Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions

[1]  A. Zhernakova,et al.  Rapidly expanding knowledge on the role of the gut microbiome in health and disease. , 2014, Biochimica et biophysica acta.

[2]  H. Brumer,et al.  A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes , 2014, Nature.

[3]  H. Kozłowski,et al.  His-rich sequences – is plagiarism from nature a good idea? , 2013 .

[4]  N. Ausmees,et al.  RapA2 Is a Calcium-binding Lectin Composed of Two Highly Conserved Cadherin-like Domains That Specifically Recognize Rhizobium leguminosarum Acidic Exopolysaccharides* , 2012, The Journal of Biological Chemistry.

[5]  Katherine H. Huang,et al.  Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.

[6]  D. Gevers,et al.  The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites. , 2012, The Journal of allergy and clinical immunology.

[7]  M. Blaser,et al.  The human microbiome: at the interface of health and disease , 2012, Nature Reviews Genetics.

[8]  S. Brunak,et al.  SignalP 4.0: discriminating signal peptides from transmembrane regions , 2011, Nature Methods.

[9]  Christoph Weber,et al.  FFAS server: novel features and applications , 2011, Nucleic Acids Res..

[10]  Michele Magrane,et al.  UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.

[11]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[12]  Adam Godzik,et al.  FFAS server: novel features and applications. Nucleic Acids Res 39:W38-W44 , 2011 .

[13]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

[14]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[15]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[16]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[17]  Chuan He,et al.  Intramolecular amide bonds stabilize pili on the surface of bacilli , 2009, Proceedings of the National Academy of Sciences.

[18]  B. Kemp,et al.  AMPK in Health and Disease. , 2009, Physiological reviews.

[19]  G. Sheldrick.  A short history of SHELX. , 2008, Acta crystallographica. Section A, Foundations of crystallography.

[20]  Serge X. Cohen,et al.  Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7 , 2008, Nature Protocols.

[21]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[22]  Hannah M. Wexler,et al.  Bacteroides: the Good, the Bad, and the Nitty-Gritty , 2007, Clinical Microbiology Reviews.

[23]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[24]  Narayanaswamy Srinivasan,et al.  Nucleic Acids Research Advance Access published June 21, 2007 PIC: Protein Interactions Calculator , 2007 .

[25]  R. Wilson,et al.  Evolution of Symbiotic Bacteria in the Distal Human Intestine , 2007, PLoS biology.

[26]  Jack Snoeyink,et al.  Nucleic Acids Research Advance Access published April 22, 2007 MolProbity: all-atom contacts and structure validation for proteins and nucleic acids , 2007 .

[27]  Eric Blanc,et al.  Automated structure solution with autoSHARP. , 2007, Methods in molecular biology.

[28]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[29]  M. Madan Babu,et al.  A Database of Bacterial Lipoproteins (DOLOP) with Functional Assignments to Predicted Lipoproteins , 2006, Journal of bacteriology.

[30]  B. Paster,et al.  The Medically Important Bacteroides spp. in Health and Disease , 2006 .

[31]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[32]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[33]  I. Goldstein,et al.  Structural Analysis of the Laetiporus sulphureus Hemolytic Pore-forming Lectin in Complex with Sugars* , 2005, Journal of Biological Chemistry.

[34]  Lisa C. Crossman,et al.  Extensive DNA Inversions in the B. fragilis Genome Control Variable Gene Expression , 2005, Science.

[35]  BMC Bioinformatics , 2005 .

[36]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[37]  Zukang Feng,et al.  Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. , 2004, Acta crystallographica. Section D, Biological crystallography.

[38]  D. Moss,et al.  Clostridium perfringens epsilon-toxin shows structural similarity to the pore-forming toxin aerolysin. , 2004, Nature structural & molecular biology.

[39]  Adam Godzik,et al.  Flexible structure alignment by chaining aligned fragment pairs allowing twists , 2003, ECCB.

[40]  T. Terwilliger.  Statistical density modification using local pattern matching , 2003, Acta crystallographica. Section D, Biological crystallography.

[41]  A. Barclay,et al.  Membrane proteins with immunoglobulin-like domains--a master superfamily of interaction molecules. , 2003, Seminars in immunology.

[42]  A. Krogh,et al.  Prediction of lipoprotein signal peptides in Gram‐negative bacteria , 2003, Protein science : a publication of the Protein Society.

[43]  L. Aravind,et al.  Provenance of SET-Domain Histone Methyltransferases Through Duplication of a Simple Structural Unit , 2003, Cell cycle.

[44]  Martyn D Winn,et al.  Macromolecular TLS refinement in REFMAC at moderate resolutions. , 2003, Methods in enzymology.

[45]  Peter Kuhn,et al.  Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. , 2002, Journal of synchrotron radiation.

[46]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[47]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[48]  M. Carson,et al.  Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein. , 2000, Structure.

[49]  F. X. Avilés,et al.  Crystal structure of avian carboxypeptidase D domain II: a prototype for the regulatory metallocarboxypeptidase subfamily , 1999, The EMBO journal.

[50]  Werner Braun,et al.  Exact and efficient analytical calculation of the accessible surface areas and their gradients for macromolecules , 1998, J. Comput. Chem..

[51]  D. Tsernoglou,et al.  Aerolysin--a paradigm for membrane insertion of beta-sheet protein toxins? , 1998, Journal of structural biology.

[52]  P. Reeds,et al.  Nitrogen cycling in the gut. , 1998, Annual review of nutrition.

[53]  J. Gouaux,et al.  Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore , 1996, Science.

[54]  A. Salyers,et al.  Bacteroides of the human lower intestinal tract. , 1984, Annual review of microbiology.