Journal of structural and functional genomics最新文献

{"title":"Finding non-crystallographic symmetry in density maps of macromolecular structures.","authors":"Thomas C Terwilliger","doi":"10.1007/s10969-013-9157-7","DOIUrl":"https://doi.org/10.1007/s10969-013-9157-7","url":null,"abstract":"<p><p>The internal symmetry of a macromolecule is both an important aspect of its function and a useful feature in obtaining a structure by X-ray crystallography and other techniques. A method is presented for finding internal symmetry and other non-crystallographic symmetry in a structure based on patterns of density in a density map for that structure. Regions in map that are similar are identified by cutting out a sphere of density from a region that has high local variation and using an FFT-based correlation search to find other regions that match. The relationships among correlated regions are then refined to maximize their correlations and are found to accurately represent non-crystallographic symmetry in the map. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 3","pages":"91-5"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9157-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31603125","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}

{"title":"Reduced dimensionality (4,3)D-hnCOCANH experiment: an efficient backbone assignment tool for NMR studies of proteins.","authors":"Dinesh Kumar","doi":"10.1007/s10969-013-9161-y","DOIUrl":"https://doi.org/10.1007/s10969-013-9161-y","url":null,"abstract":"<p><p>Sequence specific resonance assignment of proteins forms the basis for variety of structural and functional proteomics studies by NMR. In this context, an efficient standalone method for rapid assignment of backbone ((1)H, (15)N, (13)C(α) and (13)C') resonances of proteins has been presented here. Compared to currently available strategies used for the purpose, the method employs only a single reduced dimensionality experiment--(4,3)D-hnCOCANH and exploits the linear combinations of backbone ((13)C(α) and (13)C') chemical shifts to achieve a dispersion relatively better compared to those of individual chemical shifts (see the text). The resulted increased dispersion of peaks--which is different in sum (CA + CO) and difference (CA - CO) frequency regions--greatly facilitates the analysis of the spectrum by resolving the problems (associated with routine assignment strategies) arising because of degenerate amide (15)N and backbone (13)C chemical shifts. Further, the spectrum provides direct distinction between intra- and inter-residue correlations because of their opposite peak signs. The other beneficial feature of the spectrum is that it provides: (a) multiple unidirectional sequential (i→i + 1) (15)N and (13)C correlations and (b) facile identification of certain specific triplet sequences which serve as check points for mapping the stretches of sequentially connected HSQC cross peaks on to the primary sequence for assigning the resonances sequence specifically. On top of all this, the F₂-F₃ planes of the spectrum corresponding to sum (CA + CO) and difference (CA - CO) chemical shifts enable rapid and unambiguous identification of sequential HSQC peaks through matching their coordinates in these two planes (see the text). Overall, the experiment presented here will serve as an important backbone assignment tool for variety of structural and functional proteomics and drug discovery research programs by NMR involving well behaved small folded proteins (MW < 15 kDa) or a range of intrinsically disordered proteins.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 3","pages":"109-18"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9161-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31687613","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}

{"title":"Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and complementary structural coverage of dark operative protochlorophyllide oxidoreductase complexes.","authors":"Surya V S R K Pulavarti,&nbsp;Yunfen He,&nbsp;Erik A Feldmann,&nbsp;Alexander Eletsky,&nbsp;Thomas B Acton,&nbsp;Rong Xiao,&nbsp;John K Everett,&nbsp;Gaetano T Montelione,&nbsp;Michael A Kennedy,&nbsp;Thomas Szyperski","doi":"10.1007/s10969-013-9159-5","DOIUrl":"https://doi.org/10.1007/s10969-013-9159-5","url":null,"abstract":"<p><p>High-quality NMR structures of the C-terminal domain comprising residues 484-537 of the 537-residue protein Bacterial chlorophyll subunit B (BchB) from Chlorobium tepidum and residues 9-61 of 61-residue Asr4154 from Nostoc sp. (strain PCC 7120) exhibit a mixed α/β fold comprised of three α-helices and a small β-sheet packed against second α-helix. These two proteins share 29% sequence similarity and their structures are globally quite similar. The structures of BchB(484-537) and Asr4154(9-61) are the first representative structures for the large protein family (Pfam) PF08369, a family of unknown function currently containing 610 members in bacteria and eukaryotes. Furthermore, BchB(484-537) complements the structural coverage of the dark-operating protochlorophyllide oxidoreductase.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 3","pages":"119-26"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9159-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31672941","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}

{"title":"Cross-linking and mass spectrometry methodologies to facilitate structural biology: finding a path through the maze.","authors":"Eric D Merkley,&nbsp;John R Cort,&nbsp;Joshua N Adkins","doi":"10.1007/s10969-013-9160-z","DOIUrl":"https://doi.org/10.1007/s10969-013-9160-z","url":null,"abstract":"<p><p>Multiprotein complexes, rather than individual proteins, make up a large part of the biological macromolecular machinery of a cell. Understanding the structure and organization of these complexes is critical to understanding cellular function. Chemical cross-linking coupled with mass spectrometry is emerging as a complementary technique to traditional structural biology methods and can provide low-resolution structural information for a multitude of purposes, such as distance constraints in computational modeling of protein complexes. In this review, we discuss the experimental considerations for successful application of chemical cross-linking-mass spectrometry in biological studies and highlight three examples of such studies from the recent literature. These examples (as well as many others) illustrate the utility of a chemical cross-linking-mass spectrometry approach in facilitating structural analysis of large and challenging complexes. </p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 3","pages":"77-90"},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9160-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31634679","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}

{"title":"Crystal structure of AcrB complexed with linezolid at 3.5 Å resolution.","authors":"Li-Wei Hung,&nbsp;Heung-Bok Kim,&nbsp;Satoshi Murakami,&nbsp;Goutam Gupta,&nbsp;Chang-Yub Kim,&nbsp;Thomas C Terwilliger","doi":"10.1007/s10969-013-9154-x","DOIUrl":"https://doi.org/10.1007/s10969-013-9154-x","url":null,"abstract":"<p><p>AcrB is an inner membrane resistance-nodulation-cell division efflux pump and is part of the AcrAB-TolC tripartite efflux system. We have determined the crystal structure of AcrB with bound Linezolid at a resolution of 3.5 Å. The structure shows that Linezolid binds to the A385/F386 loops of the symmetric trimer of AcrB. A conformational change of a loop in the bottom of the periplasmic cleft is also observed.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 2","pages":"71-5"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9154-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10481680","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}

{"title":"Computational identification and analysis of arsenate reductase protein in Cronobacter sakazakii ATCC BAA-894 suggests potential microorganism for reducing arsenate.","authors":"Navaneet Chaturvedi,&nbsp;Vinay Kumar Singh,&nbsp;Paras Nath Pandey","doi":"10.1007/s10969-013-9153-y","DOIUrl":"https://doi.org/10.1007/s10969-013-9153-y","url":null,"abstract":"<p><p>This study focuses a bioinformatics-based prediction of arsC gene product arsenate reductase (ArsC) protein in Cronobacter sakazakii BAA-894 strain. A protein structure-based study encloses three-dimensional structural modeling of target ArsC protein, was carried out by homology modeling method. Ultimately, the detection of active binding regions was carried out for characterization of functional sites in protein. The ten probable ligand binding sites were predicted for target protein structure and highlighted the common binding residues between target and template protein. It has been first time identified that modeled ArsC protein structure in C. sakazakii was structurally and functionally similar to well-characterized ArsC protein of Escherichia coli because of having same structural motifs and fold with similar protein topology and function. Investigation revealed that ArsC from C. sakazakii can play significant role during arsenic resistance and potential microorganism for bioremediation of arsenic toxicity.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":" ","pages":"37-45"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9153-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31517172","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}

{"title":"Crystal structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2.","authors":"Michael Soniat,&nbsp;Parthasarathy Sampathkumar,&nbsp;Garen Collett,&nbsp;Anthony S Gizzi,&nbsp;Radhika N Banu,&nbsp;Rahul C Bhosle,&nbsp;Swetha Chamala,&nbsp;Sukanya Chowdhury,&nbsp;Andras Fiser,&nbsp;Alan S Glenn,&nbsp;James Hammonds,&nbsp;Brandan Hillerich,&nbsp;Kamil Khafizov,&nbsp;James D Love,&nbsp;Bridget Matikainen,&nbsp;Ronald D Seidel,&nbsp;Rafael Toro,&nbsp;P Rajesh Kumar,&nbsp;Jeffery B Bonanno,&nbsp;Yuh Min Chook,&nbsp;Steven C Almo","doi":"10.1007/s10969-013-9150-1","DOIUrl":"https://doi.org/10.1007/s10969-013-9150-1","url":null,"abstract":"<p><p>Import-Karyopherin or Importin proteins bind nuclear localization signals (NLSs) to mediate the import of proteins into the cell nucleus. Karyopherin β2 or Kapβ2, also known as Transportin, is a member of this transporter family responsible for the import of numerous RNA binding proteins. Kapβ2 recognizes a targeting signal termed the PY-NLS that lies within its cargos to target them through the nuclear pore complex. The recognition of PY-NLS by Kapβ2 is conserved throughout eukaryotes. Kap104, the Kapβ2 homolog in Saccharomyces cerevisiae, recognizes PY-NLSs in cargos Nab2, Hrp1, and Tfg2. We have determined the crystal structure of Kapβ2 bound to the PY-NLS of the mRNA processing protein Nab2 at 3.05-Å resolution. A seven-residue segment of the PY-NLS of Nab2 is observed to bind Kapβ2 in an extended conformation and occupies the same PY-NLS binding site observed in other Kapβ2·PY-NLS structures.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":" ","pages":"31-5"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9150-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40230757","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}

{"title":"Crystal structure analysis of L-fuculose-1-phosphate aldolase from Thermus thermophilus HB8 and its catalytic action: as explained through in silico.","authors":"L Karthik,&nbsp;M Nachiappan,&nbsp;D Velmurugan,&nbsp;J Jeyakanthan,&nbsp;K Gunasekaran","doi":"10.1007/s10969-013-9156-8","DOIUrl":"https://doi.org/10.1007/s10969-013-9156-8","url":null,"abstract":"<p><p>Fuculose phosphate aldolase catalyzes the reversible cleavage of fuculose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde. A tetramer by nature, this enzyme from Thermus thermophilus HB8 represents the group of Class II aldolases. The structure was solved in two different space groups using the crystals obtained from slow evaporation vapour-diffusion and microbatch techniques. The detailed crystallization description has been reported previously. In this study, the structural features of fuculose phosphate aldolase from T. thermophilus have been explored extensively through sequence and structure comparisons with fuculose phosphate aldolases of different species. Finally, an in silico analysis using induced fit docking was attempted to deduce the binding mode of fuculose phosphate aldolase with its natural substrate fuculose-1-phosphate along with a substrate analog dihydroxyacetone phosphate and phosphoglycolohydroxymate--a potential aldolase inhibitor. The results show the mechanism of action may be similar to that of Escherichia coli fuculose aldolase.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":" ","pages":"59-70"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9156-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31580239","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}

{"title":"Crystal structure of a macrophage migration inhibitory factor from Giardia lamblia.","authors":"Garry W Buchko,&nbsp;Jan Abendroth,&nbsp;Howard Robinson,&nbsp;Yanfeng Zhang,&nbsp;Stephen N Hewitt,&nbsp;Thomas E Edwards,&nbsp;Wesley C Van Voorhis,&nbsp;Peter J Myler","doi":"10.1007/s10969-013-9155-9","DOIUrl":"https://doi.org/10.1007/s10969-013-9155-9","url":null,"abstract":"<p><p>Macrophage migration inhibitory factor (MIF) is a eukaryotic cytokine that affects a broad spectrum of immune responses and its activation/inactivation is associated with numerous diseases. During protozoan infections MIF is not only expressed by the host, but, has also been observed to be expressed by some parasites and released into the host. To better understand the biological role of parasitic MIF proteins, the crystal structure of the MIF protein from Giardia lamblia (Gl-MIF), the etiological agent responsible for giardiasis, has been determined at 2.30 Å resolution. The 114-residue protein adopts an α/β fold consisting of a four-stranded β-sheet with two anti-parallel α-helices packed against a face of the β-sheet. An additional short β-strand aligns anti-parallel to β4 of the β-sheet in the adjacent protein unit to help stabilize a trimer, the biologically relevant unit observed in all solved MIF crystal structures to date, and form a discontinuous β-barrel. The structure of Gl-MIF is compared to the MIF structures from humans (Hs-MIF) and three Plasmodium species (falciparum, berghei, and yoelii). The structure of all five MIF proteins are generally similar with the exception of a channel that runs through the center of each trimer complex. Relative to Hs-MIF, there are differences in solvent accessibility and electrostatic potential distribution in the channel of Gl-MIF and the Plasmodium-MIFs due primarily to two \"gate-keeper\" residues in the parasitic MIFs. For the Plasmodium MIFs the gate-keeper residues are at positions 44 (Y --> R) and 100 (V --> D) and for Gl-MIF it is at position 100 (V --> R). If these gate-keeper residues have a biological function and contribute to the progression of parasitemia they may also form the basis for structure-based drug design targeting parasitic MIF proteins.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":" ","pages":"47-57"},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9155-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31457686","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}

{"title":"Structural and functional based identification of the bean (Phaseolus) microRNAs and their targets from expressed sequence tags.","authors":"Muhammad Younas Khan Barozai,&nbsp;Muhammad Din,&nbsp;Iftikhar Ahmed Baloch","doi":"10.1007/s10969-013-9152-z","DOIUrl":"https://doi.org/10.1007/s10969-013-9152-z","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) are small, 18-26 nucleotides long, non-coding RNAs that play role in post-transcriptional gene regulation. Many of these are evolutionarily conserved. This suggests a powerful approach to predict new miRNAs in other species. In this research, structural and functional approaches were combined to make computational prediction of potential miRNAs and their targets in Bean (Phaseolus). Total 55 novel miRNAs were detected from 38 miRNAs families in Bean (Phaseolus). These families are; miR156, 160, 164, 168, 170, 171, 172, 319, 393, 396, 397, 398, 408, 414, 438, 444, 535, 1310, 1424, 1426, 1848, 1860, 1863, 2055, 2091, 2093, 2094, 2102, 2103, 2105, 2864, 2866, 2925, 2926, 4221, 4245, 4246 and 4250. In the 55 putative miRNAs; 28 miRNAs belong to Phaseolus acutifolius, 23 to Phaseolus vulgaris, 4 to Phaseolus coccineus. All the mature miRNAs reside in the stem portion of the hairpin structures. Total 146 potential protein targets were predicted for these miRNAs.</p>","PeriodicalId":73957,"journal":{"name":"Journal of structural and functional genomics","volume":"14 1","pages":"11-8"},"PeriodicalIF":0.0,"publicationDate":"2013-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10969-013-9152-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31375497","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}