Pub Date : 2012-06-01Epub Date: 2012-05-27DOI: 10.1007/s10969-012-9138-2
David M Lawson, Clare E M Stevenson
Aminocoumarin antibiotics are natural products of soil-dwelling bacteria called Streptomycetes. They are potent inhibitors of DNA gyrase, an essential bacterial enzyme and validated drug target, and thus have attracted considerable interest as potential templates for drug development. To date, aminocoumarins have not seen widespread clinical application on account of their poor pharmacological properties. Through studying the structures and mechanisms of enzymes from their biosynthetic pathways we will be better informed to redesign these compounds through rational pathway engineering. Novobiocin, the simplest compound, requires at least seventeen gene products to convert primary metabolites into the mature antibiotic. We have solved the crystal structures of four diverse biosynthetic enzymes from the novobiocin pathway, and used these as three-dimensional frameworks for the interpretation of functional and mechanistic data, and to speculate about how they might have evolved. The structure determinations have ranged from the routine to the challenging, necessitating a variety of different approaches.
{"title":"Structural and functional dissection of aminocoumarin antibiotic biosynthesis: a review.","authors":"David M Lawson, Clare E M Stevenson","doi":"10.1007/s10969-012-9138-2","DOIUrl":"https://doi.org/10.1007/s10969-012-9138-2","url":null,"abstract":"<p><p>Aminocoumarin antibiotics are natural products of soil-dwelling bacteria called Streptomycetes. They are potent inhibitors of DNA gyrase, an essential bacterial enzyme and validated drug target, and thus have attracted considerable interest as potential templates for drug development. To date, aminocoumarins have not seen widespread clinical application on account of their poor pharmacological properties. Through studying the structures and mechanisms of enzymes from their biosynthetic pathways we will be better informed to redesign these compounds through rational pathway engineering. Novobiocin, the simplest compound, requires at least seventeen gene products to convert primary metabolites into the mature antibiotic. We have solved the crystal structures of four diverse biosynthetic enzymes from the novobiocin pathway, and used these as three-dimensional frameworks for the interpretation of functional and mechanistic data, and to speculate about how they might have evolved. The structure determinations have ranged from the routine to the challenging, necessitating a variety of different approaches.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9138-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30652137","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}
Pub Date : 2012-06-01Epub Date: 2011-11-19DOI: 10.1007/s10969-011-9118-y
Yvonne Thielmann, Juergen Koepke, Hartmut Michel
Structure determination of membrane proteins and membrane protein complexes is still a very challenging field. To facilitate the work on membrane proteins the Core Centre follows a strategy that comprises four labs of protein analytics and crystal handling, covering mass spectrometry, calorimetry, crystallization and X-ray diffraction. This general workflow is presented and a capacity of 20% of the operating time of all systems is provided to the European structural biology community within the ESFRI Instruct program. A description of the crystallization service offered at the Core Centre is given with detailed information on screening strategy, screens used and changes to adapt high throughput for membrane proteins. Our aim is to constantly develop the Core Centre towards the usage of more efficient methods. This strategy might also include the ability to automate all steps from crystallization trials to crystal screening; here we look ahead how this aim might be realized at the Core Centre.
{"title":"The ESFRI Instruct Core Centre Frankfurt: automated high-throughput crystallization suited for membrane proteins and more.","authors":"Yvonne Thielmann, Juergen Koepke, Hartmut Michel","doi":"10.1007/s10969-011-9118-y","DOIUrl":"https://doi.org/10.1007/s10969-011-9118-y","url":null,"abstract":"<p><p>Structure determination of membrane proteins and membrane protein complexes is still a very challenging field. To facilitate the work on membrane proteins the Core Centre follows a strategy that comprises four labs of protein analytics and crystal handling, covering mass spectrometry, calorimetry, crystallization and X-ray diffraction. This general workflow is presented and a capacity of 20% of the operating time of all systems is provided to the European structural biology community within the ESFRI Instruct program. A description of the crystallization service offered at the Core Centre is given with detailed information on screening strategy, screens used and changes to adapt high throughput for membrane proteins. Our aim is to constantly develop the Core Centre towards the usage of more efficient methods. This strategy might also include the ability to automate all steps from crystallization trials to crystal screening; here we look ahead how this aim might be realized at the Core Centre.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-011-9118-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30269724","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}
Pub Date : 2012-06-01Epub Date: 2012-04-06DOI: 10.1007/s10969-012-9133-7
Lida K Gifford, Lester G Carter, Margaret J Gabanyi, Helen M Berman, Paul D Adams
The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.
{"title":"The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource.","authors":"Lida K Gifford, Lester G Carter, Margaret J Gabanyi, Helen M Berman, Paul D Adams","doi":"10.1007/s10969-012-9133-7","DOIUrl":"10.1007/s10969-012-9133-7","url":null,"abstract":"<p><p>The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/ ) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB ( http://sbkb.org ), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3588887/pdf/nihms376741.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40177477","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}
Pub Date : 2012-06-01Epub Date: 2012-03-15DOI: 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
The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement.
{"title":"phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.","authors":"Thomas C Terwilliger, Frank Dimaio, Randy J Read, David Baker, Gábor Bunkóczi, Paul D Adams, Ralf W Grosse-Kunstleve, Pavel V Afonine, Nathaniel Echols","doi":"10.1007/s10969-012-9129-3","DOIUrl":"https://doi.org/10.1007/s10969-012-9129-3","url":null,"abstract":"<p><p>The combination of algorithms from the structure-modeling field with those of crystallographic structure determination can broaden the range of templates that are useful for structure determination by the method of molecular replacement. Automated tools in phenix.mr_rosetta simplify the application of these combined approaches by integrating Phenix crystallographic algorithms and Rosetta structure-modeling algorithms and by systematically generating and evaluating models with a combination of these methods. The phenix.mr_rosetta algorithms can be used to automatically determine challenging structures. The approaches used in phenix.mr_rosetta are described along with examples that show roles that structure-modeling can play in molecular replacement.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9129-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40166686","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}
Pub Date : 2012-06-01DOI: 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
Ligands interacting with Mycobacterium tuberculosis recombinant proteins were identified through use of the ability of Cibacron Blue F3GA dye to interact with nucleoside/nucleotide binding proteins, and the effects of these ligands on crystallization were examined. Co-crystallization with ligands enhanced crystallization and enabled X-ray diffraction data to be collected to a resolution of atleast 2.7 Å for 5 of 10 proteins tested. Additionally, clues about individual proteins’ functions were obtained from their interactions with each of a panel of ligands.
通过利用 Cibacron Blue F3GA 染料与核苷酸/核苷酸结合蛋白相互作用的能力,确定了与结核分枝杆菌重组蛋白相互作用的配体,并研究了这些配体对结晶的影响。与配体共结晶增强了结晶效果,并使所测试的 10 个蛋白质中的 5 个蛋白质的 X 射线衍射数据的分辨率至少达到 2.7 Å。此外,还从蛋白质与配体的相互作用中获得了有关单个蛋白质功能的线索。
{"title":"Enhancement of crystallization with nucleotide ligands identified by dye-ligand affinity chromatography.","authors":"Heungbok Kim, Cecelia Webster, Justin K M Roberts, Juthamas Kositsawat, Li-Wei Hung, Thomas C Terwilliger, Chang-Yub Kim","doi":"10.1007/s10969-012-9124-8","DOIUrl":"10.1007/s10969-012-9124-8","url":null,"abstract":"<p><p>Ligands interacting with Mycobacterium tuberculosis recombinant proteins were identified through use of the ability of Cibacron Blue F3GA dye to interact with nucleoside/nucleotide binding proteins, and the effects of these ligands on crystallization were examined. Co-crystallization with ligands enhanced crystallization and enabled X-ray diffraction data to be collected to a resolution of atleast 2.7 Å for 5 of 10 proteins tested. Additionally, clues about individual proteins’ functions were obtained from their interactions with each of a panel of ligands.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3375012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30420526","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}
Pub Date : 2012-06-01Epub Date: 2012-01-21DOI: 10.1007/s10969-012-9125-7
Elchin S Julfayev, Ryan J McLaughlin, Yi-Ping Tao, William A McLaughlin
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.
{"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":"<p><p>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.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"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}
Pub Date : 2012-06-01Epub Date: 2012-02-22DOI: 10.1007/s10969-012-9128-4
Nadezda V Kovalevskaya, Fedir M Bokhovchuk, Geerten W Vuister
The epithelial Ca(2+) channels TRPV5/6 (transient receptor potential vanilloid 5/6) are thoroughly regulated in order to fine-tune the amount of Ca(2+) reabsorption. Calmodulin has been shown to be involved into calcium-dependent inactivation of TRPV5/6 channels by binding directly to the distal C-terminal fragment of the channels (de Groot et al. in Mol Cell Biol 31:2845-2853, 12). Here, we investigate this binding in detail and find significant differences between TRPV5 and TRPV6. We also identify and characterize in vitro four other CaM binding fragments of TRPV5/6, which likely are also involved in TRPV5/6 channel regulation. The five CaM binding sites display diversity in binding modes, binding stoichiometries and binding affinities, which may fine-tune the response of the channels to varying Ca(2+)-concentrations.
上皮Ca(2+)通道TRPV5/6(瞬时受体电位香草蛋白5/6)被彻底调节,以微调Ca(2+)重吸收量。钙调素已被证明通过直接结合通道的远端c端片段参与TRPV5/6通道的钙依赖性失活(de Groot et al. in Mol Cell Biol 31:2845- 2853,12)。在这里,我们详细研究了这种结合,发现TRPV5和TRPV6之间存在显著差异。我们还在体外鉴定并表征了TRPV5/6的另外四个CaM结合片段,它们可能也参与了TRPV5/6通道的调节。5个CaM结合位点在结合模式、结合化学计量学和结合亲和力方面表现出多样性,这可能微调了通道对不同Ca(2+)浓度的响应。
{"title":"The TRPV5/6 calcium channels contain multiple calmodulin binding sites with differential binding properties.","authors":"Nadezda V Kovalevskaya, Fedir M Bokhovchuk, Geerten W Vuister","doi":"10.1007/s10969-012-9128-4","DOIUrl":"https://doi.org/10.1007/s10969-012-9128-4","url":null,"abstract":"<p><p>The epithelial Ca(2+) channels TRPV5/6 (transient receptor potential vanilloid 5/6) are thoroughly regulated in order to fine-tune the amount of Ca(2+) reabsorption. Calmodulin has been shown to be involved into calcium-dependent inactivation of TRPV5/6 channels by binding directly to the distal C-terminal fragment of the channels (de Groot et al. in Mol Cell Biol 31:2845-2853, 12). Here, we investigate this binding in detail and find significant differences between TRPV5 and TRPV6. We also identify and characterize in vitro four other CaM binding fragments of TRPV5/6, which likely are also involved in TRPV5/6 channel regulation. The five CaM binding sites display diversity in binding modes, binding stoichiometries and binding affinities, which may fine-tune the response of the channels to varying Ca(2+)-concentrations.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9128-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30476586","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}
Pub Date : 2012-03-01Epub Date: 2012-01-06DOI: 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
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.
{"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":"<p><p>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.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"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}
Pub Date : 2012-03-01Epub Date: 2012-02-22DOI: 10.1007/s10969-012-9130-x
James E Bray
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.
{"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":"<p><p>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.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"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}
Pub Date : 2012-03-01Epub Date: 2012-03-10DOI: 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
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.
{"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":"<p><p>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.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"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}