Journal of structural and functional genomics最新文献_第4页

Structural genomics studies of human caries pathogen Streptococcus mutans. 人类龋齿致病菌变形链球菌的结构基因组学研究。

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2014-01-29 DOI: 10.1007/s10969-014-9172-3

Lanfen Li, Jie Nan, Dan Li, Erik Brostromer, Zixi Wang, Cong Liu, Qiaoming Hou, Xuexin Fan, Zhaoyang Ye, Xiao-Dong Su

{"title":"Structural genomics studies of human caries pathogen Streptococcus mutans.","authors":"Lanfen Li, Jie Nan, Dan Li, Erik Brostromer, Zixi Wang, Cong Liu, Qiaoming Hou, Xuexin Fan, Zhaoyang Ye, Xiao-Dong Su","doi":"10.1007/s10969-014-9172-3","DOIUrl":"https://doi.org/10.1007/s10969-014-9172-3","url":null,"abstract":"Gram-positive bacterium Streptococcus mutans is the primary causative agent of human dental caries. To better understand this pathogen at the atomic structure level and to establish potential drug and vaccine targets, we have carried out structural genomics research since 2005. To achieve the goal, we have developed various in-house automation systems including novel high-throughput crystallization equipment and methods, based on which a large-scale, high-efficiency and low-cost platform has been establish in our laboratory. From a total of 1,963 annotated open reading frames, 1,391 non-membrane targets were selected prioritized by protein sequence similarities to unknown structures, and clustered by restriction sites to allow for cost-effective high-throughput conventional cloning. Selected proteins were over-expressed in different strains of Escherichia coli. Clones expressed soluble proteins were selected, expanded, and expressed proteins were purified and subjected to crystallization trials. Finally, protein crystals were subjected to X-ray analysis and structures were determined by crystallographic methods. Using the previously established procedures, we have so far obtained more than 200 kinds of protein crystals and 100 kinds of crystal structures involved in different biological pathways. In this paper we demonstrate and review a possibility of performing structural genomics studies at moderate laboratory scale. Furthermore, the techniques and methods developed in our study can be widely applied to conventional structural biology research practice. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9172-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32070202","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 the S6K1 kinase domain in complexes with inhibitors. 抑制剂配合物中S6K1激酶结构域的晶体结构。

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2014-07-31 DOI: 10.1007/s10969-014-9188-8

Hideaki Niwa, Junko Mikuni, Shunta Sasaki, Yuri Tomabechi, Keiko Honda, Mariko Ikeda, Noboru Ohsawa, Motoaki Wakiyama, Noriko Handa, Mikako Shirouzu, Teruki Honma, Akiko Tanaka, Shigeyuki Yokoyama

{"title":"Crystal structures of the S6K1 kinase domain in complexes with inhibitors.","authors":"Hideaki Niwa, Junko Mikuni, Shunta Sasaki, Yuri Tomabechi, Keiko Honda, Mariko Ikeda, Noboru Ohsawa, Motoaki Wakiyama, Noriko Handa, Mikako Shirouzu, Teruki Honma, Akiko Tanaka, Shigeyuki Yokoyama","doi":"10.1007/s10969-014-9188-8","DOIUrl":"https://doi.org/10.1007/s10969-014-9188-8","url":null,"abstract":"Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. The crystal structures of the five inhibitors in complexes with the S6K1 kinase domain were determined at resolutions between 1.85 and 2.10 Å. All of the inhibitors bound to the ATP binding site, lying along the P-loop, while the activation loop stayed in the inactive form. Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123. Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9188-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32548127","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: 13

Evaluation of intensity and pulse width of different moderators for designing a new diffractometer for protein crystals with large unit cells in J-PARC/MLF. J-PARC/MLF大细胞蛋白晶体衍射仪设计中不同缓冲剂的强度和脉宽评价

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2014-01-18 DOI: 10.1007/s10969-014-9170-5

Katsuaki Tomoyori, Katsuhiro Kusaka, Taro Yamada, Taro Tamada

{"title":"Evaluation of intensity and pulse width of different moderators for designing a new diffractometer for protein crystals with large unit cells in J-PARC/MLF.","authors":"Katsuaki Tomoyori, Katsuhiro Kusaka, Taro Yamada, Taro Tamada","doi":"10.1007/s10969-014-9170-5","DOIUrl":"https://doi.org/10.1007/s10969-014-9170-5","url":null,"abstract":"We plan to design a high-resolution biomacromolecule neutron time-of-flight diffractometer, which allows us to collect data from crystals with unit cells above 250 Å, in the materials and life science experimental facility at the Japan Proton Accelerator Research Complex. This new diffractometer can be used for a detailed analysis of large proteins such as membrane proteins and supermolecular complex. A quantitative comparison of the intensity and pulse width of a decoupled moderator (DM) against a coupled moderator (CM) considering the pulse width time resolution indicated that the DM satisfies the criteria for our diffractometer rather than the CM. The results suggested that a characteristic feature of the DM, i.e., narrow pulse width with a short tail, is crucial for the separation of Bragg reflections from crystals with large unit cells. On the other hand, it should be noted that the weak signals from the DM are buried under the high-level background caused by the incoherent scattering of hydrogen atoms, especially, in the case of large unit cells. We propose a profile-fitting integration method combined with the energy loss functions and a background subtraction method achieved by employing the statistics-sensitive nonlinear iterative peak-clipping algorithm. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9170-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32043797","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: 4

Carbohydrate recognition by rotaviruses. 轮状病毒对碳水化合物的识别

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2013-11-19 DOI: 10.1007/s10969-013-9167-5

Xing Yu, Helen Blanchard

引用次数: 4

Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine. 水鸡tRNA m(1)A58甲基转移酶TrmI与s -腺苷- l-蛋氨酸配合物的晶体结构

Journal of structural and functional genomics Pub Date : 2014-09-01 DOI: 10.1007/s10969-014-9183-0

Mitsuo Kuratani, Tatsuo Yanagisawa, Ryohei Ishii, Michiyo Matsuno, Shu-Yi Si, Kazushige Katsura, Ryoko Ushikoshi-Nakayama, Rie Shibata, Mikako Shirouzu, Yoshitaka Bessho, Shigeyuki Yokoyama

{"title":"Crystal structure of tRNA m(1)A58 methyltransferase TrmI from Aquifex aeolicus in complex with S-adenosyl-L-methionine.","authors":"Mitsuo Kuratani, Tatsuo Yanagisawa, Ryohei Ishii, Michiyo Matsuno, Shu-Yi Si, Kazushige Katsura, Ryoko Ushikoshi-Nakayama, Rie Shibata, Mikako Shirouzu, Yoshitaka Bessho, Shigeyuki Yokoyama","doi":"10.1007/s10969-014-9183-0","DOIUrl":"https://doi.org/10.1007/s10969-014-9183-0","url":null,"abstract":"The N (1)-methyladenosine residue at position 58 of tRNA is found in the three domains of life, and contributes to the stability of the three-dimensional L-shaped tRNA structure. In thermophilic bacteria, this modification is important for thermal adaptation, and is catalyzed by the tRNA m(1)A58 methyltransferase TrmI, using S-adenosyl-L-methionine (AdoMet) as the methyl donor. We present the 2.2 Å crystal structure of TrmI from the extremely thermophilic bacterium Aquifex aeolicus, in complex with AdoMet. There are four molecules per asymmetric unit, and they form a tetramer. Based on a comparison of the AdoMet binding mode of A. aeolicus TrmI to those of the Thermus thermophilus and Pyrococcus abyssi TrmIs, we discuss their similarities and differences. Although the binding modes to the N6 amino group of the adenine moiety of AdoMet are similar, using the side chains of acidic residues as well as hydrogen bonds, the positions of the amino acid residues involved in binding are diverse among the TrmIs from A. aeolicus, T. thermophilus, and P. abyssi.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9183-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10832361","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

Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR. 迈向综合结构生物学方法:结合冷冻透射电镜，x射线晶体学和核磁共振。

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2014-04-20 DOI: 10.1007/s10969-014-9179-9

Jeffrey Lengyel, Eric Hnath, Marc Storms, Thomas Wohlfarth

{"title":"Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.","authors":"Jeffrey Lengyel, Eric Hnath, Marc Storms, Thomas Wohlfarth","doi":"10.1007/s10969-014-9179-9","DOIUrl":"https://doi.org/10.1007/s10969-014-9179-9","url":null,"abstract":"Cryo-transmission electron microscopy (Cryo-TEM) and particularly single particle analysis is rapidly becoming the premier method for determining the three-dimensional structure of protein complexes, and viruses. In the last several years there have been dramatic technological improvements in Cryo-TEM, such as advancements in automation and use of improved detectors, as well as improved image processing techniques. While Cryo-TEM was once thought of as a low resolution structural technique, the method is currently capable of generating nearly atomic resolution structures on a routine basis. Moreover, the combination of Cryo-TEM and other methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics modeling are allowing researchers to address scientific questions previously thought intractable. Future technological developments are widely believed to further enhance the method and it is not inconceivable that Cryo-TEM could become as routine as X-ray crystallography for protein structure determination. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9179-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32277258","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: 18

Structural insights of post-translational modification sites in the proteome of Thermus thermophilus. 嗜热热菌蛋白质组翻译后修饰位点的结构分析。

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2014-01-10 DOI: 10.1007/s10969-013-9169-3

Ryoji Masui, Yoshio Takahata, Masao Inoue, Yota Iio, Hiroki Okanishi, Kwang Kim, Noriko Nakagawa, Kei Yura, Seiki Kuramitsu

{"title":"Structural insights of post-translational modification sites in the proteome of Thermus thermophilus.","authors":"Ryoji Masui, Yoshio Takahata, Masao Inoue, Yota Iio, Hiroki Okanishi, Kwang Kim, Noriko Nakagawa, Kei Yura, Seiki Kuramitsu","doi":"10.1007/s10969-013-9169-3","DOIUrl":"https://doi.org/10.1007/s10969-013-9169-3","url":null,"abstract":"Phosphorylation and acetylation are the most prevalent post-translational modifications (PTMs) detected in not only eukaryotes but also bacteria. We performed phosphoproteome and acetylome analyses of proteins from an extremely thermophilic eubacterium Thermus thermophilus HB8, and identified numerous phosphorylation and acetylation sites. To facilitate the elucidation of the structural aspects of these PTM events, we mapped the PTM sites on the known tertiary structures for the respective proteins and their homologs. Wu et al. (Mol Cell Proteomics 12:2701-2713, 2013) recently reported phosphoproteome analysis of proteins from T. thermophilus HB27. Therefore, we assessed the structural characteristics of these phosphorylation and acetylation sites on the tertiary structures of the identified proteins or their homologs. Our study revealed that many of the identified phosphosites are in close proximity to bound ligands, i.e., the numbers of 'nearby' and 'peripheral' phosphorylation sites represent 56 % (48/86 sites) of total identified phosphorylation sites. In addition, approximately 60 % of all phosphosites exhibited <10 % accessible surface area of their side chains, suggesting some structural rearrangement is required for phosphoryl transfer by kinases. Our findings also indicate that phosphorylation of a residue occurs more frequently at a flexible region of the protein, whereas lysine acetylation occurs more frequently in an ordered structure.","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9169-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32015223","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

Conformational variation of the translocon enhancing chaperone SecDF. 转位增强伴侣蛋白SecDF的构象变化。

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2013-12-25 DOI: 10.1007/s10969-013-9168-4

Kazuhiro Mio, Tomoya Tsukazaki, Hiroyuki Mori, Masaaki Kawata, Toshio Moriya, Yoshikazu Sasaki, Ryuichiro Ishitani, Koreaki Ito, Osamu Nureki, Chikara Sato

{"title":"Conformational variation of the translocon enhancing chaperone SecDF.","authors":"Kazuhiro Mio, Tomoya Tsukazaki, Hiroyuki Mori, Masaaki Kawata, Toshio Moriya, Yoshikazu Sasaki, Ryuichiro Ishitani, Koreaki Ito, Osamu Nureki, Chikara Sato","doi":"10.1007/s10969-013-9168-4","DOIUrl":"https://doi.org/10.1007/s10969-013-9168-4","url":null,"abstract":"The Sec translocon facilitates transportation of newly synthesized polypeptides from the cytoplasm to the lumen/periplasm across the phospholipid membrane. Although the polypeptide-conducting machinery is formed by the SecYEG-SecA complex in bacteria, its transportation efficiency is markedly enhanced by SecDF. A previous study suggested that SecDF assumes at least two conformations differing by a 120° rotation in the spatial orientation of the P1 head subdomain to the rigid base, and that the conformational dynamics plays a critical role in polypeptide translocation. Here we addressed this hypothesis by analyzing the 3D structure of SecDF using electron tomography and single particle reconstruction. Reconstruction of wt SecDF showed two major conformations; one resembles the crystal structure of full-length SecDF (F-form structure), while the other is similar to the hypothetical structural variant based on the crystal structure of the isolated P1 domain (I-form structure). The transmembrane domain of the I-form structure has a scissor like cleft open to the periplasmic side. We also report the structure of a double cysteine mutant designed to constrain SecDF to the I-form. This reconstruction has a protrusion at the periplasmic end that nicely fits the orientation of P1 in the I-from. These results provide firm evidence for the occurrence of the I-form in solution and support the proposed F- to I-transition of wt SecDF during polypeptide translocation. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9168-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31982350","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: 9

A new manual dispensing system for in meso membrane protein crystallization with using a stepping motor-based dispenser. 一种采用步进电机的新型中膜蛋白结晶手动点胶系统。

Journal of structural and functional genomics Pub Date : 2014-09-01 Epub Date: 2014-07-24 DOI: 10.1007/s10969-014-9187-9

Masakatsu Hato, Toshiaki Hosaka, Hiroaki Tanabe, Tokuji Kitsunai, Shigeyuki Yokoyama

引用次数: 8

Conformational landscapes for KMSKS loop in tyrosyl-tRNA synthetases. 酪氨酸- trna合成酶中KMSKS环的构象图。

Journal of structural and functional genomics Pub Date : 2014-06-01 Epub Date: 2014-04-11 DOI: 10.1007/s10969-014-9178-x

Manish Datt, Amit Sharma

引用次数: 14