Journal of structural and functional genomics最新文献_第9页

phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta. 凤凰。mr_rosetta:用Phenix和Rosetta进行分子替换和模型重建。

Journal of structural and functional genomics Pub Date : 2012-06-01 Epub Date: 2012-03-15 DOI: 10.1007/s10969-012-9129-3

Thomas C Terwilliger, Frank Dimaio, Randy J Read, David Baker, Gábor Bunkóczi, Paul D Adams, Ralf W Grosse-Kunstleve, Pavel V Afonine, Nathaniel Echols

引用次数: 128

Enhancement of crystallization with nucleotide ligands identified by dye-ligand affinity chromatography. 通过染料配体亲和层析法识别核苷酸配体，增强结晶效果。

Journal of structural and functional genomics Pub Date : 2012-06-01 DOI: 10.1007/s10969-012-9124-8

Heungbok Kim, Cecelia Webster, Justin K M Roberts, Juthamas Kositsawat, Li-Wei Hung, Thomas C Terwilliger, Chang-Yub Kim

引用次数: 0

KB-Rank: efficient protein structure and functional annotation identification via text query. KB-Rank：通过文本查询高效识别蛋白质结构和功能注释。

Journal of structural and functional genomics Pub Date : 2012-06-01 Epub Date: 2012-01-21 DOI: 10.1007/s10969-012-9125-7

Elchin S Julfayev, Ryan J McLaughlin, Yi-Ping Tao, William A McLaughlin

{"title":"KB-Rank: efficient protein structure and functional annotation identification via text query.","authors":"Elchin S Julfayev, Ryan J McLaughlin, Yi-Ping Tao, William A McLaughlin","doi":"10.1007/s10969-012-9125-7","DOIUrl":"10.1007/s10969-012-9125-7","url":null,"abstract":"The KB-Rank tool was developed to help determine the functions of proteins. A user provides text query and protein structures are retrieved together with their functional annotation categories. Structures and annotation categories are ranked according to their estimated relevance to the queried text. The algorithm for ranking first retrieves matches between the query text and the text fields associated with the structures. The structures are next ordered by their relative content of annotations that are found to be prevalent across all the structures retrieved. An interactive web interface was implemented to navigate and interpret the relevance of the structures and annotation categories retrieved by a given search. The aim of the KB-Rank tool is to provide a means to quickly identify protein structures of interest and the annotations most relevant to the queries posed by a user. Informational and navigational searches regarding disease topics are described to illustrate the tool's utilities. The tool is available at the URL http://protein.tcmedc.org/KB-Rank.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 2","pages":"101-10"},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b1/42/10969_2012_Article_9125.PMC3375009.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30407066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The TRPV5/6 calcium channels contain multiple calmodulin binding sites with differential binding properties. TRPV5/6钙通道含有多个具有不同结合特性的钙调蛋白结合位点。

Journal of structural and functional genomics Pub Date : 2012-06-01 Epub Date: 2012-02-22 DOI: 10.1007/s10969-012-9128-4

Nadezda V Kovalevskaya, Fedir M Bokhovchuk, Geerten W Vuister

引用次数: 29

Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771. 溶液核磁共振结构揭示了独特的同源二聚体形成的翼螺旋-转-螺旋motif，并提供了蛋白质结构域家族PF10771的第一个结构。

Journal of structural and functional genomics Pub Date : 2012-03-01 Epub Date: 2012-01-06 DOI: 10.1007/s10969-011-9121-3

Alexander Eletsky, Donald Petrey, Qiangfeng Cliff Zhang, Hsiau-Wei Lee, Thomas B Acton, Rong Xiao, John K Everett, James H Prestegard, Barry Honig, Gaetano T Montelione, Thomas Szyperski

{"title":"Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771.","authors":"Alexander Eletsky, Donald Petrey, Qiangfeng Cliff Zhang, Hsiau-Wei Lee, Thomas B Acton, Rong Xiao, John K Everett, James H Prestegard, Barry Honig, Gaetano T Montelione, Thomas Szyperski","doi":"10.1007/s10969-011-9121-3","DOIUrl":"10.1007/s10969-011-9121-3","url":null,"abstract":"High-quality NMR structures of the homo-dimeric proteins Bvu3908 (69-residues in monomeric unit) from Bacteroides vulgatus and Bt2368 (74-residues) from Bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (wHTH) motifs mediating tight complex formation. Such homo-dimer formation by winged HTH motifs is otherwise found only in two DNA-binding proteins with known structure: the C-terminal wHTH domain of transcriptional activator FadR from E. coli and protein TubR from B. thurigensis, which is involved in plasmid DNA segregation. However, the relative orientation of the wHTH motifs is different and residues involved in DNA-binding are not conserved in Bvu3908 and Bt2368. Hence, the proteins of the present study are not very likely to bind DNA, but are likely to exhibit a function that has thus far not been ascribed to homo-dimers formed by winged HTH motifs. The structures of Bvu3908 and Bt2368 are the first atomic resolution structures for PFAM family PF10771, a family of unknown function (DUF2582) currently containing 128 members.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-011-9121-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30367745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome. 基于折叠识别和结晶预测相结合的结构基因组学靶点选择:在人类蛋白质组中的应用。

Journal of structural and functional genomics Pub Date : 2012-03-01 Epub Date: 2012-02-22 DOI: 10.1007/s10969-012-9130-x

James E Bray

{"title":"Target selection for structural genomics based on combining fold recognition and crystallisation prediction methods: application to the human proteome.","authors":"James E Bray","doi":"10.1007/s10969-012-9130-x","DOIUrl":"https://doi.org/10.1007/s10969-012-9130-x","url":null,"abstract":"The objective of this study is to automatically identify regions of the human proteome that are suitable for 3D structure determination by X-ray crystallography and to annotate them according to their likelihood to produce diffraction quality crystals. The results provide a powerful tool for structural genomics laboratories who wish to select human proteins based on the statistical likelihood of crystallisation success. Combining fold recognition and crystallisation prediction algorithms enables the efficient calculation of the crystallisability of the entire human proteome. This novel study estimates that there are approximately 40,000 crystallisable regions in the human proteome. Currently, only 15% of these regions (approx. 6,000 sequences) have been solved to at least 95% sequence identity. The remaining unsolved regions have been categorised into 5 crystallisation classes and an integral membrane protein (IMP) class, based on established structure prediction, crystallisation prediction and transmembrane (TM) helix prediction algorithms. Approximately 750 unsolved regions (2% of the proteome) have been identified as having a PDB fold representative (template) and an 'optimal' likelihood of crystallisation. At the other end of the spectrum, more than 10,500 non-IMP regions with a PDB template are classified as 'very difficult' to crystallise (26%) and almost 2,500 regions (6%) were predicted to contain at least 3 TM helices. The 3D-SPECS (3D Structural Proteomics Explorer with Crystallisation Scores) website contains crystallisation predictions for the entire human proteome and can be found at http://www.bioinformaticsplus.org/3dspecs.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 1","pages":"37-46"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9130-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30476587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni. 炭疽芽胞杆菌和空肠芽胞杆菌推定磷酸甘油酸激酶的晶体结构。

Journal of structural and functional genomics Pub Date : 2012-03-01 Epub Date: 2012-03-10 DOI: 10.1007/s10969-012-9131-9

Heping Zheng, Ekaterina V Filippova, Karolina L Tkaczuk, Piotr Dworzynski, Maksymilian Chruszcz, Przemyslaw J Porebski, Zdzislaw Wawrzak, Olena Onopriyenko, Marina Kudritska, Sarah Grimshaw, Alexei Savchenko, Wayne F Anderson, Wladek Minor

{"title":"Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni.","authors":"Heping Zheng, Ekaterina V Filippova, Karolina L Tkaczuk, Piotr Dworzynski, Maksymilian Chruszcz, Przemyslaw J Porebski, Zdzislaw Wawrzak, Olena Onopriyenko, Marina Kudritska, Sarah Grimshaw, Alexei Savchenko, Wayne F Anderson, Wladek Minor","doi":"10.1007/s10969-012-9131-9","DOIUrl":"https://doi.org/10.1007/s10969-012-9131-9","url":null,"abstract":"Phosphoglycerate kinase (PGK) is indispensable during glycolysis for anaerobic glucose degradation and energy generation. Here we present comprehensive structure analysis of two putative PGKs from Bacillus anthracis str. Sterne and Campylobacter jejuni in the context of their structural homologs. They are the first PGKs from pathogenic bacteria reported in the Protein Data Bank. The crystal structure of PGK from Bacillus anthracis str. Sterne (BaPGK) has been determined at 1.68 Å while the structure of PGK from Campylobacter jejuni (CjPGK) has been determined at 2.14 Å resolution. The proteins' monomers are composed of two domains, each containing a Rossmann fold, hinged together by a helix which can be used to adjust the relative position between two domains. It is also shown that apo-forms of both BaPGK and CjPGK adopt open conformations as compared to the substrate and ATP bound forms of PGK from other species.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":" ","pages":"15-26"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9131-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40152509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica. 一种推定的来自南极洲的等chorismatase水解酶的晶体结构。

Journal of structural and functional genomics Pub Date : 2012-03-01 Epub Date: 2012-02-15 DOI: 10.1007/s10969-012-9127-5

Anna M Goral, Karolina L Tkaczuk, Maksymilian Chruszcz, Olga Kagan, Alexei Savchenko, Wladek Minor

{"title":"Crystal structure of a putative isochorismatase hydrolase from Oleispira antarctica.","authors":"Anna M Goral, Karolina L Tkaczuk, Maksymilian Chruszcz, Olga Kagan, Alexei Savchenko, Wladek Minor","doi":"10.1007/s10969-012-9127-5","DOIUrl":"https://doi.org/10.1007/s10969-012-9127-5","url":null,"abstract":"Isochorismatase-like hydrolases (IHL) constitute a large family of enzymes divided into five structural families (by SCOP). IHLs are crucial for siderophore-mediated ferric iron acquisition by cells. Knowledge of the structural characteristics of these molecules will enhance the understanding of the molecular basis of iron transport, and perhaps resolve which of the mechanisms previously proposed in the literature is the correct one. We determined the crystal structure of the apo-form of a putative isochorismatase hydrolase OaIHL (PDB code: 3LQY) from the antarctic γ-proteobacterium Oleispira antarctica, and did comparative sequential and structural analysis of its closest homologs. The characteristic features of all analyzed structures were identified and discussed. We also docked isochorismate to the determined crystal structure by in silico methods, to highlight the interactions of the active center with the substrate. The putative isochorismate hydrolase OaIHL from O. antarctica possesses the typical catalytic triad for IHL proteins. Its active center resembles those IHLs with a D-K-C catalytic triad, rather than those variants with a D-K-X triad. OaIHL shares some structural and sequential features with other members of the IHL superfamily. In silico docking results showed that despite small differences in active site composition, isochorismate binds to in the structure of OaIHL in a similar mode to its binding in phenazine biosynthesis protein PhzD (PDB code 1NF8).","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 1","pages":"27-36"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9127-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30474600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536. 溶液核磁共振结构揭示了一个独特的结构，并提供了蛋白质结构域家族PF04536的第一个结构。

Journal of structural and functional genomics Pub Date : 2012-03-01 Epub Date: 2011-12-24 DOI: 10.1007/s10969-011-9122-2

Alexander Eletsky, Thomas B Acton, Rong Xiao, John K Everett, Gaetano T Montelione, Thomas Szyperski

{"title":"Solution NMR structures reveal a distinct architecture and provide first structures for protein domain family PF04536.","authors":"Alexander Eletsky, Thomas B Acton, Rong Xiao, John K Everett, Gaetano T Montelione, Thomas Szyperski","doi":"10.1007/s10969-011-9122-2","DOIUrl":"10.1007/s10969-011-9122-2","url":null,"abstract":"The protein family (Pfam) PF04536 is a broadly conserved domain family of unknown function (DUF477), with more than 1,350 members in prokaryotic and eukaryotic proteins. High-quality NMR structures of the N-terminal domain comprising residues 41-180 of the 684-residue protein CG2496 from Corynebacterium glutamicum and the N-terminal domain comprising residues 35-182 of the 435-residue protein PG0361 from Porphyromonas gingivalis both exhibit an α/β fold comprised of a four-stranded β-sheet, three α-helices packed against one side of the sheet, and a fourth α-helix attached to the other side. In spite of low sequence similarity (18%) assessed by structure-based sequence alignment, the two structures are globally quite similar. However, moderate structural differences are observed for the relative orientation of two of the four helices. Comparison with known protein structures reveals that the α/β architecture of CG2496(41-180) and PG0361(35-182) has previously not been characterized. Moreover, calculation of surface charge potential and identification of surface clefts indicate that the two domains very likely have different functions.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 1","pages":"9-14"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-011-9122-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30348113","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Erratum to: Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771 核磁共振结构揭示了独特的同型二聚体形成有翼的螺旋-螺旋-螺旋motif，并为蛋白质结构域家族PF10771提供了第一个结构

Journal of structural and functional genomics Pub Date : 2012-01-01 DOI: 10.1007/s10969-012-9132-8

A. Eletsky, Donald Petrey, Q. Zhang, Hsiau-Wei Lee, T. Acton, R. Xiao, J. Everett, J. Prestegard, B. Honig, G. Montelione, T. Szyperski

引用次数: 0