Journal of structural and functional genomics最新文献_第7页

Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum. 长双歧杆菌II型脱氢奎酸脱水酶样蛋白的晶体结构。

Journal of structural and functional genomics Pub Date : 2013-03-01 Epub Date: 2013-03-29 DOI: 10.1007/s10969-013-9149-7

Samuel H Light, Sankar N Krishna, Raymond C Bergan, Arnon Lavie, Wayne F Anderson

引用次数: 1

New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium. 新的溶菌酶样蛋白亚家族没有催化活性:鼠伤寒沙门氏菌STM3605蛋白的晶体学和生化研究

Journal of structural and functional genomics Pub Date : 2013-03-01 Epub Date: 2013-04-10 DOI: 10.1007/s10969-013-9151-0

Karolina Michalska, Roslyn N Brown, Hui Li, Robert Jedrzejczak, George S Niemann, Fred Heffron, John R Cort, Joshua N Adkins, Gyorgy Babnigg, Andrzej Joachimiak

{"title":"New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium.","authors":"Karolina Michalska, Roslyn N Brown, Hui Li, Robert Jedrzejczak, George S Niemann, Fred Heffron, John R Cort, Joshua N Adkins, Gyorgy Babnigg, Andrzej Joachimiak","doi":"10.1007/s10969-013-9151-0","DOIUrl":"https://doi.org/10.1007/s10969-013-9151-0","url":null,"abstract":"Phage viruses that infect prokaryotes integrate their genome into the host chromosome; thus, microbial genomes typically contain genetic remnants of both recent and ancient phage infections. Often phage genes occur in clusters of atypical G+C content that reflect integration of the foreign DNA. However, some phage genes occur in isolation without other phage gene neighbors, probably resulting from horizontal gene transfer. In these cases, the phage gene product is unlikely to function as a component of a mature phage particle, and instead may have been co-opted by the host for its own benefit. The product of one such gene from Salmonella enterica serovar Typhimurium, STM3605, encodes a protein with modest sequence similarity to phage-like lysozyme (N-acetylmuramidase) but appears to lack essential catalytic residues that are strictly conserved in all lysozymes. Close homologs in other bacteria share this characteristic. The structure of the STM3605 protein was characterized by X-ray crystallography, and functional assays showed that it is a stable, folded protein whose structure closely resembles lysozyme. However, this protein is unlikely to hydrolyze peptidoglycan. Instead, STM3605 is presumed to have evolved an alternative function because it shows some lytic activity and partitions to micelles.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9151-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31438285","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: 4

Solution NMR structure of the helicase associated domain BVU_0683(627-691) from Bacteroides vulgatus provides first structural coverage for protein domain family PF03457 and indicates domain binding to DNA. 解解旋酶相关结构域BVU_0683(627-691)的NMR结构为蛋白结构域家族PF03457提供了第一个结构覆盖，表明该结构域与DNA结合。

Journal of structural and functional genomics Pub Date : 2013-03-01 Epub Date: 2012-11-16 DOI: 10.1007/s10969-012-9148-0

Jeffrey L Mills, Thomas B Acton, Rong Xiao, John K Everett, Gaetano T Montelione, Thomas Szyperski

引用次数: 0

A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs. 对于非专业的生物信息学家来说，这是一个简单的方法，可以为没有已知同源物的蛋白质建立可实验验证的假设。

Journal of structural and functional genomics Pub Date : 2012-12-01 Epub Date: 2012-09-07 DOI: 10.1007/s10969-012-9141-7

Alexander Zawaira, Youtaro Shibayama

{"title":"A simple recipe for the non-expert bioinformaticist for building experimentally-testable hypotheses for proteins with no known homologs.","authors":"Alexander Zawaira, Youtaro Shibayama","doi":"10.1007/s10969-012-9141-7","DOIUrl":"https://doi.org/10.1007/s10969-012-9141-7","url":null,"abstract":"The study of the protein-protein interactions (PPIs) of unique ORFs is a strategy for deciphering the biological roles of unique ORFs of interest. For uniform reference, we define unique ORFs as those for which no matching protein is found after PDB-BLAST search with default parameters. The uniqueness of the ORFs generally precludes the straightforward use of structure-based approaches in the design of experiments to explore PPIs. Many open-source bioinformatics tools, from the commonly-used to the relatively esoteric, have been built and validated to perform analyses and/or predictions of sorts on proteins. How can these available tools be combined into a protocol that helps the non-expert bioinformaticist researcher to design experiments to explore the PPIs of their unique ORF? Here we define a pragmatic protocol based on accessibility of software to achieve this and we make it concrete by applying it on two proteins-the ImuB and ImuA' proteins from Mycobacterium tuberculosis. The protocol is pragmatic in that decisions are made largely based on the availability of easy-to-use freeware. We define the following basic and user-friendly software pathway to build testable PPI hypotheses for a query protein sequence: PSI-PRED → MUSTER → metaPPISP → ASAView and ConSurf. Where possible, other analytical and/or predictive tools may be included. Our protocol combines the software predictions and analyses with general bioinformatics principles to arrive at consensus, prioritised and testable PPI hypotheses.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 4","pages":"185-200"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9141-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30885582","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: 0

The crystal structures of the α-subunit of the α(2)β (2) tetrameric Glycyl-tRNA synthetase. α(2)β(2)四聚体甘氨酸- trna合成酶α-亚基的晶体结构。

Journal of structural and functional genomics Pub Date : 2012-12-01 Epub Date: 2012-10-06 DOI: 10.1007/s10969-012-9142-6

Kemin Tan, Min Zhou, Rongguang Zhang, Wayne F Anderson, Andrzej Joachimiak

{"title":"The crystal structures of the α-subunit of the α(2)β (2) tetrameric Glycyl-tRNA synthetase.","authors":"Kemin Tan, Min Zhou, Rongguang Zhang, Wayne F Anderson, Andrzej Joachimiak","doi":"10.1007/s10969-012-9142-6","DOIUrl":"https://doi.org/10.1007/s10969-012-9142-6","url":null,"abstract":"Aminoacyl-tRNA synthetases (AARSs) are ligases (EC.6.1.1.-) that catalyze the acylation of amino acids to their cognate tRNAs in the process of translating genetic information from mRNA to protein. Their amino acid and tRNA specificity are crucial for correctly translating the genetic code. Glycine is the smallest amino acid and the glycyl-tRNA synthetase (GlyRS) belongs to Class II AARSs. The enzyme is unusual because it can assume different quaternary structures. In eukaryotes, archaebacteria and some bacteria, it forms an α(2) homodimer. In some bacteria, GlyRS is an α(2)β(2) heterotetramer and shows a distant similarity to α(2) GlyRSs. The human pathogen eubacterium Campylobacter jejuni GlyRS (CjGlyRS) is an α(2)β(2) heterotetramer and is similar to Escherichia coli GlyRS; both are members of Class IIc AARSs. The two-step aminoacylation reaction of tetrameric GlyRSs requires the involvement of both α- and β-subunits. At present, the structure of the GlyRS α(2)β(2) class and the details of the enzymatic mechanism of this enzyme remain unknown. Here we report the crystal structures of the catalytic α-subunit of CjGlyRS and its complexes with ATP, and ATP and glycine. These structures provide detailed information on substrate binding and show evidence for a proposed mechanism for amino acid activation and the formation of the glycyl-adenylate intermediate for Class II AARSs.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 4","pages":"233-9"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9142-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30966518","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: 9

A unified NMR strategy for high-throughput determination of backbone fold of small proteins. 一种统一的核磁共振策略，用于小蛋白质主干折叠的高通量测定。

Journal of structural and functional genomics Pub Date : 2012-12-01 Epub Date: 2012-09-28 DOI: 10.1007/s10969-012-9144-4

Dinesh Kumar, Anmol Gautam, Ramakrishna V Hosur

{"title":"A unified NMR strategy for high-throughput determination of backbone fold of small proteins.","authors":"Dinesh Kumar, Anmol Gautam, Ramakrishna V Hosur","doi":"10.1007/s10969-012-9144-4","DOIUrl":"https://doi.org/10.1007/s10969-012-9144-4","url":null,"abstract":"An efficient semi-automated strategy called PFBD (i.e. Protein Fold from Backbone Data only) has been presented for rapid backbone fold determination of small proteins. It makes use of NMR parameters involving backbone atoms only. These include chemical shifts, amide-amide NOEs and H-bonds. The backbone chemical shifts are obtained in an automated manner from the orthogonal 2D projections of variants of HNN and HN(C)N experiments (Kumar et al., in Magn Reson Chem 50(5):357-363, 2012) using AUTOBA (Borkar et al. in J Biomol NMR 50(3):285-297, 2011); backbone H-bonds are manually derived from constant time long-range 2D-HnCO spectrum (Cordier and Grzesiek in J Am Chem Soc 121:1601-1602, 1999); and amide-amide NOEs are derived from 3D HNCO NOESY experiment which provides NOEs along the direct (1)H dimension that has maximum resolution (Lohr and Ruterjans in J Biomol NMR 9(1):371-388, 1997). All the experiments needed for the execution of PFBD can be recorded and analyzed in about 24-48 h depending upon the concentration of the protein and dispersion of amide cross-peaks in the (1)H-(15)N correlation spectrum. Thus, we believe that the strategy, because of its speed and simplicity will be very valuable in Biomolecular NMR community for high-throughput structural proteomics of small folded proteins of MW < 10-12 kDa, the regime where NMR is generally preferred over X-ray crystallography. The strategy has been validated and demonstrated here on two small globular proteins: human ubiquitin (76 aa) and chicken SH3 domain (62 aa).","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 4","pages":"201-12"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9144-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30966519","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: 3

Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures. 通过与结构基因组学结构的比较评估基于模板的结构预测元服务器的准确性。

Journal of structural and functional genomics Pub Date : 2012-12-01 Epub Date: 2012-10-20 DOI: 10.1007/s10969-012-9146-2

Dominik Gront, Marek Grabowski, Matthew D Zimmerman, John Raynor, Karolina L Tkaczuk, Wladek Minor

{"title":"Assessing the accuracy of template-based structure prediction metaservers by comparison with structural genomics structures.","authors":"Dominik Gront, Marek Grabowski, Matthew D Zimmerman, John Raynor, Karolina L Tkaczuk, Wladek Minor","doi":"10.1007/s10969-012-9146-2","DOIUrl":"https://doi.org/10.1007/s10969-012-9146-2","url":null,"abstract":"The 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.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 4","pages":"213-25"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9146-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30990519","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

Pitfalls in the interpretation of structural changes in mutant proteins from crystal structures. 从晶体结构解读突变蛋白质结构变化的陷阱。

Journal of structural and functional genomics Pub Date : 2012-12-01 Epub Date: 2012-10-26 DOI: 10.1007/s10969-012-9147-1

P R Pokkuluri, X Yang, Y Y Londer, M Schiffer

{"title":"Pitfalls in the interpretation of structural changes in mutant proteins from crystal structures.","authors":"P R Pokkuluri, X Yang, Y Y Londer, M Schiffer","doi":"10.1007/s10969-012-9147-1","DOIUrl":"10.1007/s10969-012-9147-1","url":null,"abstract":"PpcA is a small protein with 71 residues that contains three covalently bound hemes. The structures of single mutants at residue 58 have shown larger deviations in another part of the protein molecule than at the site of the mutation. Closer examination of the crystal packing has revealed the origin of this unexpected structural change. The site of mutation is within Van der Waals distance from another protein molecule related by a crystallographic twofold axis within the crystal. The structural changes occurred at or near the mutation site have led to a slight adjustment of the surface residues in contact. The observed deviations between the native and the mutant molecular structures are derived from the new crystal packing even though the two crystals are essentially isomorphous. Without careful consideration of the crystal lattice a non-expert looking at only the coordinates deposited in the Protein Data Bank could draw erroneous conclusion that mutation in one part of the molecule affected the structure of the protein in a distant part of the molecule.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"13 4","pages":"227-32"},"PeriodicalIF":0.0,"publicationDate":"2012-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109977/pdf/nihms604329.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31003584","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

Crystal structure of mouse RhoA:GTPγS complex in a centered lattice. 小鼠RhoA: gtp - γ s配合物在中心晶格中的晶体结构。

Journal of structural and functional genomics Pub Date : 2012-12-01 Epub Date: 2012-09-22 DOI: 10.1007/s10969-012-9143-5

Chacko Jobichen, Kuntal Pal, Kunchithapadam Swaminathan

引用次数: 8

Utility of anion and cation combinations for phasing of protein structures. 阴离子和阳离子组合在蛋白质结构相化中的应用。

Journal of structural and functional genomics Pub Date : 2012-09-01 Epub Date: 2012-05-06 DOI: 10.1007/s10969-012-9137-3

Ashwani Sharma, Manickam Yogavel, Amit Sharma

引用次数: 9