74,"2013":49,"2014":60,"2015":74,"2016":75},{"2004":78,"2005":79,"2007":80,"2008":81,"2009":82,"2010":83,"2011":84,"2012":85,"2013":86,"2014":87,"2015":88,"2016":89},{"pages":548,"volume":550},{"VOID":549},"167-172",{"VOID":551},"5",{"total":21,"publishYear":553,"statisticByYear":554},2004,{},"2004-03-01","2026-05-09T02:21:13.775+00:00",[39],{"id":559,"createTime":560,"updateTime":561,"relativeEntities":562,"slug":563,"properties":564,"entityType":112,"verifyStatus":113,"verifyTime":575,"verifyNote":115,"languages":576,"translateLanguages":20,"viewCount":21,"primaryUrl":578,"fullTextUrl":20,"authors":579,"publicationType":419,"publisherRelationship":597,"citationCount":21,"citationInfo":623,"publishDate":626,"publishYear":624,"citationAnalyzeStatus":19,"lastCitationAnalyze":561,"indexDatabases":627,"openAccess":20,"references":628,"isForceReanalyzing":449},"521e29ad-45ec-42ba-800d-901c0759f444","2024-04-17T07:26:12.823+00:00","2026-03-18T03:38:50.864+00:00",[],"More-genes-in-vertebrates-",{"abstract":565,"title":567,"gsPaper":569,"keywords":571,"doi":573},{"EN":566},"With the acquisition of complete genome sequences from several animals, there is renewed interest in the pattern of genome evolution on our own lineage. One key question is whether gene number increased during chordate or vertebrate evolution. It is argued here that comparing the total number of genes between a fly, a nematode and human is not appropriate to address this question. Extensive gene loss after duplication is one complication; another is the problem of comparing taxa that are phylogenetically very distant. Amphioxus and tunicates are more appropriate animals for comparison to vertebrates. Comparisons of clustered homeobox genes, where gene loss can be identified, reveals a one to four mode of evolution for Hox and ParaHox genes. Analyses of other gene families in amphioxus and vertebrates confirm that gene duplication was very widespread on the vertebrate lineage. These data confirm that vertebrates have more genes than their closest invertebrate relatives, acquired through gene duplication. abbreviations IHGSC, International Human Genome Sequencing Consortium; TCESC, The C. elegans Sequencing Consortium.",{"EN":568},"More genes in vertebrates?",{"VOID":570},"[\"1375475155915320703\"]",{"EN":572},"",{"VOID":574},"10.1023\u002FA:1022656931587","2024-04-29T06:12:12.415+00:00",[577],"EN","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FA:1022656931587",[580],{"id":581,"sortIndex":21,"researcher":20,"roles":582,"affiliations":583,"properties":592,"displayName":594,"givenName":20,"familyName":20},"36c8500a-8890-49fd-85ce-6973b21b9ff4",[],[584],{"id":585,"sortIndex":21,"affiliation":586,"properties":20},"7e565381-3b32-48b9-a9e3-7aa5342ecd1f",{"id":585,"createTime":20,"updateTime":20,"relativeEntities":587,"slug":20,"properties":588,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":591,"statistic":20},[],{"title":589},{"EN":590},"School of Animal & Microbial Sciences, The University of Reading, Whiteknights, Reading, United Kingdom",[],{"title":593,"gsAuthor":595},{"EN":594},"Peter W.H. 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(2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185-2195.",{"id":20,"text":632,"url":20,"identifiers":20},"Aguinaldo, A.M., Turbeville, J.M., Linford, L.S., Rivera, M.C., Garey, J.R., Raff, R. and Lake, J.A. (1997) Evidence for a clade of nematodes, arthropods and other moulting animals. Nature, 387, 489-493.",{"id":20,"text":634,"url":20,"identifiers":20},"Arai, R., Suzuki, A. and Akai Y. (1988) The karyotype and DNA value of a cypriniform algae eater, Gyrinocheilus aymonieri. Jpn. J. Ichthyol., 34, 515-517.",{"id":20,"text":636,"url":20,"identifiers":20},"Araki, I., Terazawa, K. and Satoh, N. (1996) Duplication of an amphioxus myogenic bHLH gene is independent of vertebrate myogenic bHLH gene duplication. Gene, 171, 231-236.",{"id":20,"text":638,"url":20,"identifiers":20},"Aristotle (350 BC) History of Animals (Translation, D'Arcy Wentworth Thompson). Library of the Future, Second Series 1991, World Library, Inc., Garden Grove, CA.",{"id":20,"text":640,"url":20,"identifiers":20},"Atkin, N.B. and Ohno, S. (1967) DNA values of four primitive chordates. Chromosoma, 23, 10-13.",{"id":20,"text":642,"url":20,"identifiers":20},"Baltimore, D. (2001) Our genome unveiled. Nature, 409, 814-816.",{"id":20,"text":644,"url":20,"identifiers":20},"Brooke, N.M., Garcia-Fernàndez, J. and Holland, P.W.H. (1998) The ParaHox gene cluster is an evolutionary sister of the Hox gene cluster. Nature, 392, 920-922.",{"id":20,"text":646,"url":20,"identifiers":20},"Claverie, J.-M. (2001) What if there are only 30,000 genes? Science, 291, 1255-1257.",{"id":20,"text":648,"url":20,"identifiers":20},"de Rosa, R., Grenier, J.K., Andreeva, T., Cook, C.E., Adoutte, A., Akam, M., Carroll, S.B. and Balavoine, G. (1999) Hox genes in brachiopods and priapulids and protostome evolution. Nature, 399, 772-776.",{"id":20,"text":650,"url":20,"identifiers":20},"Ferrier, D.E.K. and Holland, P.W.H. (2001) Ancient origins of the Hox gene cluster. Nature Rev. Genet. 2, 33-38.",{"id":20,"text":652,"url":20,"identifiers":20},"Ferrier, D.E.K., Minguillon, C., Holland, P.W.H. and Garcia-Fernandez, J. (2000) The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evol. Dev., 2, 284-293.",{"id":20,"text":654,"url":20,"identifiers":20},"Flybase (1999) The Flybase database of the Drosophila genome projects and community literature. Nucleic Acids Res., 27, 85-88.",{"id":20,"text":656,"url":20,"identifiers":20},"Furlong, R.F. and Holland, P.W.H. (2002) Were vertebrates octoploid? Phil. Trans. R. Soc. Ser. B, 357, 531-544.",{"id":20,"text":658,"url":20,"identifiers":20},"Garcia-Fernández, J. and Holland, P.W.H. (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370, 563-566.",{"id":20,"text":660,"url":20,"identifiers":20},"Hinegardner, R. and Rosen, D.E. (1972) Cellular DNA content and the evolution of teleostean fishes. Amer. Naturalist, 106, 621-644.",{"id":20,"text":662,"url":20,"identifiers":20},"Holland, P.W.H. (1999) Gene duplication: past, present and future. Semin. Cell Dev. Biol., 10, 541-547.",{"id":20,"text":664,"url":20,"identifiers":20},"Holland, P.W.H. and Garcia-Fernàndez, J. (1996) Hox genes and chordate evolution. Dev. Biol., 173, 382-395.",{"id":20,"text":666,"url":20,"identifiers":20},"Holland, P.W.H., Holland, L.Z., Williams, N.A. and Holland, N.D. (1992) An amphioxus homeobox gene: sequence conservation, spatial expression during development and insights into vertebrate evolution. Development, 116, 653-661.",{"id":20,"text":668,"url":20,"identifiers":20},"International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860-921.",{"id":20,"text":670,"url":20,"identifiers":20},"Jefferies, R.P.S. and Lewis, D.N. (1978) The English Silurian fossil Placocystites forbesianus and the ancestry of the vertebrates. Phil. Trans. R. Soc. Ser. B, 282, 205-323.",{"id":20,"text":672,"url":20,"identifiers":20},"Krakauer, D.C. and Nowak, M. (1999) Evolutionary preservation of redundant duplicated genes. Semin. Cell Dev. Biol., 10, 555-559.",{"id":20,"text":674,"url":20,"identifiers":20},"Ohno, S. (1970) Evolution by Gene Duplication, Springer-Verlag, Heidelberg.",{"id":20,"text":676,"url":20,"identifiers":20},"Ohno, S. (1999) Gene duplication and the uniqueness of vertebrate genomes circa 1970-1999. Semin. Cell Dev. Biol., 10, 517-522.",{"id":20,"text":678,"url":20,"identifiers":20},"Patton, S.J., Luke, G.N. and Holland, P.W.H. (1998) Complex history of a chromosomal paralogy regions: insights from amphioxus aromatic amino acid hydroxylase genes and insulinrelated genes. Mol. Biol. Evol., 15, 1373-1380.",{"id":20,"text":680,"url":20,"identifiers":20},"Pendleton, J.W., Nagai, B.K., Murtha, M.T. and Ruddle, F.H. (1993) Expansion of the Hox gene family and the evolution of chordates. Proc. Natl. Acad. Sci. USA, 90, 6300-6304.",{"id":20,"text":682,"url":20,"identifiers":20},"Pollard, S.L. and Holland, P.W.H. (2000) Evidence for fourteen homeobox gene clusters in human genome ancestry, Curr. Biol., 10, 1059-1062.",{"id":20,"text":684,"url":20,"identifiers":20},"Robinson, E.S., Potter, I.C. and Atkin, N.B. (1975) The nuclear DNA content of lampreys. Experientia, 31, 912-913.",{"id":20,"text":686,"url":20,"identifiers":20},"Rubin, G.M. (2001) Comparing species. Nature, 409, 820-821.",{"id":20,"text":688,"url":20,"identifiers":20},"Shimeld, S.M. and Holland, P.W.H. (2000) Vertebrate innovations. Proc. Natl. Acad. Sci. USA 97, 4449-4452.",{"id":20,"text":690,"url":20,"identifiers":20},"Schmidtke, J., Weiler, C., Kunz, B. and Engel, W. (1977) Isozymes of a tunicate and a cephalochordate as a test of polyploidisation in chordate evolution. Nature, 266, 532-533.",{"id":20,"text":692,"url":20,"identifiers":20},"Shu, D.-G., Conway Morris, S. and Zhang, X.-L. (1996) A Pikaialike chordate from the Lower Cambrian of China. Nature, 384, 157-158.",{"id":20,"text":694,"url":20,"identifiers":20},"The C. elegans Sequencing Consortium (1998) Genome Sequence of the nematode Caenorhabditis elegans: a platform for investigating biology. Science, 282, 2012-2018.",{"id":20,"text":696,"url":20,"identifiers":20},"Venter, J.C., Adams, M.D., Myers, E.W. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.",{"id":20,"text":698,"url":20,"identifiers":20},"Wada, H. and Satoh, N. (1993) Details of the evolutionary history from invertebrates, as deduced from the sequences of 18S rDNA. Proc. Natl. Acad. Sci. USA, 91, 1801-1804.",{"id":700,"createTime":701,"updateTime":702,"relativeEntities":703,"slug":704,"properties":705,"entityType":112,"verifyStatus":113,"verifyTime":716,"verifyNote":115,"languages":20,"translateLanguages":20,"viewCount":160,"primaryUrl":717,"fullTextUrl":20,"authors":718,"publicationType":419,"publisherRelationship":773,"citationCount":20,"citationInfo":20,"publishDate":555,"publishYear":553,"citationAnalyzeStatus":19,"lastCitationAnalyze":702,"indexDatabases":798,"openAccess":20,"references":20,"isForceReanalyzing":449},"a14b50c6-0d90-4b21-80c6-72cd97a53f10","2023-11-27T23:39:55.071+00:00","2026-01-29T16:06:41.402+00:00",[],"An-automated-small-scale-protein-expression-and-purification-screening-provides-beneficial-information-for-protein-production",{"abstract":706,"title":708,"gsPaper":710,"references":712,"doi":714},{"EN":707},"One of the first key steps in structural genomics is high-throughput expression and rapid screening to select highly soluble proteins, the preferred candidates for crystal production. Here we describe the methodology used at the Berkeley Structural Genomics Center (BSGC) for automated parallel expression and small-scale purification of fusion proteins using a 96-well format. Our robotic method includes cell lysis, soluble fraction separation and purification with affinity resins. For detection of His-tagged proteins in the soluble fractions and after affinity resin elution, a dot-blot procedure with an anti-His-antibody is used. The expression level and molecular mass of recombinant proteins are checked by SDS-PAGE. With this approach, we are able to obtain beneficial information to be used for large-scale protein expression and purification.",{"EN":709},"An automated small-scale protein expression and purification screening provides beneficial information for protein production",{"VOID":711},"[\"11302921312525652626\"]",{"VOID":713},"Yokoyama, S. (2003) Curr. Opin. Chem. Biol. 7, 39–43.\nHou, J., Sims, G., Zhang, C. and Kim, S.-H. (2003) Proc. Natl. Acad. Sci. USA 100, 2386–2390.\nPaul, D.C., Van Frank, R.M., Muth, W.L., Ross, J.W. and Williams, D.C. (1983) Eur. J. Cell Biol. 31, 171–174.\nDieckman, L., Gu, M., Stols, L., Donneley, M.I. and Collart, F.R. (2002) Protein Expr. Purif. 25, 1–7.\nKnaust, R.K. and Nordlund, P. (2001) Ann. Biochem. 297, 79–85.\nGrabski, A., Drott, D. and Mehler, M. (2003) inNovations, 16, 11–13.\nKim, R., Sandler, S.J., Goldman, S., Yokota, H., Clark, A.J. and Kim, S.-H. (1998) Biotechnol. Lett. 20, 207–210.",{"VOID":715},"10.1023\u002FB:JSFG.0000029195.73810.86","2024-05-12T03:08:47.234+00:00","http:\u002F\u002Flink.springer.com\u002F10.1023\u002FB:JSFG.0000029195.73810.86",[719,734,747,760],{"id":720,"sortIndex":21,"researcher":20,"roles":721,"affiliations":722,"properties":731,"displayName":733,"givenName":20,"familyName":20},"a2a188cd-7669-4897-8699-854a5ca8878a",[121],[723],{"id":724,"sortIndex":21,"affiliation":725,"properties":20},"9b2b1c0d-b967-46aa-b1a5-531132e9e5e1",{"id":724,"createTime":20,"updateTime":20,"relativeEntities":726,"slug":20,"properties":727,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":730,"statistic":20},[],{"title":728},{"VI":729},"Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, USA",[],{"title":732},{"VI":733},"Henry 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explosion of the size of the universe of known protein sequences has stimulated two complementary approaches to structural mapping of these sequences: theoretical structure prediction and experimental determination by structural genomics (SG). In this work, we assess the accuracy of structure prediction by two automated template-based structure prediction metaservers (genesilico.pl and bioinfo.pl) by measuring the structural similarity of the predicted models to corresponding experimental models determined a posteriori. Of 199 targets chosen from SG programs, the metaservers predicted the structures of about a fourth of them “correctly.” (In this case, “correct” was defined as placing more than 70 % of the alpha carbon atoms in the model within 2 Å of the experimentally determined positions.) Almost all of the targets that could be modeled to this accuracy were those with an available template in the Protein Data Bank (PDB) with more than 25 % sequence identity. The majority of those SG targets with lower sequence identity to structures in the PDB were not predicted by the metaservers with this accuracy. We also compared metaserver results to CASP8 results, finding that the models obtained by participants in the CASP competition were significantly better than those produced by the metaservers.",{"EN":809},"Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures",{"VOID":811},"[]",{"EN":572},{"VOID":814},"Grabowski M et al (2007) Structural genomics: keeping up with expanding knowledge of the protein universe. Curr Opin Struct Biol 17(3):347–353\nLevitt M (2009) Nature of the protein universe. Proc Natl Acad Sci USA 106(27):11079–11084\nAnfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(96):223–230\nBradley P, Misura KM, Baker D (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309(5742):1868–1871\nVitkup D et al (2001) Completeness in structural genomics. Nat Struct Biol 8(6):559–566\nMoult J (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol\nSali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815\nKolinski A, Gront D (2007) Comparative modeling without implicit sequence alignments. Bioinformatics 23(19):2522–2527\nBujnicki JM et al (2001) Structure prediction meta server. Bioinformatics 17(8):750–751\nChen L et al (2004) TargetDB: a target registration database for structural genomics projects. Bioinformatics 20(16):2860–2862\nGinalski K et al (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 19(8):1015–1018\nKurowski MA, Bujnicki JM (2003) GeneSilico protein structure prediction meta-server. Nucleic Acids Res 31(13):3305–3307\nWallner B, Elofsson A (2005) Pcons5: combining consensus, structural evaluation and fold recognition scores. Bioinformatics 21(23):4248–4254\nAlexandrov N, Shindyalov I (2003) PDP: protein domain parser. Bioinformatics 19(3):429–430\nKabsch W (1976) Solution for best rotation to relate two sets of vectors. Acta Crystallogr A 32:922–923\nGront D, Kolinski A (2006) BioShell—a package of tools for structural biology computations. Bioinformatics 22(5):621–622\nGront D, Kolinski A (2008) Utility library for structural bioinformatics. Bioinformatics 24(4):584–585\nSmith TF, Waterman MS (1981) Identification of common molecular subsequences. J Mol Biol 147(1):195–197\nHenikoff S, Henikoff JG (1992) Amino acid substitution matrices from protein blocks. Proc Nat Acad Sci USA 89(22):10915–10919\nSander C, Schneider R (1991) Database of homology-derived protein sequences and the structural meaning of sequence alignment. Proteins: Struct Function Genetics 9:56–68\nAltschul SF et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402\nMoult J et al (2009) Critical assessment of methods of protein structure prediction-Round VIII. Prot-Struct Funct Bioinform 77:1–4\nVenclovas C, Margelevicius M (2009) The use of automatic tools and human expertise in template-based modeling of CASP8 target proteins. Prot-Struct Funct Bioinform 77:81–88\nMoult J et al (2011) Critical assessment of methods of protein structure prediction (CASP)—round IX. Proteins 79(Suppl 10):1–5\nKryshtafovych A, Fidelis K, Moult J (2011) CASP9 results compared to those of previous CASP experiments. Proteins 79(Suppl 10):196–207\nMoult J et al (2009) Critical assessment of methods of protein structure prediction-Round VIII. Proteins 77(Suppl 9):1–4\nSoding J (2005) Protein homology detection by HMM–HMM comparison. Bioinformatics 21(7):951–960\nZhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40\nXu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80(7):1715–1735\nGront D et al (2011) Generalized fragment picking in Rosetta: design, protocols and applications. PLoS ONE 6(8):e23294\nCameo Project (2012) Available from: www.cameo3d.org\nKolinski A (2004) Protein modeling and structure prediction with a reduced representation. Acta Biochim Pol 51(2):349–371\nKim DE, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32(Web Server issue):W526-31\nLevitt M (2007) Growth of novel protein structural data. Proc Natl Acad Sci USA 104(9):3183–3188\nMurzin AG et al (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247(4):536–540\nBaker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294(5540):93–96",{"VOID":816},"10.1007\u002Fs10969-012-9146-2","2024-05-07T05:52:49.896+00:00","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10969-012-9146-2",[820,854,875,896,917,938],{"id":821,"sortIndex":21,"researcher":20,"roles":822,"affiliations":823,"properties":851,"displayName":853,"givenName":20,"familyName":20},"7e5acc0b-c080-4565-bf78-75f1bc3bc8f9",[121],[824,832,840],{"id":825,"sortIndex":21,"affiliation":826,"properties":20},"e5f08d76-90eb-452b-96d6-209311007706",{"id":825,"createTime":20,"updateTime":20,"relativeEntities":827,"slug":20,"properties":828,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":831,"statistic":20},[],{"title":829},{"VI":830},"Midwest Center for Structural Genomics, New York, USA",[],{"id":833,"sortIndex":21,"affiliation":834,"properties":20},"975f054c-83da-417b-8b7c-f880bb571d3a",{"id":833,"createTime":20,"updateTime":20,"relativeEntities":835,"slug":20,"properties":836,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":839,"statistic":20},[],{"title":837},{"VI":838},"Faculty of Chemistry, University of Warsaw, Warsaw, Poland",[],{"id":841,"sortIndex":21,"affiliation":842,"properties":848},"caa1bf00-bfd0-4cc7-af84-320bcfa8b2d3",{"id":841,"createTime":20,"updateTime":20,"relativeEntities":843,"slug":20,"properties":844,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":847,"statistic":20},[],{"title":845},{"VI":846},"Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, U.S.A",[],{"title":849},{"VI":850},"Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA",{"title":852},{"VI":853},"Dominik Gront",{"id":855,"sortIndex":44,"researcher":20,"roles":856,"affiliations":857,"properties":872,"displayName":874,"givenName":20,"familyName":20},"e1c3b789-646a-49cd-b20f-bc0c36259714",[121],[858,864],{"id":825,"sortIndex":21,"affiliation":859,"properties":20},{"id":825,"createTime":20,"updateTime":20,"relativeEntities":860,"slug":20,"properties":861,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":863,"statistic":20},[],{"title":862},{"VI":830},[],{"id":841,"sortIndex":21,"affiliation":865,"properties":870},{"id":841,"createTime":20,"updateTime":20,"relativeEntities":866,"slug":20,"properties":867,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":869,"statistic":20},[],{"title":868},{"VI":846},[],{"title":871},{"VI":850},{"title":873},{"VI":874},"Marek Grabowski",{"id":876,"sortIndex":160,"researcher":20,"roles":877,"affiliations":878,"properties":893,"displayName":895,"givenName":20,"familyName":20},"851bcded-945d-4de6-a9a6-4d8a090b00a1",[121],[879,885],{"id":825,"sortIndex":21,"affiliation":880,"properties":20},{"id":825,"createTime":20,"updateTime":20,"relativeEntities":881,"slug":20,"properties":882,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":884,"statistic":20},[],{"title":883},{"VI":830},[],{"id":841,"sortIndex":21,"affiliation":886,"properties":891},{"id":841,"createTime":20,"updateTime":20,"relativeEntities":887,"slug":20,"properties":888,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":890,"statistic":20},[],{"title":889},{"VI":846},[],{"title":892},{"VI":850},{"title":894},{"VI":895},"Matthew D. 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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":994},"Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination",{"VOID":996},"Aloy, P. and Russell, R. 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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":998},"10.1023\u002FA:1026113408773","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FA:1026113408773",[1001,1016,1031],{"id":1002,"sortIndex":21,"researcher":20,"roles":1003,"affiliations":1004,"properties":1013,"displayName":1015,"givenName":20,"familyName":20},"9f3074c9-7def-4bdc-997b-1bb4bea60ace",[121],[1005],{"id":1006,"sortIndex":21,"affiliation":1007,"properties":20},"28942e79-89b9-4e48-b062-8225944ac429",{"id":1006,"createTime":20,"updateTime":20,"relativeEntities":1008,"slug":20,"properties":1009,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1012,"statistic":20},[],{"title":1010},{"EN":1011},"MRC Laboratory of Molecular Biology, Cambridge, UK",[],{"title":1014},{"VI":1015},"Gordana Apic",{"id":1017,"sortIndex":44,"researcher":20,"roles":1018,"affiliations":1019,"properties":1028,"displayName":1030,"givenName":20,"familyName":20},"9483c3c7-b096-44b2-b34d-77e2b359d0be",[121],[1020],{"id":1021,"sortIndex":21,"affiliation":1022,"properties":20},"1c6b6a50-0a57-4bd8-893d-5ed14f9cafaa",{"id":1021,"createTime":20,"updateTime":20,"relativeEntities":1023,"slug":20,"properties":1024,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1027,"statistic":20},[],{"title":1025},{"VI":1026},"DKFZ (German Cancer Research Center), Heidelberg, Germany",[],{"title":1029},{"VI":1030},"Wolfgang Huber",{"id":1032,"sortIndex":160,"researcher":20,"roles":1033,"affiliations":1034,"properties":1041,"displayName":1043,"givenName":20,"familyName":20},"ef34292f-c4cf-4d0b-bdc1-7451305a9fe2",[121],[1035],{"id":1006,"sortIndex":21,"affiliation":1036,"properties":20},{"id":1006,"createTime":20,"updateTime":20,"relativeEntities":1037,"slug":20,"properties":1038,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1040,"statistic":20},[],{"title":1039},{"EN":1011},[],{"title":1042},{"VI":1043},"Sarah A. Teichmann",{"url":999,"publisher":1045,"properties":1065},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":1046,"slug":10,"properties":1047,"entityType":18,"verifyStatus":19,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":21,"subjectFields":1051,"manageAffiliations":1052,"indexDatabases":1053,"url":40,"thumbnailPath":20,"statistic":1060,"gsStatistic":20,"type":90,"analyzePriority":20},[],{"issn":1048,"title":1049,"eissn":1050},{"VOID":13},{"EN":15},{"VOID":17},[],[],[1054],{"id":26,"indexDatabase":1055,"url":37,"indexYears":38,"academicFieldIds":20,"indexDatabaseRanking":39},{"id":28,"createTime":20,"updateTime":20,"relativeEntities":1056,"label":1057,"description":1058,"key":34,"publicationTags":1059,"standard":20},[],{"EN":31,"VI":31},{"EN":31,"VI":33},[36],{"impactFactor":21,"impactFactorByYear":1061,"i10Index":49,"i10IndexLast5Year":21,"totalPublication":50,"totalPublicationByYear":1062,"totalCitation":66,"totalCitationByYear":1063,"totalCitationPerPublication":76,"totalCitationPerPublicationByYear":1064,"hindexLast5Year":60,"hindex":60},{"2012":43,"2013":44,"2014":45,"2015":46,"2016":47,"2017":48,"2018":46},{"2000":52,"2002":53,"2003":54,"2004":55,"2005":56,"2006":57,"2007":58,"2008":59,"2009":60,"2010":61,"2011":62,"2012":62,"2013":63,"2014":64,"2015":65,"2016":53,"2017":52},{"2004":68,"2005":69,"2007":68,"2008":70,"2009":71,"2010":72,"2011":73,"2012":74,"2013":49,"2014":60,"2015":74,"2016":75},{"2004":78,"2005":79,"2007":80,"2008":81,"2009":82,"2010":83,"2011":84,"2012":85,"2013":86,"2014":87,"2015":88,"2016":89},{"pages":1066,"volume":1068},{"VOID":1067},"67-78",{"VOID":1069},"4","2003-06-01",[39],{"id":1073,"createTime":1074,"updateTime":1075,"relativeEntities":1076,"slug":1077,"properties":1078,"entityType":112,"verifyStatus":113,"verifyTime":1075,"verifyNote":115,"languages":20,"translateLanguages":20,"viewCount":21,"primaryUrl":1087,"fullTextUrl":20,"authors":1088,"publicationType":419,"publisherRelationship":1359,"citationCount":20,"citationInfo":20,"publishDate":1385,"publishYear":981,"citationAnalyzeStatus":19,"lastCitationAnalyze":20,"indexDatabases":1386,"openAccess":20,"references":20,"isForceReanalyzing":449},"6e66a007-f7c2-414f-b466-c64778e44ad4","2024-01-22T10:24:48.068+00:00","2025-02-25T10:49:38.253+00:00",[],"Solution-NMR-and-X-ray-crystal-structures-of-Pseudomonas-syringae-Pspto-3016-from-protein-domain-family-PF04237-DUF419-adopt-a-double-wing-DNA-binding-motif",{"abstract":1079,"title":1081,"references":1083,"doi":1085},{"EN":1080},"The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of Pspto_3016 adopts a “double wing” α\u002Fβ sandwich fold similar to that of protein YjbR from Escherichia coli and to the C-terminal DNA binding domain of the MotA transcription factor (MotCF) from T4 bacteriophage, along with other uncharacterized proteins. Pspto_3016 was selected by the Protein Structure Initiative of the National Institutes of Health and the Northeast Structural Genomics Consortium (NESG ID PsR293).",{"EN":1082},"Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a “double wing” DNA binding motif",{"VOID":1084},"Acton TB, Xiao R, Anderson S, Aramini J, Buchwald W, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang Y, Janjua H, Kornhaber G, Lau J, Lee D, Liu G, Maglaqui M, Ma L, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GVT, Tang Y, Tong S, Wang D, Wang H, Zhao L, Montelione GT (2010) Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 493:21–60\nAshkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N (2010) ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. 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Bioinformatics 20:3702–3704\nGabanyi MJ, Adams PD, Arnold K, Bordoli L, Carter LG, Flippen-Andersen J, Gifford L, Haas J, Kouranov A, McLaughlin WA, Micallef DI, Minor W, Shah R, Schwede T, Tao YP, Westbrook JD, Zimmerman M, Berman HM (2011) The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods. J Struct Funct Genomics 12:45–54\nGüntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378\nHerrmann T, Güntert P, Wüthrich K (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol 319:209–227\nHolm L, Rosenström P (2010) Dali server: conservation mapping in 3D. Nucleic Acids Res 38:W545–W549\nHuang YJ, Moseley HN, Baran MC, Arrowsmith C, Powers R, Tejero R, Szyperski T, Montelione GT (2005) An integrated platform for automated analysis of protein NMR structures. Methods Enzymol 394:111–141\nHuang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision, and F-measure scores (RPF scores): structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665–1674\nKanehisa M, Goto S (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30\nLi N, Sickmier EA, Zhang R, Joachimiak A, White SW (2002) The MotA transcription factor from bacteriophage T4 contains a novel DNA-binding domain: the ‘double wing’ motif. Mol Microbiol 43:1079–1088\nLi N, Zhang W, White SW, Kriwacki RW (2001) Solution structure of the transcriptional activation domain of the bacteriophage T4 protein, MotA. Biochemistry 40:4293–4302\nLiu J, Montelione GT, Rost B (2007) Novel leverage of structural genomics. Nat Biotechnol 25:849–851\nMoseley HN, Monleon D, Montelione GT (2001) Automatic determination of protein backbone resonance assignments from triple resonance nuclear magnetic resonance data. Methods Enzymol 339:91–108\nOtwinowski Z, Minor W (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods Enzymol 276:307–326\nPerrakis A, Morris R, Lamzin VS (1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6:458–463\nSchrödinger L (2002) The PyMOL Molecular Graphics System, Version 0.99rc6\nSchwieters C, Kuszewski J, Clore G (2006) Using Xplor-NIH for NMR molecular structure determination. Prog Nucl Mag Res Spectrosc 48:47–62\nSheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122\nSingarapu KK, Liu G, Xiao R, Bertonati C, Honig B, Montelione GT, Szyperski T (2007) NMR structure of protein yjbR from Escherichia coli reveals ‘double-wing’ DNA binding motif. Proteins 67:501–504\nTerwilliger TC (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr 59:38–44\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",{"VOID":1086},"10.1007\u002Fs10969-012-9140-8","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1007\u002Fs10969-012-9140-8",[1089,1113,1135,1155,1175,1190,1210,1230,1250,1270,1290,1310,1339],{"id":1090,"sortIndex":21,"researcher":20,"roles":1091,"affiliations":1092,"properties":1110,"displayName":1112,"givenName":20,"familyName":20},"1a4041ff-35b7-46a9-909a-02c352c18af7",[121],[1093,1101],{"id":1094,"sortIndex":21,"affiliation":1095,"properties":20},"38c0db18-2776-4833-809a-c8001bb8cb78",{"id":1094,"createTime":20,"updateTime":20,"relativeEntities":1096,"slug":20,"properties":1097,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1100,"statistic":20},[],{"title":1098},{"VI":1099},"Department of Chemistry and Biochemistry, Miami University, Oxford, USA",[],{"id":1102,"sortIndex":44,"affiliation":1103,"properties":1109},"8834e95d-a526-4f78-930d-ad9cc897c0fe",{"id":1102,"createTime":20,"updateTime":20,"relativeEntities":1104,"slug":20,"properties":1105,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1108,"statistic":20},[],{"title":1106},{"VI":1107},"Northeast Structural Genomics Consortium, Piscataway, USA",[],{},{"title":1111},{"VI":1112},"Erik A. Feldmann",{"id":1114,"sortIndex":44,"researcher":20,"roles":1115,"affiliations":1116,"properties":1132,"displayName":1134,"givenName":20,"familyName":20},"29b00d4b-23d1-4bbd-b818-1d9b24fd8bfe",[121],[1117,1123],{"id":1102,"sortIndex":21,"affiliation":1118,"properties":20},{"id":1102,"createTime":20,"updateTime":20,"relativeEntities":1119,"slug":20,"properties":1120,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1122,"statistic":20},[],{"title":1121},{"VI":1107},[],{"id":1124,"sortIndex":44,"affiliation":1125,"properties":1131},"61507e9a-6e44-4732-b2a9-2399d6103a09",{"id":1124,"createTime":20,"updateTime":20,"relativeEntities":1126,"slug":20,"properties":1127,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1130,"statistic":20},[],{"title":1128},{"VI":1129},"Department of Biological Sciences, Columbia University, New York, USA",[],{},{"title":1133},{"VI":1134},"Jayaraman Seetharaman",{"id":1136,"sortIndex":160,"researcher":20,"roles":1137,"affiliations":1138,"properties":1152,"displayName":1154,"givenName":20,"familyName":20},"fe0f1746-724f-4491-acf6-2deb5550d739",[121],[1139,1145],{"id":1094,"sortIndex":21,"affiliation":1140,"properties":20},{"id":1094,"createTime":20,"updateTime":20,"relativeEntities":1141,"slug":20,"properties":1142,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1144,"statistic":20},[],{"title":1143},{"VI":1099},[],{"id":1102,"sortIndex":44,"affiliation":1146,"properties":1151},{"id":1102,"createTime":20,"updateTime":20,"relativeEntities":1147,"slug":20,"properties":1148,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1150,"statistic":20},[],{"title":1149},{"VI":1107},[],{},{"title":1153},{"VI":1154},"Theresa A. 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The 3-D fold of MJ0882 at 1.8 Å highly resembles that of a methyltransferase, despite limited sequence similarity to any confirmed methyltransferase. The structure has an S-adenosylmethionine (AdoMet) binding pocket surrounded by motifs with similarities to those commonly found among AdoMet binding proteins. Preliminary biochemical experiments show that MJ0882 specifically binds to AdoMet, which is the essential co-factor for methyltransferases.",{"EN":1397},"Structure-based experimental confirmation of biochemical function to a methyltransferase, MJ0882, from hyperthermophile Methanococcus jannaschii",{"VOID":1399},"Schluckebier, G., O'Gara, M., Saenger, W. and Cheng, X. (1995) J. Mol. Biol. 247, 16–20.\nCheng, X., Kumar, S., Posfai, J., Pflugrath, J.W. and Roberts, R.J. (1993) Cell 74, 299–307.\nKlimasauskas, S., Kumar, S., Roberts, R.J. and Cheng, X. (1994) Cell 76, 357–369.\nLabahn, J. et al. (1994) Proc. Natl. Acad. Sci. USA 91, 10957–10961.\nReinisch, K.M., Chen, L., Verdine, G.L. and Lipscomb, W.N. (1995) Cell 82, 143–153.\nGong, W., O'Gara, M., Blumenthal, R.M. and Cheng, X. (1997) Nucleic Acids Res 25, 2702-2715.\nVidgren, J., Svensson, L.A. and Liljas, A. (1994) Nature 368, 354–358.\nFu, Z. et al. (1996) Biochemistry 35, 11985–11993.\nHodel, A.E., Gershon, P.D., Shi, X. and Quiocho, F.A. (1996) Cell 85, 247–256.\nBussiere, D.E. et al. (1998) Biochemistry 37, 7103–7112.\nDjordjevic, S. and Stock, A.M. (1997) Structure 5, 545–558.\nAravind, L. and Koonin, E.V. (2001) Trends Biochem. Sci. 26, 215–217.\nHolm, L. and Sander, C. (1993) J. Mol. Biol. 233, 123–138.\nHendrickson, W.A. (1991) Science 254, 51-58.\nCheng, X. (1995) Annu. Rev. Biophys. Biomol. Struct. 24, 293–318.\nKim, R. et al. (1998) Biotech. Lett 20, 207-210.\nJancarik, J., Scott, W.G., Milligan, D.L., Koshland, D.E., Jr. and Kim, S.H. (1991) J. Mol. Biol. 221, 31-34.\nOtwinowski, Z. and Minor, W. (1997) Methods Enzymol. 276, 307–326.\nTerwilliger, T.C. (1997) Methods Enzymol. 276, 530.\nCowtan, K. and Main, P. (1998) Acta Crystallogr. D Biol. Crystallogr. 54, 487–493.\nJones, T.A., Zou, J.-Y., Cowan, S.W. and Kjeldgaard, M. (1991) Acta Crystallogr. A47, 110–119.\nBrunger, A.T. et al. (1998) Acta Crystallogr. D54, 905–921.\nKraulis, P.J. (1991) J. Appl. 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automated NOE assignment and structure calculation on the basis of a largely complete, assigned input chemical shift list and a list of unassigned NOESY cross peaks has recently become feasible for routine NMR protein structure calculation and has been shown to yield results that are equivalent to those of the conventional, manual approach. However, these algorithms rely on the availability of a virtually complete list of the chemical shifts. This paper investigates the influence of incomplete chemical shift assignments on the reliability of NMR structures obtained with automated NOESY cross peak assignment. The program CYANA was used for combined automated NOESY assignment with the CANDID algorithm and structure calculations with torsion angle dynamics at various degrees of completeness of the chemical shift assignment which was simulated by random omission of entries in the experimental 1H chemical shift lists that had been used for the earlier, conventional structure determinations of two proteins. Sets of structure calculations were performed choosing the omitted chemical shifts randomly among all assigned hydrogen atoms, or among aromatic hydrogen atoms. For comparison, automated NOESY assignment and structure calculations were performed with the complete experimental chemical shift but under random omission of NOESY cross peaks. When heteronuclear-resolved three-dimensional NOESY spectra are available the current CANDID algorithm yields in the absence of up to about 10% of the experimental 1H chemical shifts reliable NOE assignments and three-dimensional structures that deviate by less than 2 Å from the reference structure obtained using all experimental chemical shift assignments. In contrast, the algorithm can accommodate the omission of up to 50% of the cross peaks in heteronuclear- resolved NOESY spectra without producing structures with a RMSD of more than 2 Å to the reference structure. When only homonuclear NOESY spectra are available, the algorithm is slightly more susceptible to missing data and can tolerate the absence of up to about 7% of the experimental 1H chemical shifts or of up to 30% of the NOESY peaks. Abbreviations: BmPBPA – Bombyx mori pheromone binding protein form A; CYANA – combined assignment and dynamics algorithm for NMR applications; NMR – nuclear magnetic resonance; NOE – nuclear Overhauser effect; NOESY – NOE spectroscopy; RMSD – root-mean-square deviation; WmKT – Williopsis mrakii killer toxin",{"EN":1537},"Influence of the completeness of chemical shift assignments on NMR structures obtained with automated NOE assignment",{"VOID":1539},"Moseley, H. N. B. and Montelione, G. T. (1999) Curr. Opin. Struct. Biol. 9, 635–642.\nPrestegard J. H., Valafar, H., Glushka, J. and Tian, F. (2001) Biochemistry 31, 8677-8685\nMontelione, G. T., Zheng, D., Huang, Y. J., Gunsalus, K. C. and Szyperski, T. (2000) Nat. Struct. Biol. 7, 982-985.\nMumenthaler, C. and Braun, W. (1995) J. Mol. Biol. 254 465–480.\nMumenthaler, C., Güntert, P., Braun, W. and Wüthrich, K. (1997) J. Biomol. NMR 10 351–362.\nNilges, M., Macias, M. J., O'Donoghue, S. I. and Oschkinat, H. (1997) J. Mol. Biol. 269, 408–422.\nLinge, J. P., O'Donoghue, S. I. and Nilges, M. (2001) Meth. Enzymol. 339, 71–90.\nSavarin, P., Zinn-Justin, S. and Gilquin, B. (2001) J. Biomol. NMR 19, 49–62.\nHerrmann, T., Güntert, P. and Wüthrich, K. (2002) J. Mol. Biol. 319, 209–227.\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.\nGüntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol. 273, 283–298.\nHorst, R., Damberger, F., Luginbühl, P., Güntert, P., Peng, G., Nikonova, L., Leal, W. S. and Wüthrich, K. (2001) Proc. Natl. Acad. Sci. USA 98, 14374–14379.\nAntuch, W., Güntert, P. and Wüthrich, K. (1996) Nat. Struct. Biol. 3, 662–665.\nGüntert, P. (1998) Q. Rev. Biophys. 31, 145–237.\nGüntert, P., Braun, W. and Wüthrich, K. (1991) J. Mol. Biol. 217, 517–530.\nKoradi, R., Billeter, M. and Wüthrich, K. (1996). J. Mol. Graph. 14, 51–55.",{"VOID":1541},"10.1023\u002FA:1026122726574","https:\u002F\u002Flink.springer.com\u002Farticle\u002F10.1023\u002FA:1026122726574",[1544,1559],{"id":1545,"sortIndex":21,"researcher":20,"roles":1546,"affiliations":1547,"properties":1556,"displayName":1558,"givenName":20,"familyName":20},"9812c09f-3808-4d54-a8d3-22ec7a7c487b",[121],[1548],{"id":1549,"sortIndex":21,"affiliation":1550,"properties":20},"563f187f-18ce-46da-bf8e-89338a6a17f0",{"id":1549,"createTime":20,"updateTime":20,"relativeEntities":1551,"slug":20,"properties":1552,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1555,"statistic":20},[],{"title":1553},{"VI":1554},"Genomic Sciences Center, RIKEN Yokohama Institute, Yokohama, Japan",[],{"title":1557},{"VI":1558},"JunGoo Jee",{"id":1560,"sortIndex":44,"researcher":20,"roles":1561,"affiliations":1562,"properties":1569,"displayName":1571,"givenName":20,"familyName":20},"12db17d2-11f5-4ca8-96ad-92e4c3fd4c8c",[121],[1563],{"id":1549,"sortIndex":21,"affiliation":1564,"properties":20},{"id":1549,"createTime":20,"updateTime":20,"relativeEntities":1565,"slug":20,"properties":1566,"entityType":20,"verifyStatus":20,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":20,"url":20,"parentIds":1568,"statistic":20},[],{"title":1567},{"VI":1554},[],{"title":1570},{"VI":1571},"Peter Güntert",{"url":1542,"publisher":1573,"properties":1593},{"id":6,"createTime":7,"updateTime":8,"relativeEntities":1574,"slug":10,"properties":1575,"entityType":18,"verifyStatus":19,"verifyTime":20,"verifyNote":20,"languages":20,"translateLanguages":20,"viewCount":21,"subjectFields":1579,"manageAffiliations":1580,"indexDatabases":1581,"url":40,"thumbnailPath":20,"statistic":1588,"gsStatistic":20,"type":90,"analyzePriority":20},[],{"issn":1576,"title":1577,"eissn":1578},{"VOID":13},{"EN":15},{"VOID":17},[],[],[1582],{"id":26,"indexDatabase":1583,"url":37,"indexYears":38,"academicFieldIds":20,"indexDatabaseRanking":39},{"id":28,"createTime":20,"updateTime":20,"relativeEntities":1584,"label":1585,"description":1586,"key":34,"publicationTags":1587,"standard":20},[],{"EN":31,"VI":31},{"EN":31,"VI":33},[36],{"impactFactor":21,"impactFactorByYear":1589,"i10Index":49,"i10IndexLast5Year":21,"totalPublication":50,"totalPublicationByYear":1590,"totalCitation":66,"totalCitationByYear":1591,"totalCitationPerPublication":76,"totalCitationPerPublicationByYear":1592,"hindexLast5Year":60,"hindex":60},{"2012":43,"2013":44,"2014":45,"2015":46,"2016":47,"2017":48,"2018":46},{"2000":52,"2002":53,"2003":54,"2004":55,"2005":56,"2006":57,"2007":58,"2008":59,"2009":60,"2010":61,"2011":62,"2012":62,"2013":63,"2014":64,"2015":65,"2016":53,"2017":52},{"2004":68,"2005":69,"2007":68,"2008":70,"2009":71,"2010":72,"2011":73,"2012":74,"2013":49,"2014":60,"2015":74,"2016":75},{"2004":78,"2005":79,"2007":80,"2008":81,"2009":82,"2010":83,"2011":84,"2012":85,"2013":86,"2014":87,"2015":88,"2016":89},{"pages":1594,"volume":1596},{"VOID":1595},"179-189",{"VOID":1069},[39],{"id":1599,"createTime":1600,"updateTime":1601,"relativeEntities":1602,"slug":1603,"properties":1604,"entityType":112,"verifyStatus":113,"verifyTime":1601,"verifyNote":115,"languages":20,"translateLanguages":20,"viewCount":160,"primaryUrl":1613,"fullTextUrl":20,"authors":1614,"publicationType":419,"publisherRelationship":1778,"citationCount":20,"citationInfo":20,"publishDate":1804,"publishYear":1805,"citationAnalyzeStatus":19,"lastCitationAnalyze":20,"indexDatabases":1806,"openAccess":20,"references":20,"isForceReanalyzing":449},"37331340-09bc-463b-b3f2-4b44e956f77d","2023-11-25T03:28:57.146+00:00","2025-02-24T16:08:13.441+00:00",[],"The-crystal-structure-of-pyrimidine-thiamin-biosynthesis-precursor-like-domain-containing-protein-CAE31940-from-proteobacterium-Bordetella-bronchiseptica-RB50-and-evolutionary-insight-into-the-NMT1-THI5-family",{"abstract":1605,"title":1607,"references":1609,"doi":1611},{"EN":1606},"We report a 2.0 Å structure of the CAE31940 protein, a proteobacterial NMT1\u002FTHI5-like domain-containing protein. We also discuss the primary and tertiary structure similarity with its homologs. The highly conserved FGGXMP motif was identified in CAE31940, which corresponds to the GCCCX motif located in the vicinity of the active center characteristic for THi5-like proteins found in yeast. This suggests that the FGGXMP motif may be a unique hallmark of proteobacterial NMT1\u002FTHI5-like proteins.",{"EN":1608},"The crystal structure of pyrimidine\u002Fthiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1\u002FTHI5 family",{"VOID":1610},"Zurlinden A, Schweingruber ME (1994) Cloning, nucleotide sequence, and regulation of Schizosaccharomyces pombe thi4, a thiamine biosynthetic gene. J Bacteriol 176:6631–6635\nBegley TP, Chatterjee A, Hanes JW, Hazra A, Ealick SE (2008) Cofactor biosynthesis–still yielding fascinating new biological chemistry. Curr Opin Chem Biol 12(2):118–125\nBale S, Rajashankar KR, Perry K, Begley TP, Ealick SE (2010) HMP binding protein ThiY and HMP-P synthase THI5 are structural homologues. Biochemistry 49(41):8929–8936\nMaundrell K (1990) nmt1 of fission yeast. A highly transcribed gene completely repressed by thiamine. J Biol Chem 265(19):10857–10864\nWightman R, Meacock PA (2003) The THI5 gene family of Saccharomyces cerevisiae: distribution of homologues among the hemiascomycetes and functional redundancy in the aerobic biosynthesis of thiamin from pyridoxine. Microbiology 149(Pt 6):1447–1460\nZhang RG, Skarina T, Katz JE, Beasley S, Khachatryan A, Vyas S, Arrowsmith CH, Clarke S, Edwards A, Joachimiak A et al (2001) Structure of thermo toga maritima stationary phase survival protein SurE: a novel acid phosphatase. Structure 9(11):1095–1106\nEschenfeldt WH, Lucy S, Millard CS, Joachimiak A, Mark ID (2009) A family of LIC vectors for high-throughput cloning and purification of proteins. Methods Mol Biol 498:105–115\nAslanidis C, de Jong PJ (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res 18(20):6069–6074\nHaun RS, Serventi IM, Moss J (1992) Rapid, reliable ligation-independent cloning of PCR products using modified plasmid vectors. Biotechniques 13(4):515–518\nRosenbaum G, Alkire RW, Evans G, Rotella FJ, Lazarski K, Zhang RG, Ginell SL, Duke N, Naday I, Lazarz J et al (2006) The Structural Biology Center 19ID undulator beamline: facility specifications and protein crystallographic results. J Synchrotron Radiat 13(Pt 1):30–45\nMinor W, Cymborowski M, Otwinowski Z, Chruszcz M (2006) HKL-3000: the integration of data reduction and structure solution—from diffraction images to an initial model in minutes. Acta Crystallogr D Biol Crystallogr 62:859–866\nSheldrick GM (2008) A short history of SHELX. 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Proteins 53(Suppl 6):369–379\nWallner B, Elofsson A (2007) Prediction of global and local model quality in CASP7 using Pcons and ProQ. Proteins 69(Suppl 8):184–193\nPawlowski M, Gajda MJ, Matlak R, Bujnicki JM (2008) MetaMQAP: a meta-server for the quality assessment of protein models. BMC Bioinformatics 9:403\nLi Z, Ye Y, Godzik A (2006) Flexible structural neighbourhood: a database of proteins structural similarities and alignments. Nucleic Acids Res 34:D277–D280\nSonnhammer EL, Eddy SR, Durbin R (1997) Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 28(3):405–420\nSantini S, Claverie JM, Mouz N, Rousselle T, Maza C, Monchois V, Abergel C (2011) The conserved Candida albicans CA3427 gene product defines a new family of proteins exhibiting the generic periplasmic binding protein structural fold. PLoS ONE 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