CrossTope: a curate repository of 3D structures of immunogenic peptide: MHC complexes

The CrossTope is a highly curate repository of three-dimensional structures of peptide:major histocompatibility complex (MHC) class I complexes (pMHC-I). The complexes hosted by this databank were obtained in protein databases and by large-scale in silico construction of pMHC-I structures, using a new approach developed by our group. At this moment, the database contains 182 ‘non-redundant’ pMHC-I complexes from two human and two murine alleles. A web server provides interface for database query. The user can download (i) structure coordinate files and (ii) topological and charges distribution maps images from the T-cell receptor-interacting surface of pMHC-I complexes. The retrieved structures and maps can be used to cluster similar epitopes in cross-reactivity approaches, to analyse viral escape mutations in a structural level or even to improve the immunogenicity of tumour antigens. Database URL: http://www.crosstope.com.br

[1]  Arthur J. Olson,et al.  AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading , 2009, J. Comput. Chem..

[2]  L. Watkin,et al.  Cross-reactive influenza virus-specific CD8+ T cells contribute to lymphoproliferation in Epstein-Barr virus-associated infectious mononucleosis. , 2005, The Journal of clinical investigation.

[3]  Marialva Sinigaglia,et al.  Structural Allele-Specific Patterns Adopted by Epitopes in the MHC-I Cleft and Reconstruction of MHC:peptide Complexes to Cross-Reactivity Assessment , 2010, PloS one.

[4]  Marialva Sinigaglia,et al.  Structural in silico analysis of cross-genotype-reactivity among naturally occurring HCV NS3-1073-variants in the context of HLA-A*02:01 allele. , 2011, Molecular immunology.

[5]  Robyn L Stanfield,et al.  How TCRs bind MHCs, peptides, and coreceptors. , 2006, Annual review of immunology.

[6]  M. Kayikci,et al.  Toward the atomistic simulation of T cell epitopes automated construction of MHC: peptide structures for free energy calculations. , 2008, Journal of molecular graphics & modelling.

[7]  Marialva Sinigaglia,et al.  Reconstruction of MHC Alleles by Cross Modeling and Structural Assessment , 2010, BIOCOMP.

[8]  Raymond T Chung,et al.  Spontaneous control of HCV is associated with expression of HLA-B 57 and preservation of targeted epitopes. , 2011, Gastroenterology.

[9]  Angel Herráez,et al.  Biomolecules in the computer: Jmol to the rescue , 2006, Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology.

[10]  G. Schneider,et al.  A Structural Basis for CD8+ T Cell-dependent Recognition of Non-homologous Peptide Ligands , 2005, Journal of Biological Chemistry.

[11]  R. Abagyan,et al.  Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypes , 2006, Proteins.

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

[13]  M. Brown.  Progress in the genetics of ankylosing spondylitis. , 2011, Briefings in functional genomics.

[14]  J. Chies,et al.  Immunodominant viral peptides as determinants of cross-reactivity in the immune system – Can we develop wide spectrum viral vaccines?☆ , 2005, Medical Hypotheses.

[15]  F. Celada,et al.  CD8 memory T cells: cross-reactivity and heterologous immunity , 2004, Seminars in Immunology.

[16]  A. Ebringer,et al.  “B27 Disease” Is a New Autoimmune Disease That Affects Millions of People , 2007, Annals of the New York Academy of Sciences.

[17]  Yang Zhang,et al.  I-TASSER: a unified platform for automated protein structure and function prediction , 2010, Nature Protocols.

[18]  A. Khanolkar,et al.  T cell responses to viral infections , 2002, Immunologic research.

[19]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.

[20]  Gunter Schneider,et al.  Determination of Structural Principles Underlying Three Different Modes of Lymphocytic Choriomeningitis Virus Escape from CTL Recognition1 , 2004, The Journal of Immunology.

[21]  Shoba Ranganathan,et al.  pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes , 2010, Immunome research.

[22]  R. Welsh,et al.  CD8 T cell responses to viral infections in sequence , 2004, Cellular microbiology.

[23]  Jack T Stapleton,et al.  The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation , 2010, Science.

[24]  O. Pybus,et al.  Dominant influence of an HLA‐B27 restricted CD8+ T cell response in mediating HCV clearance and evolution , 2006, Hepatology.

[25]  M. Sternberg,et al.  Protein structure prediction on the Web: a case study using the Phyre server , 2009, Nature Protocols.

[26]  Barry Honig,et al.  GRASP2: visualization, surface properties, and electrostatics of macromolecular structures and sequences. , 2003, Methods in enzymology.

[27]  Marc A. Martí-Renom,et al.  MODBASE: a database of annotated comparative protein structure models and associated resources , 2005, Nucleic Acids Res..

[28]  R. Welsh,et al.  Heterologous immunity between viruses , 2010, Immunological reviews.