Journal of structural and functional genomics最新文献_第2页

Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation. 基于相互作用能和序列守恒的蛋白质-配体结合位点预测方法的建立。

Journal of structural and functional genomics Pub Date : 2016-09-01 Epub Date: 2016-07-11 DOI: 10.1007/s10969-016-9204-2

Hiroto Tsujikawa, Kenta Sato, Cao Wei, Gul Saad, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Kentaro Shimizu

{"title":"Development of a protein-ligand-binding site prediction method based on interaction energy and sequence conservation.","authors":"Hiroto Tsujikawa, Kenta Sato, Cao Wei, Gul Saad, Kazuya Sumikoshi, Shugo Nakamura, Tohru Terada, Kentaro Shimizu","doi":"10.1007/s10969-016-9204-2","DOIUrl":"https://doi.org/10.1007/s10969-016-9204-2","url":null,"abstract":"We present a new method for predicting protein-ligand-binding sites based on protein three-dimensional structure and amino acid conservation. This method involves calculation of the van der Waals interaction energy between a protein and many probes placed on the protein surface and subsequent clustering of the probes with low interaction energies to identify the most energetically favorable locus. In addition, it uses amino acid conservation among homologous proteins. Ligand-binding sites were predicted by combining the interaction energy and the amino acid conservation score. The performance of our prediction method was evaluated using a non-redundant dataset of 348 ligand-bound and ligand-unbound protein structure pairs, constructed by filtering entries in a ligand-binding site structure database, LigASite. Ligand-bound structure prediction (bound prediction) indicated that 74.0 % of predicted ligand-binding sites overlapped with real ligand-binding sites by over 25 % of their volume. Ligand-unbound structure prediction (unbound prediction) indicated that 73.9 % of predicted ligand-binding residues overlapped with real ligand-binding residues. The amino acid conservation score improved the average prediction accuracy by 17.0 and 17.6 points for the bound and unbound predictions, respectively. These results demonstrate the effectiveness of the combined use of the interaction energy and amino acid conservation in the ligand-binding site prediction. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-016-9204-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34721445","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: 10

Expression, purification, and crystallization of Schizosaccharomyces pombe eIF2B Schizosaccharomyces pombe eIF2B的表达、纯化和结晶

Journal of structural and functional genomics Pub Date : 2016-03-29 DOI: 10.1007/s10969-016-9203-3

K. Kashiwagi, T. Shigeta, H. Imataka, Takuhiro Ito, S. Yokoyama

引用次数: 4

The impact of structural genomics: the first quindecennial 结构基因组学的影响:第一个十年

Journal of structural and functional genomics Pub Date : 2016-03-02 DOI: 10.1007/s10969-016-9201-5

M. Grabowski, E. Niedzialkowska, M. Zimmerman, W. Minor

引用次数: 57

Automated protein motif generation in the structure-based protein function prediction tool ProMOL. 在基于结构的蛋白质功能预测工具 ProMOL 中自动生成蛋白质主题。

Journal of structural and functional genomics Pub Date : 2015-12-01 Epub Date: 2015-11-16 DOI: 10.1007/s10969-015-9199-0

Mikhail Osipovitch, Mitchell Lambrecht, Cameron Baker, Shariq Madha, Jeffrey L Mills, Paul A Craig, Herbert J Bernstein

{"title":"Automated protein motif generation in the structure-based protein function prediction tool ProMOL.","authors":"Mikhail Osipovitch, Mitchell Lambrecht, Cameron Baker, Shariq Madha, Jeffrey L Mills, Paul A Craig, Herbert J Bernstein","doi":"10.1007/s10969-015-9199-0","DOIUrl":"10.1007/s10969-015-9199-0","url":null,"abstract":"ProMOL, a plugin for the PyMOL molecular graphics system, is a structure-based protein function prediction tool. ProMOL includes a set of routines for building motif templates that are used for screening query structures for enzyme active sites. Previously, each motif template was generated manually and required supervision in the optimization of parameters for sensitivity and selectivity. We developed an algorithm and workflow for the automation of motif building and testing routines in ProMOL. The algorithm uses a set of empirically derived parameters for optimization and requires little user intervention. The automated motif generation algorithm was first tested in a performance comparison with a set of manually generated motifs based on identical active sites from the same 112 PDB entries. The two sets of motifs were equally effective in identifying alignments with homologs and in rejecting alignments with unrelated structures. A second set of 296 active site motifs were generated automatically, based on Catalytic Site Atlas entries with literature citations, as an expansion of the library of existing manually generated motif templates. The new motif templates exhibited comparable performance to the existing ones in terms of hit rates against native structures, homologs with the same EC and Pfam designations, and randomly selected unrelated structures with a different EC designation at the first EC digit, as well as in terms of RMSD values obtained from local structural alignments of motifs and query structures. This research is supported by NIH grant GM078077. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684744/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81556142","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

Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes. 共同表达和生产重组蛋白-蛋白复合物的基因选择和克隆方法。

Journal of structural and functional genomics Pub Date : 2015-12-01 Epub Date: 2015-12-15 DOI: 10.1007/s10969-015-9200-y

György Babnigg, Robert Jedrzejczak, Boguslaw Nocek, Adam Stein, William Eschenfeldt, Lucy Stols, Norman Marshall, Alicia Weger, Ruiying Wu, Mark Donnelly, Andrzej Joachimiak

{"title":"Gene selection and cloning approaches for co-expression and production of recombinant protein-protein complexes.","authors":"György Babnigg, Robert Jedrzejczak, Boguslaw Nocek, Adam Stein, William Eschenfeldt, Lucy Stols, Norman Marshall, Alicia Weger, Ruiying Wu, Mark Donnelly, Andrzej Joachimiak","doi":"10.1007/s10969-015-9200-y","DOIUrl":"10.1007/s10969-015-9200-y","url":null,"abstract":"Multiprotein complexes play essential roles in all cells and X-ray crystallography can provide unparalleled insight into their structure and function. Many of these complexes are believed to be sufficiently stable for structural biology studies, but the production of protein-protein complexes using recombinant technologies is still labor-intensive. We have explored several strategies for the identification and cloning of heterodimers and heterotrimers that are compatible with the high-throughput (HTP) structural biology pipeline developed for single proteins. Two approaches are presented and compared which resulted in co-expression of paired genes from a single expression vector. Native operons encoding predicted interacting proteins were selected from a repertoire of genomes, and cloned directly to expression vector. In an alternative approach, Helicobacter pylori proteins predicted to interact strongly were cloned, each associated with translational control elements, then linked into an artificial operon. Proteins were then expressed and purified by standard HTP protocols, resulting to date in the structure determination of two H. pylori complexes. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6886524/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73311969","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 the MazG-related nucleoside triphosphate pyrophosphohydrolase from Thermotoga maritima MSB8. 海洋热藓MSB8中与mazg相关的核苷三磷酸焦磷酸水解酶的晶体结构。

Journal of structural and functional genomics Pub Date : 2015-06-01 Epub Date: 2015-03-11 DOI: 10.1007/s10969-015-9195-4

Balasundaram Padmanabhan, Prashant Deshmukh, Shigeyuki Yokoyama, Yoshitaka Bessho

{"title":"Crystal structure of the MazG-related nucleoside triphosphate pyrophosphohydrolase from Thermotoga maritima MSB8.","authors":"Balasundaram Padmanabhan, Prashant Deshmukh, Shigeyuki Yokoyama, Yoshitaka Bessho","doi":"10.1007/s10969-015-9195-4","DOIUrl":"https://doi.org/10.1007/s10969-015-9195-4","url":null,"abstract":"The MazG family proteins, which are highly conserved in bacteria, are nucleoside triphosphate pyrophosphohydrolases that hydrolyze all canonical nucleoside triphosphates, and are also involved in removing noncanonical nucleoside triphosphates to prevent their incorporation into DNA or RNA. The primary structure of TM0360 from Thermotoga maritima MSB8 suggested that TM0360 is a MazG-related nucleoside triphosphate pyrophosphohydrolase. The crystal structure of the TM0360 protein was determined by the MAD technique at 2.0 Å resolution. The asymmetric unit contains an intact dimer molecule. The overall structure of TM0360 is similar to the known structures of the dimeric MazG protein and dUTPases. The putative NTP binding pocket in TM0360, identified by considering the probable NTP-interacting residues and structural features, suggested that TM0360 resembles the C-terminal domain of Escherichia coli MazG, although TM0360 may be a truncated paralog of the N-terminal domain of T. maritima MazG (TM0913), according to its primary structure. The putative function of TM0360 is discussed, based on structural homology. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9195-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33119361","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: 2

Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT. 免疫相关锌指蛋白ZFAT dna结合域的溶液结构。

Journal of structural and functional genomics Pub Date : 2015-06-01 Epub Date: 2015-03-24 DOI: 10.1007/s10969-015-9196-3

Naoya Tochio, Takashi Umehara, Kazuhiko Nakabayashi, Misao Yoneyama, Kengo Tsuda, Mikako Shirouzu, Seizo Koshiba, Satoru Watanabe, Takanori Kigawa, Takehiko Sasazuki, Senji Shirasawa, Shigeyuki Yokoyama

{"title":"Solution structures of the DNA-binding domains of immune-related zinc-finger protein ZFAT.","authors":"Naoya Tochio, Takashi Umehara, Kazuhiko Nakabayashi, Misao Yoneyama, Kengo Tsuda, Mikako Shirouzu, Seizo Koshiba, Satoru Watanabe, Takanori Kigawa, Takehiko Sasazuki, Senji Shirasawa, Shigeyuki Yokoyama","doi":"10.1007/s10969-015-9196-3","DOIUrl":"https://doi.org/10.1007/s10969-015-9196-3","url":null,"abstract":"ZFAT is a transcriptional regulator, containing eighteen C2H2-type zinc-fingers and one AT-hook, involved in autoimmune thyroid disease, apoptosis, and immune-related cell survival. We determined the solution structures of the thirteen individual ZFAT zinc-fingers (ZF) and the tandemly arrayed zinc-fingers in the regions from ZF2 to ZF5, by NMR spectroscopy. ZFAT has eight uncommon bulged-out helix-containing zinc-fingers, and six of their structures (ZF4, ZF5, ZF6, ZF10, ZF11, and ZF13) were determined. The distribution patterns of the putative DNA-binding surface residues are different among the ZFAT zinc-fingers, suggesting the distinct DNA sequence preferences of the N-terminal and C-terminal zinc-fingers. Since ZFAT has three to five consecutive tandem zinc-fingers, which may cooperatively function as a unit, we also determined two tandemly arrayed zinc-finger structures, between ZF2 to ZF4 and ZF3 to ZF5. Our NMR spectroscopic analysis detected the interaction between ZF4 and ZF5, which are connected by an uncommon linker sequence, KKIK. The ZF4-ZF5 linker restrained the relative structural space between the two zinc-fingers in solution, unlike the other linker regions with determined structures, suggesting the involvement of the ZF4-ZF5 interfinger linker in the regulation of ZFAT function. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9196-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33155277","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: 12

Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies. 生产真核蛋白的表达平台:大肠杆菌细胞和小麦无生殖细胞合成、亲和力和溶解度标签和克隆策略的比较

Journal of structural and functional genomics Pub Date : 2015-06-01 Epub Date: 2015-04-09 DOI: 10.1007/s10969-015-9198-1

David J Aceti, Craig A Bingman, Russell L Wrobel, Ronnie O Frederick, Shin-Ichi Makino, Karl W Nichols, Sarata C Sahu, Lai F Bergeman, Paul G Blommel, Claudia C Cornilescu, Katarzyna A Gromek, Kory D Seder, Soyoon Hwang, John G Primm, Grzegorz Sabat, Frank C Vojtik, Brian F Volkman, Zsolt Zolnai, George N Phillips, John L Markley, Brian G Fox

{"title":"Expression platforms for producing eukaryotic proteins: a comparison of E. coli cell-based and wheat germ cell-free synthesis, affinity and solubility tags, and cloning strategies.","authors":"David J Aceti, Craig A Bingman, Russell L Wrobel, Ronnie O Frederick, Shin-Ichi Makino, Karl W Nichols, Sarata C Sahu, Lai F Bergeman, Paul G Blommel, Claudia C Cornilescu, Katarzyna A Gromek, Kory D Seder, Soyoon Hwang, John G Primm, Grzegorz Sabat, Frank C Vojtik, Brian F Volkman, Zsolt Zolnai, George N Phillips, John L Markley, Brian G Fox","doi":"10.1007/s10969-015-9198-1","DOIUrl":"https://doi.org/10.1007/s10969-015-9198-1","url":null,"abstract":"Vectors designed for protein production in Escherichia coli and by wheat germ cell-free translation were tested using 21 well-characterized eukaryotic proteins chosen to serve as controls within the context of a structural genomics pipeline. The controls were carried through cloning, small-scale expression trials, large-scale growth or synthesis, and purification. Successfully purified proteins were also subjected to either crystallization trials or (1)H-(15)N HSQC NMR analyses. Experiments evaluated: (1) the relative efficacy of restriction/ligation and recombinational cloning systems; (2) the value of maltose-binding protein (MBP) as a solubility enhancement tag; (3) the consequences of in vivo proteolysis of the MBP fusion as an alternative to post-purification proteolysis; (4) the effect of the level of LacI repressor on the yields of protein obtained from E. coli using autoinduction; (5) the consequences of removing the His tag from proteins produced by the cell-free system; and (6) the comparative performance of E. coli cells or wheat germ cell-free translation. Optimal promoter/repressor and fusion tag configurations for each expression system are discussed. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9198-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33075194","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

Crystal structures of Mycobacterial MeaB and MMAA-like GTPases. 分枝杆菌MeaB和mmaa样gtp酶的晶体结构。

Journal of structural and functional genomics Pub Date : 2015-06-01 Epub Date: 2015-04-02 DOI: 10.1007/s10969-015-9197-2

Thomas E Edwards, Loren Baugh, Jameson Bullen, Ruth O Baydo, Pam Witte, Kaitlin Thompkins, Isabelle Q H Phan, Jan Abendroth, Matthew C Clifton, Banumathi Sankaran, Wesley C Van Voorhis, Peter J Myler, Bart L Staker, Christoph Grundner, Donald D Lorimer

{"title":"Crystal structures of Mycobacterial MeaB and MMAA-like GTPases.","authors":"Thomas E Edwards, Loren Baugh, Jameson Bullen, Ruth O Baydo, Pam Witte, Kaitlin Thompkins, Isabelle Q H Phan, Jan Abendroth, Matthew C Clifton, Banumathi Sankaran, Wesley C Van Voorhis, Peter J Myler, Bart L Staker, Christoph Grundner, Donald D Lorimer","doi":"10.1007/s10969-015-9197-2","DOIUrl":"https://doi.org/10.1007/s10969-015-9197-2","url":null,"abstract":"The methylmalonyl Co-A mutase-associated GTPase MeaB from Methylobacterium extorquens is involved in glyoxylate regulation and required for growth. In humans, mutations in the homolog methylmalonic aciduria associated protein (MMAA) cause methylmalonic aciduria, which is often fatal. The central role of MeaB from bacteria to humans suggests that MeaB is also important in other, pathogenic bacteria such as Mycobacterium tuberculosis. However, the identity of the mycobacterial MeaB homolog is presently unclear. Here, we identify the M. tuberculosis protein Rv1496 and its homologs in M. smegmatis and M. thermoresistibile as MeaB. The crystal structures of all three homologs are highly similar to MeaB and MMAA structures and reveal a characteristic three-domain homodimer with GDP bound in the G domain active site. A structure of Rv1496 obtained from a crystal grown in the presence of GTP exhibited electron density for GDP, suggesting GTPase activity. These structures identify the mycobacterial MeaB and provide a structural framework for therapeutic targeting of M. tuberculosis MeaB. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-015-9197-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33180961","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: 6

Annotation of proteins of unknown function: initial enzyme results. 功能未知的蛋白质注释:初始酶结果。

Journal of structural and functional genomics Pub Date : 2015-03-01 Epub Date: 2015-01-29 DOI: 10.1007/s10969-015-9194-5

Talia McKay, Kaitlin Hart, Alison Horn, Haeja Kessler, Greg Dodge, Keti Bardhi, Kostandina Bardhi, Jeffrey L Mills, Herbert J Bernstein, Paul A Craig

引用次数: 15