Backbone flexibility of CDR3 and immune recognition of antigens.

[1]  J. Marsh.  Buried and accessible surface area control intrinsic protein flexibility. , 2013, Journal of molecular biology.

[2]  Yi Li,et al.  T-cell Receptor Specificity Maintained by Altered Thermodynamics* , 2013, The Journal of Biological Chemistry.

[3]  Z. Weng,et al.  A flexible docking approach for prediction of T cell receptor–peptide–MHC complexes , 2013, Protein science : a publication of the Protein Society.

[4]  Roland L. Dunbrack,et al.  S2C: A database correlating sequence and atomic coordinate residue numbering in the Protein Data Bank , 2013 .

[5]  Zhiping Weng,et al.  Cutting Edge: Evidence for a Dynamically Driven T Cell Signaling Mechanism , 2012, The Journal of Immunology.

[6]  J. Haidar,et al.  A universal combinatorial design of antibody framework to graft distinct CDR sequences: A bioinformatics approach , 2012, Proteins.

[7]  Janet E. Paulsen,et al.  Fundamental Characteristics of the Immunoglobulin VH Repertoire of Chickens in Comparison with Those of Humans, Mice, and Camelids , 2012, The Journal of Immunology.

[8]  K. Garcia,et al.  T cell receptor signaling is limited by docking geometry to peptide-major histocompatibility complex. , 2011, Immunity.

[9]  M. Sliwkowski,et al.  A two-in-one antibody against HER3 and EGFR has superior inhibitory activity compared with monospecific antibodies. , 2011, Cancer cell.

[10]  A. Pande,et al.  Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of γD-crystallin. , 2011, Journal of molecular biology.

[11]  Sarah A. Teichmann,et al.  Relative Solvent Accessible Surface Area Predicts Protein Conformational Changes upon Binding , 2011, Structure.

[12]  R. Kelley,et al.  High Affinity Antigen Recognition of the Dual Specific Variants of Herceptin Is Entropy-Driven in Spite of Structural Plasticity , 2011, PloS one.

[13]  Benjamin D. Sellers,et al.  Effects of somatic mutations on CDR loop flexibility during affinity maturation , 2011, Proteins.

[14]  C. Langmead,et al.  Accounting for conformational entropy in predicting binding free energies of protein‐protein interactions , 2011, Proteins.

[15]  Mark J van Raaij,et al.  Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction , 2011, Proteins.

[16]  Z. Weng,et al.  Combinations of affinity-enhancing mutations in a T cell receptor reveal highly nonadditive effects within and between complementarity determining regions and chains. , 2010, Biochemistry.

[17]  A. Joshua Wand,et al.  The role of conformational entropy in molecular recognition by calmodulin , 2010, Nature chemical biology.

[18]  Tanja Kortemme,et al.  Multi‐constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility , 2009, Proteins.

[19]  Franklin Peale,et al.  Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site , 2009, Science.

[20]  Zhiping Weng,et al.  Structure‐based design of a T‐cell receptor leads to nearly 100‐fold improvement in binding affinity for pepMHC , 2009, Proteins.

[21]  S. Smith‐Gill,et al.  Association energetics of cross-reactive and specific antibodies. , 2009, Biochemistry.

[22]  K. Garcia,et al.  Different thermodynamic binding mechanisms and peptide fine specificities associated with a panel of structurally similar high-affinity T cell receptors. , 2008, Biochemistry.

[23]  Andrew C. R. Martin,et al.  Analysis and improvements to Kabat and structurally correct numbering of antibody variable domains. , 2008, Molecular immunology.

[24]  K. M. Armstrong,et al.  Thermodynamics of T‐cell receptor–peptide/MHC interactions: progress and opportunities , 2008, Journal of molecular recognition : JMR.

[25]  Ettore Appella,et al.  Single MHC mutation eliminates enthalpy associated with T cell receptor binding. , 2007, Journal of molecular biology.

[26]  Bruce Tidor,et al.  Computational design of antibody-affinity improvement beyond in vivo maturation , 2007, Nature Biotechnology.

[27]  A. Wand,et al.  Conformational entropy in molecular recognition by proteins , 2007, Nature.

[28]  K. M. Armstrong,et al.  A comprehensive calorimetric investigation of an entropically driven T cell receptor-peptide/major histocompatibility complex interaction. , 2007, Biophysical journal.

[29]  Ian F. Thorpe,et al.  Molecular evolution of affinity and flexibility in the immune system , 2007, Proceedings of the National Academy of Sciences.

[30]  K Dane Wittrup,et al.  Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies. , 2007, Journal of molecular biology.

[31]  K. Garcia,et al.  How a Single T Cell Receptor Recognizes Both Self and Foreign MHC , 2007, Cell.

[32]  B. Malissen,et al.  How much can a T‐cell antigen receptor adapt to structurally distinct antigenic peptides? , 2007, The EMBO journal.

[33]  Tongqing Zhou,et al.  Structural definition of a conserved neutralization epitope on HIV-1 gp120 , 2007, Nature.

[34]  R. Varadarajan,et al.  Thermodynamic effects of proline introduction on protein stability , 2006, Proteins.

[35]  J. Sancho,et al.  α‐helix stabilization by alanine relative to glycine: Roles of polar and apolar solvent exposures and of backbone entropy , 2006, Proteins.

[36]  A. Wand,et al.  Characterization of the backbone and side chain dynamics of the CaM-CaMKIp complex reveals microscopic contributions to protein conformational entropy. , 2006, Biochemistry.

[37]  David M Kranz,et al.  Long-range cooperative binding effects in a T cell receptor variable domain. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[38]  James McCluskey,et al.  Disparate thermodynamics governing T cell receptor-MHC-I interactions implicate extrinsic factors in guiding MHC restriction. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Michael Nilges,et al.  Flexibility and conformational entropy in protein-protein binding. , 2006, Structure.

[40]  Z. Weng,et al.  Main‐chain conformational tendencies of amino acids , 2005, Proteins.

[41]  Bosco K. Ho,et al.  The Ramachandran plots of glycine and pre-proline , 2005, BMC Structural Biology.

[42]  Zhiping Weng,et al.  ZDOCK and RDOCK performance in CAPRI rounds 3, 4, and 5 , 2005, Proteins.

[43]  Abhishek K. Jha,et al.  Helix, sheet, and polyproline II frequencies and strong nearest neighbor effects in a restricted coil library. , 2005, Biochemistry.

[44]  P. Jeffrey,et al.  Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. , 2005, Cancer cell.

[45]  Yi Li,et al.  Directed evolution of human T-cell receptors with picomolar affinities by phage display , 2005, Nature Biotechnology.

[46]  Brian M Baker,et al.  Two different T cell receptors use different thermodynamic strategies to recognize the same peptide/MHC ligand. , 2005, Journal of molecular biology.

[47]  Patrice Koehl,et al.  The ASTRAL Compendium in 2004 , 2003, Nucleic Acids Res..

[48]  Mark M Davis,et al.  Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation. , 2003, Molecular cell.

[49]  D. Baker,et al.  Design of a Novel Globular Protein Fold with Atomic-Level Accuracy , 2003, Science.

[50]  R. Berry,et al.  Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. , 2003, Journal of molecular biology.

[51]  Peter G Schultz,et al.  Structural plasticity and the evolution of antibody affinity and specificity. , 2003, Journal of molecular biology.

[52]  Z. Weng,et al.  ZDOCK: An initial‐stage protein‐docking algorithm , 2003, Proteins.

[53]  S. Smith‐Gill,et al.  X-ray snapshots of the maturation of an antibody response to a protein antigen , 2003, Nature Structural Biology.

[54]  John D. Scott,et al.  Induction of Flexibility through Protein-Protein Interactions* , 2003, The Journal of Biological Chemistry.

[55]  Dan S. Tawfik,et al.  Antibody Multispecificity Mediated by Conformational Diversity , 2003, Science.

[56]  Kim K. Baldridge,et al.  Flexibility and molecular recognition in the immune system , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[57]  D. Baker,et al.  A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[58]  B. Nayak,et al.  Epitope Recognition by Diverse Antibodies Suggests Conformational Convergence in an Antibody Response1 , 2002, The Journal of Immunology.

[59]  D. A. Bosco,et al.  Enzyme Dynamics During Catalysis , 2002, Science.

[60]  R C Stevens,et al.  A comparative analysis of the immunological evolution of antibody 28B4. , 2001, Biochemistry.

[61]  R. Srinivasan,et al.  The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[62]  K. Rao,et al.  Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site. , 2000, Immunity.

[63]  K D Wittrup,et al.  In vitro evolution of a T cell receptor with high affinity for peptide/MHC. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[64]  K. Garcia,et al.  A functional hot spot for antigen recognition in a superagonist TCR/MHC complex. , 2000, Immunity.

[65]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[66]  Milos V. Novotny,et al.  Increased protein backbone conformational entropy upon hydrophobic ligand binding , 1999, Nature Structural Biology.

[67]  S. A. Marshall,et al.  Energy functions for protein design. , 1999, Current opinion in structural biology.

[68]  B K Jakobsen,et al.  TCR binding to peptide-MHC stabilizes a flexible recognition interface. , 1999, Immunity.

[69]  P. Coutinho,et al.  Stabilization of Aspergillus awamori glucoamylase by proline substitution and combining stabilizing mutations. , 1998, Protein engineering.

[70]  F. Frolow,et al.  Enhanced thermal stability of Clostridium beijerinckii alcohol dehydrogenase after strategic substitution of amino acid residues with prolines from the homologous thermophilic Thermoanaerobacter brockii alcohol dehydrogenase , 1998, Protein science : a publication of the Protein Society.

[71]  T. Tanaka,et al.  Improving the thermostability of Bacillus stearothermophilus neutral protease by introducing proline into the active site helix. , 1997, Protein engineering.

[72]  P. Reilly,et al.  Effect of introducing proline residues on the stability of Aspergillus awamori. , 1997, Protein engineering.

[73]  R C Stevens,et al.  Structural insights into the evolution of an antibody combining site. , 1997, Science.

[74]  K. Sharp,et al.  Entropy in protein folding and in protein-protein interactions. , 1997, Current opinion in structural biology.

[75]  D. Wiley,et al.  Assembly, specific binding, and crystallization of a human TCR-alphabeta with an antigenic Tax peptide from human T lymphotropic virus type 1 and the class I MHC molecule HLA-A2. , 1996, Journal of immunology.

[76]  Partho Ghosh,et al.  Structure of the complex between human T-cell receptor, viral peptide and HLA-A2 , 1996, Nature.

[77]  Andrew C. R. Martin,et al.  Accessing the Kabat antibody sequence database by computer , 1996, Proteins.

[78]  Pascal Rigolet,et al.  Structure of influenza virus haemagglutinin complexed with a neutralizing antibody , 1995, Nature.

[79]  Luis Serrano,et al.  Elucidating the folding problem of helical peptides using empirical parameters , 1994, Nature Structural Biology.

[80]  S. Vajda.  Conformational filtering in polypeptides and proteins. , 1993, Journal of molecular biology.

[81]  T. Herning,et al.  Role of proline residues in human lysozyme stability: a scanning calorimetric study combined with X-ray structure analysis of proline mutants. , 1994, Biochemistry.

[82]  D. Wiley,et al.  HLA-A2-peptide complexes: refolding and crystallization of molecules expressed in Escherichia coli and complexed with single antigenic peptides. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[83]  N R Kallenbach,et al.  Side chain contributions to the stability of alpha-helical structure in peptides. , 1990, Science.

[84]  H. Scheraga,et al.  Theoretical determination of sterically allowed conformations of a polypeptide chain by a computer method , 1965 .

[85]  G. N. Ramachandran,et al.  Stereochemistry of polypeptide chain configurations. , 1963, Journal of molecular biology.

[86]  L. Pauling,et al.  Configurations of Polypeptide Chains With Favored Orientations Around Single Bonds: Two New Pleated Sheets. , 1951, Proceedings of the National Academy of Sciences of the United States of America.