Journal of Structural and Functional Genomics

Enhancement of crystallization with nucleotide ligands identified by dye-ligand affinity chromatography.

Publication Date: 2012 Jan 28 PMID: 22286688
Authors: Kim, H. - Webster, C. - Roberts, J. K. - Kositsawat, J. - Hung, L. W. - Terwilliger, T. C. - Kim, C. Y.
Journal: J Struct Funct Genomics

Ligands interacting with Mycobacterium tuberculosis recombinant proteins were identified through use of the ability of Cibacron Blue F3GA dye to interact with nucleoside/nucleotide binding proteins, and the effects of these ligands on crystallization were examined. Co-crystallization with ligands enhanced crystallization and enabled X-ray diffraction data to be collected to a resolution of at least 2.7 A for 5 of 10 proteins tested. Additionally, clues about individual proteins' functions were obtained from their interactions with each of a panel of ligands.

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Structure- and sequence-based function prediction for non-homologous proteins.

Publication Date: 2012 Jan 22 PMID: 22270458
Authors: Sael, L. - Chitale, M. - Kihara, D.
Journal: J Struct Funct Genomics

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.

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KB-Rank: efficient protein structure and functional annotation identification via text query.

Publication Date: 2012 Jan 21 PMID: 22270457
Authors: Julfayev, E. S. - McLaughlin, R. J. - Tao, Y. P. - McLaughlin, W. A.
Journal: J Struct Funct Genomics

The KB-Rank tool was developed to help determine the functions of proteins. A user provides text query and protein structures are retrieved together with their functional annotation categories. Structures and annotation categories are ranked according to their estimated relevance to the queried text. The algorithm for ranking first retrieves matches between the query text and the text fields associated with the structures. The structures are next ordered by their relative content of annotations that are found to be prevalent across all the structures retrieved. An interactive web interface was implemented to navigate and interpret the relevance of the structures and annotation categories retrieved by a given search. The aim of the KB-Rank tool is to provide a means to quickly identify protein structures of interest and the annotations most relevant to the queries posed by a user. Informational and navigational searches regarding disease topics are described to illustrate the tool's utilities. The tool is available at the URL http://protein.tcmedc.org/KB-Rank .

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Canadian macromolecular crystallography facility: a suite of fully automated beamlines.

Publication Date: 2012 Jan 21 PMID: 22270456
Authors: Grochulski, P. - Fodje, M. - Labiuk, S. - Gorin, J. - Janzen, K. - Berg, R.
Journal: J Struct Funct Genomics

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.

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Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771.

Publication Date: 2012 Jan 6 PMID: 22223187
Authors: Eletsky, A. - Petrey, D. - Zhang, Q. C. - Lee, H. W. - Acton, T. B. - Xiao, R. - Everett, J. K. - Prestegard, J. H. - Honig, B. - Montelione, G. T. - Szyperski, T.
Journal: J Struct Funct Genomics

High-quality NMR structures of the homo-dimeric proteins Bvu3908 (69-residues in monomeric unit) from Bacteroides vulgatus and Bt2368 (74-residues) from Bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (wHTH) motifs mediating tight complex formation. Such homo-dimer formation by winged HTH motifs is otherwise found only in two DNA-binding proteins with known structure: the C-terminal wHTH domain of transcriptional activator FadR from E. coli and protein TubR from B. thurigensis, which is involved in plasmid DNA segregation. However, the relative orientation of the wHTH motifs is different and residues involved in DNA-binding are not conserved in Bvu3908 and Bt2368. Hence, the proteins of the present study are not very likely to bind DNA, but are likely to exhibit a function that has thus far not been ascribed to homo-dimers formed by winged HTH motifs. The structures of Bvu3908 and Bt2368 are the first atomic resolution structures for PFAM family PF10771, a family of unknown function (DUF2582) currently containing 128 members.

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