Journal of structural and functional genomics最新文献_第8页

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":null,"pages":null},"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

Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain-like folds and different functions. 来自金黄色葡萄球菌和枯草芽孢杆菌的PF06855蛋白结构域家族的三个结构代表具有类似SAM结构域的折叠，功能不同。

Journal of structural and functional genomics Pub Date : 2012-09-01 Epub Date: 2012-07-29 DOI: 10.1007/s10969-012-9134-6

G V T Swapna, Paolo Rossi, Alexander F Montelione, Jordi Benach, Bomina Yu, Mariam Abashidze, Jayaraman Seetharaman, Rong Xiao, Thomas B Acton, Liang Tong, Gaetano T Montelione

{"title":"Three structural representatives of the PF06855 protein domain family from Staphyloccocus aureus and Bacillus subtilis have SAM domain-like folds and different functions.","authors":"G V T Swapna, Paolo Rossi, Alexander F Montelione, Jordi Benach, Bomina Yu, Mariam Abashidze, Jayaraman Seetharaman, Rong Xiao, Thomas B Acton, Liang Tong, Gaetano T Montelione","doi":"10.1007/s10969-012-9134-6","DOIUrl":"https://doi.org/10.1007/s10969-012-9134-6","url":null,"abstract":"Protein domain family PF06855 (DUF1250) is a family of small domains of unknown function found only in bacteria, and mostly in the order Bacillales and Lactobacillales. Here we describe the solution NMR or X-ray crystal structures of three representatives of this domain family, MW0776 and MW1311 from Staphyloccocus aureus and yozE from Bacillus subtilis. All three proteins adopt a four-helix motif similar to sterile alpha motif (SAM) domains. Phylogenetic analysis classifies MW1311 and yozE as functionally equivalent proteins of the UPF0346 family of unknown function, but excludes MW0776, which likely has a different biological function. Our structural characterization of the three domains supports this separation of function. The structures of MW0776, MW1311, and yozE constitute the first structural representatives from this protein domain family.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9134-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30797636","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: 1

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. 来自蛋白结构域家族PF04237 (DUF419)的丁香假单胞菌Pspto_3016的核磁共振和x射线晶体结构采用“双翼”DNA结合基元。

Journal of structural and functional genomics Pub Date : 2012-09-01 Epub Date: 2012-08-03 DOI: 10.1007/s10969-012-9140-8

Erik A Feldmann, Jayaraman Seetharaman, Theresa A Ramelot, Scott Lew, Li Zhao, Keith Hamilton, Colleen Ciccosanti, Rong Xiao, Thomas B Acton, John K Everett, Liang Tong, Gaetano T Montelione, Michael A Kennedy

{"title":"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.","authors":"Erik A Feldmann, Jayaraman Seetharaman, Theresa A Ramelot, Scott Lew, Li Zhao, Keith Hamilton, Colleen Ciccosanti, Rong Xiao, Thomas B Acton, John K Everett, Liang Tong, Gaetano T Montelione, Michael A Kennedy","doi":"10.1007/s10969-012-9140-8","DOIUrl":"https://doi.org/10.1007/s10969-012-9140-8","url":null,"abstract":"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/β 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).","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9140-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30813023","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

Solution NMR structure of Alr2454 from Nostoc sp. PCC 7120, the first structural representative of Pfam domain family PF11267. 来自Nostoc sp. PCC 7120的Alr2454的溶液核磁共振结构，Pfam结构域家族PF11267的第一个结构代表。

Journal of structural and functional genomics Pub Date : 2012-09-01 Epub Date: 2012-05-17 DOI: 10.1007/s10969-012-9135-5

James M Aramini, Donald Petrey, Dong Yup Lee, Haleema Janjua, Rong Xiao, Thomas B Acton, John K Everett, Gaetano T Montelione

引用次数: 3

TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan. TP图谱:整合和传播靶向蛋白研究计划(TPRP)-日本结构生物学项目二期的进展。

Journal of structural and functional genomics Pub Date : 2012-09-01 Epub Date: 2012-05-29 DOI: 10.1007/s10969-012-9139-1

Takao Iwayanagi, Sei Miyamoto, Takeshi Konno, Hisashi Mizutani, Tomohiro Hirai, Yasumasa Shigemoto, Takashi Gojobori, Hideaki Sugawara

{"title":"TP Atlas: integration and dissemination of advances in Targeted Proteins Research Program (TPRP)-structural biology project phase II in Japan.","authors":"Takao Iwayanagi, Sei Miyamoto, Takeshi Konno, Hisashi Mizutani, Tomohiro Hirai, Yasumasa Shigemoto, Takashi Gojobori, Hideaki Sugawara","doi":"10.1007/s10969-012-9139-1","DOIUrl":"https://doi.org/10.1007/s10969-012-9139-1","url":null,"abstract":"The Targeted Proteins Research Program (TPRP) promoted by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan is the phase II of structural biology project (2007-2011) following the Protein 3000 Project (2002-2006) in Japan. While the phase I Protein 3000 Project put partial emphasis on the construction and maintenance of pipelines for structural analyses, the TPRP is dedicated to revealing the structures and functions of the targeted proteins that have great importance in both basic research and industrial applications. To pursue this objective, 35 Targeted Proteins (TP) Projects selected in the three areas of fundamental biology, medicine and pharmacology, and food and environment are tightly collaborated with 10 Advanced Technology (AT) Projects in the four fields of protein production, structural analyses, chemical library and screening, and information platform. Here, the outlines and achievements of the 35 TP Projects are summarized in the system named TP Atlas. Progress in the diversified areas is described in the modules of Graphical Summary, General Summary, Tabular Summary, and Structure Gallery of the TP Atlas in the standard and unified format. Advances in TP Projects owing to novel technologies stemmed from AT Projects and collaborative research among TP Projects are illustrated as a hallmark of the Program. The TP Atlas can be accessed at http://net.genes.nig.ac.jp/tpatlas/index_e.html .","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9139-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30652138","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

Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product. 结合c-二gmp产物的水绿海洋杆菌GG(D/E)EF二胍酸环化酶结构域的晶体结构

Journal of structural and functional genomics Pub Date : 2012-09-01 Epub Date: 2012-07-29 DOI: 10.1007/s10969-012-9136-4

Sergey M Vorobiev, Helen Neely, Bomina Yu, Jayaraman Seetharaman, Rong Xiao, Thomas B Acton, Gaetano T Montelione, John F Hunt

{"title":"Crystal structure of a catalytically active GG(D/E)EF diguanylate cyclase domain from Marinobacter aquaeolei with bound c-di-GMP product.","authors":"Sergey M Vorobiev, Helen Neely, Bomina Yu, Jayaraman Seetharaman, Rong Xiao, Thomas B Acton, Gaetano T Montelione, John F Hunt","doi":"10.1007/s10969-012-9136-4","DOIUrl":"https://doi.org/10.1007/s10969-012-9136-4","url":null,"abstract":"Recent studies of signal transduction in bacteria have revealed a unique second messenger, bis-(3'-5')-cyclic dimeric GMP (c-di-GMP), which regulates transitions between motile states and sessile states, such as biofilms. C-di-GMP is synthesized from two GTP molecules by diguanylate cyclases (DGC). The catalytic activity of DGCs depends on a conserved GG(D/E)EF domain, usually part of a larger multi-domain protein organization. The domains other than the GG(D/E)EF domain often control DGC activation. This paper presents the 1.83 Å crystal structure of an isolated catalytically competent GG(D/E)EF domain from the A1U3W3_MARAV protein from Marinobacter aquaeolei. Co-crystallization with GTP resulted in enzymatic synthesis of c-di-GMP. Comparison with previously solved DGC structures shows a similar orientation of c-di-GMP bound to an allosteric regulatory site mediating feedback inhibition of the enzyme. Biosynthesis of c-di-GMP in the crystallization reaction establishes that the enzymatic activity of this DGC domain does not require interaction with regulatory domains.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2012-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-012-9136-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30797638","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: 15

Canadian macromolecular crystallography facility: a suite of fully automated beamlines. 加拿大大分子晶体学设备:一套全自动光束线。

Journal of structural and functional genomics Pub Date : 2012-06-01 Epub Date: 2012-01-21 DOI: 10.1007/s10969-012-9123-9

Pawel Grochulski, Michel Fodje, Shaunivan Labiuk, James Gorin, Kathryn Janzen, Russ Berg

{"title":"Canadian macromolecular crystallography facility: a suite of fully automated beamlines.","authors":"Pawel Grochulski, Michel Fodje, Shaunivan Labiuk, James Gorin, Kathryn Janzen, Russ Berg","doi":"10.1007/s10969-012-9123-9","DOIUrl":"https://doi.org/10.1007/s10969-012-9123-9","url":null,"abstract":"The Canadian light source is a 2.9 GeV national synchrotron radiation facility located on the University of Saskatchewan campus in Saskatoon. The small-gap in-vacuum undulator illuminated beamline, 08ID-1, together with the bending magnet beamline, 08B1-1, constitute the Canadian Macromolecular Crystallography Facility (CMCF). The CMCF provides service to more than 50 Principal Investigators in Canada and the United States. Up to 25% of the beam time is devoted to commercial users and the general user program is guaranteed up to 55% of the useful beam time through a peer-review process. CMCF staff provides \"Mail-In\" crystallography service to users with the highest scored proposals. Both beamlines are equipped with very robust end-stations including on-axis visualization systems, Rayonix 300 CCD series detectors and Stanford-type robotic sample auto-mounters. MxDC, an in-house developed beamline control system, is integrated with a data processing module, AutoProcess, allowing full automation of data collection and data processing with minimal human intervention. Sample management and remote monitoring of experiments is enabled through interaction with a Laboratory Information Management System developed at the facility.","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/s10969-012-9123-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30407065","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: 16

Structure- and sequence-based function prediction for non-homologous proteins. 基于结构和序列的非同源蛋白功能预测。

Journal of structural and functional genomics Pub Date : 2012-06-01 Epub Date: 2012-01-22 DOI: 10.1007/s10969-012-9126-6

Lee Sael, Meghana Chitale, Daisuke Kihara

{"title":"Structure- and sequence-based function prediction for non-homologous proteins.","authors":"Lee Sael, Meghana Chitale, Daisuke Kihara","doi":"10.1007/s10969-012-9126-6","DOIUrl":"https://doi.org/10.1007/s10969-012-9126-6","url":null,"abstract":"The structural genomics projects have been accumulating an increasing number of protein structures, many of which remain functionally unknown. In parallel effort to experimental methods, computational methods are expected to make a significant contribution for functional elucidation of such proteins. However, conventional computational methods that transfer functions from homologous proteins do not help much for these uncharacterized protein structures because they do not have apparent structural or sequence similarity with the known proteins. Here, we briefly review two avenues of computational function prediction methods, i.e. structure-based methods and sequence-based methods. The focus is on our recent developments of local structure-based and sequence-based methods, which can effectively extract function information from distantly related proteins. Two structure-based methods, Pocket-Surfer and Patch-Surfer, identify similar known ligand binding sites for pocket regions in a query protein without using global protein fold similarity information. Two sequence-based methods, protein function prediction and extended similarity group, make use of weakly similar sequences that are conventionally discarded in homology based function annotation. Combined together with experimental methods we hope that computational methods will make leading contribution in functional elucidation of the protein structures.","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/s10969-012-9126-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30407068","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: 34