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

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":"15 3","pages":"173-80"},"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":" ","pages":"117-24"},"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":" ","pages":"137-51"},"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":" ","pages":"107-15"},"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

Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin. 克拉多菌素抑制疟原虫赖氨酸- trna合成酶的结构基础。

Journal of structural and functional genomics Pub Date : 2014-06-01 Epub Date: 2014-06-17 DOI: 10.1007/s10969-014-9182-1

Sameena Khan, Arvind Sharma, Hassan Belrhali, Manickam Yogavel, Amit Sharma

{"title":"Structural basis of malaria parasite lysyl-tRNA synthetase inhibition by cladosporin.","authors":"Sameena Khan, Arvind Sharma, Hassan Belrhali, Manickam Yogavel, Amit Sharma","doi":"10.1007/s10969-014-9182-1","DOIUrl":"https://doi.org/10.1007/s10969-014-9182-1","url":null,"abstract":"Malaria parasites inevitably develop drug resistance to anti-malarials over time. Hence the immediacy for discovering new chemical scaffolds to include in combination malaria drug therapy. The desirable attributes of new chemotherapeutic agents currently include activity against both liver and blood stage malaria parasites. One such recently discovered compound called cladosporin abrogates parasite growth via inhibition of Plasmodium falciparum lysyl-tRNA synthetase (PfKRS), an enzyme central to protein translation. Here, we present crystal structure of ternary PfKRS-lysine-cladosporin (PfKRS-K-C) complex that reveals cladosporin's remarkable ability to mimic the natural substrate adenosine and thereby colonize PfKRS active site. The isocoumarin fragment of cladosporin sandwiches between critical adenine-recognizing residues while its pyran ring fits snugly in the ribose-recognizing cavity. PfKRS-K-C structure highlights ample space within PfKRS active site for further chemical derivatization of cladosporin. Such derivatives may be useful against additional human pathogens that retain high conservation in cladosporin chelating residues within their lysyl-tRNA synthetase. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"15 2","pages":"63-71"},"PeriodicalIF":0.0,"publicationDate":"2014-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9182-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32430255","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: 53

The crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein CAE31940 from proteobacterium Bordetella bronchiseptica RB50, and evolutionary insight into the NMT1/THI5 family. 博德氏杆菌RB50中嘧啶/硫胺素生物合成前体样结构域蛋白CAE31940的晶体结构及其对NMT1/THI5家族的进化见解

Journal of structural and functional genomics Pub Date : 2014-06-01 Epub Date: 2014-06-08 DOI: 10.1007/s10969-014-9180-3

Jacek Bajor, Karolina L Tkaczuk, Maksymilian Chruszcz, Hutton Chapman, Olga Kagan, Alexei Savchenko, Wladek Minor

引用次数: 0

Principal components analysis of protein sequence clusters. 蛋白质序列簇的主成分分析。

Journal of structural and functional genomics Pub Date : 2014-03-01 Epub Date: 2014-02-05 DOI: 10.1007/s10969-014-9173-2

Bo Wang, Michael A Kennedy

{"title":"Principal components analysis of protein sequence clusters.","authors":"Bo Wang, Michael A Kennedy","doi":"10.1007/s10969-014-9173-2","DOIUrl":"https://doi.org/10.1007/s10969-014-9173-2","url":null,"abstract":"Sequence analysis of large protein families can produce sub-clusters even within the same family. In some cases, it is of interest to know precisely which amino acid position variations are most responsible for driving separation into sub-clusters. In large protein families composed of large proteins, it can be quite challenging to assign the relative importance to specific amino acid positions. Principal components analysis (PCA) is ideal for such a task, since the problem is posed in a large variable space, i.e. the number of amino acids that make up the protein sequence, and PCA is powerful at reducing the dimensionality of complex problems by projecting the data into an eigenspace that represents the directions of greatest variation. However, PCA of aligned protein sequence families is complicated by the fact that protein sequences are traditionally represented by single letter alphabetic codes, whereas PCA of protein sequence families requires conversion of sequence information into a numerical representation. Here, we introduce a new amino acid sequence conversion algorithm optimized for PCA data input. The method is demonstrated using a small artificial dataset to illustrate the characteristics and performance of the algorithm, as well as a small protein sequence family consisting of nine members, COG2263, and finally with a large protein sequence family, Pfam04237, which contains more than 1,800 sequences that group into two sub-clusters. ","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"15 1","pages":"1-11"},"PeriodicalIF":0.0,"publicationDate":"2014-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-014-9173-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32089747","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: 21