Protein-protein recognition.

BSc Degree Examination 2018-9 Department​: BIOLOGY Title of Exam: Protein protein recognition Time Allowed: 2 hours Marking Scheme: Total marks available for this paper: 100 The marks available for each question are indicated on the paper Instructions: Section A​: Answer all questions in the spaces provided on the examination paper Section B​: Answer ​either​ question A ​or​ question B. Write your answer on the separate paper provided and attach it to the back of the question paper using the cable tie provided Materials Supplied: GREEN ANSWER BOOKLET For marker use only: Office use only: 1 2 3 4 5 6 A B Total as %

[1]  K. Struhl,et al.  The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α Helices: Crystal structure of the protein-DNA complex , 1992, Cell.

[2]  J. Janin,et al.  Computer studies of interactions between macromolecules. , 1987, Progress in biophysics and molecular biology.

[3]  G. Rose,et al.  Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[4]  M J Sippl,et al.  Knowledge-based potentials for proteins. , 1995, Current opinion in structural biology.

[5]  J. Janin,et al.  Quantifying biological specificity: the statistical mechanics of molecular recognition. , 1996, Proteins.

[6]  R L Stanfield,et al.  Antibody-antigen interactions: new structures and new conformational changes. , 1994, Current opinion in structural biology.

[7]  J. Janin,et al.  Principles of protein-protein recognition from structure to thermodynamics. , 1995, Biochimie.

[8]  A. Olson,et al.  Texture mapping parametric molecular surfaces. , 1995, Journal of molecular graphics.

[9]  R. Webster,et al.  N9 neuraminidase complexes with antibodies NC41 and NC10: empirical free energy calculations capture specificity trends observed with mutant binding data. , 1994, Biochemistry.

[10]  P. Privalov,et al.  A thermodynamic approach to the problem of stabilization of globular protein structure: a calorimetric study. , 1974, Journal of molecular biology.

[11]  H. Erickson,et al.  Co-operativity in protein-protein association. The structure and stability of the actin filament. , 1989, Journal of molecular biology.

[12]  Stephen K. Burley,et al.  Co-crystal structure of TBP recognizing the minor groove of a TATA element , 1993, Nature.

[13]  C. Tanford.  Protein denaturation. , 1968, Advances in protein chemistry.

[14]  André Matagne,et al.  Structural and kinetic characterization of a β-lactamase-inhibitor protein , 1994, Nature.

[15]  H. Wolfson,et al.  Molecular surface complementarity at protein-protein interfaces: the critical role played by surface normals at well placed, sparse, points in docking. , 1995, Journal of molecular biology.

[16]  J. Scott Dixon,et al.  Flexible ligand docking using a genetic algorithm , 1995, J. Comput. Aided Mol. Des..

[17]  Gennady M Verkhivker,et al.  Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. , 1995, Protein engineering.

[18]  M. Mizutani,et al.  Rational automatic search method for stable docking models of protein and ligand. , 1994, Journal of molecular biology.

[19]  P. Privalov,et al.  Hydration effects in protein unfolding. , 1994, Biophysical chemistry.

[20]  E. Katchalski‐Katzir,et al.  Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[21]  S Vajda,et al.  Effect of conformational flexibility and solvation on receptor-ligand binding free energies. , 1994, Biochemistry.

[22]  B. Bush,et al.  Macromolecular shape and surface maps by solvent exclusion. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[23]  J. Janin,et al.  Protein‐protein recognition analyzed by docking simulation , 1991, Proteins.

[24]  W. Kauzmann.  Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.

[25]  A. Leach,et al.  Ligand docking to proteins with discrete side-chain flexibility. , 1994, Journal of molecular biology.

[26]  I. Kuntz,et al.  Structure-based discovery of inhibitors of thymidylate synthase. , 1993, Science.

[27]  S. Fields,et al.  Protein-protein interactions: methods for detection and analysis , 1995, Microbiological reviews.

[28]  B C Finzel,et al.  Three-dimensional structure of an antibody-antigen complex. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[29]  J. Janin,et al.  Protein docking algorithms: simulating molecular recognition , 1993 .

[30]  J. Janin,et al.  Reaction pathway for the quaternary structure change in hemoglobin , 1985, Biopolymers.

[31]  S. Wodak,et al.  Hemoglobin interaction in sickle cell fibers. I: Theoretical approaches to the molecular contacts. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[32]  H. Scheraga,et al.  Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Stewart,et al.  Rethinking "shape space": evidence from simulated docking suggests that steric shape complementarity is not limiting for antibody-antigen recognition and idiotypic interactions. , 1994, Journal of theoretical biology.

[34]  C. Chothia,et al.  Principles of protein–protein recognition , 1975, Nature.

[35]  R. S. Spolar,et al.  Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. , 1992, Biochemistry.

[36]  R. Huber,et al.  Refined structure of the hirudin-thrombin complex. , 1991, Journal of molecular biology.

[37]  A Tramontano,et al.  PUZZLE: a new method for automated protein docking based on surface shape complementarity. , 1994, Journal of molecular biology.

[38]  R. Abagyan,et al.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.

[39]  S. Kim,et al.  "Soft docking": matching of molecular surface cubes. , 1991, Journal of molecular biology.

[40]  H. Wolfson,et al.  Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[41]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[42]  G. Cohen,et al.  Structure of an antibody-lysozyme complex unexpected effect of conservative mutation. , 1995, Journal of molecular biology.

[43]  G. Rose,et al.  Molecular recognition. I. Automatic identification of topographic surface features , 1985, Biopolymers.

[44]  J. Janin,et al.  Computer analysis of protein-protein interaction. , 1978, Journal of molecular biology.

[45]  C. Chothia,et al.  Hydrophobic bonding and accessible surface area in proteins , 1974, Nature.

[46]  H. Wolfson,et al.  Shape complementarity at protein–protein interfaces , 1994, Biopolymers.

[47]  R. Nussinov,et al.  A geometry-based suite of molecular docking processes. , 1995, Journal of molecular biology.

[48]  T. Bhat,et al.  Solvent rearrangement in an antigen-antibody interface introduced by site-directed mutagenesis of the antibody combining site. , 1994, Journal of molecular biology.

[49]  Antigen-antibody recognition. Model calculations. , 1994, Biophysical chemistry.

[50]  M L Connolly,et al.  Shape distributions of protein topography , 1992, Biopolymers.

[51]  A. Olson,et al.  Approximation and characterization of molecular surfaces , 1993, Biopolymers.

[52]  M J Sternberg,et al.  Protein side-chain conformational entropy derived from fusion data--comparison with other empirical scales. , 1994, Protein engineering.

[53]  L M Amzel,et al.  Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation , 1994, Proteins.

[54]  J A McCammon,et al.  Combined conformational search and finite-difference Poisson-Boltzmann approach for flexible docking. Application to an operator mutation in the lambda repressor-operator complex. , 1994, Journal of molecular biology.

[55]  R. S. Spolar,et al.  Hydrophobic effect in protein folding and other noncovalent processes involving proteins. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[56]  A Caflisch,et al.  Monte Carlo docking of oligopeptides to proteins , 1992, Proteins.

[57]  B Honig,et al.  Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. , 1991, Biochemistry.

[58]  M. L. Connolly.  Solvent-accessible surfaces of proteins and nucleic acids. , 1983, Science.

[59]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[60]  M. L. Connolly.  Analytical molecular surface calculation , 1983 .

[61]  T. Stouch,et al.  Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures. , 1993, Journal of molecular biology.

[62]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[63]  M. L. Connolly.  Shape complementarity at the hemoglobin α1β1 subunit interface , 1986 .

[64]  Christopher Lee.  Calculating binding energies: Current Opinion in Structural Biology 1992, 2:217–222 , 1992 .

[65]  M. Lewis,et al.  Calculation of the free energy of association for protein complexes , 1992, Protein science : a publication of the Protein Society.

[66]  I. Kuntz,et al.  Structure-based design of nonpeptide inhibitors specific for the human immunodeficiency virus 1 protease. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[67]  P A Kollman,et al.  Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches , 1993, Proteins.

[68]  Ruben Abagyan,et al.  Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy , 1994, Nature Structural Biology.

[69]  M J Sternberg,et al.  Empirical scale of side-chain conformational entropy in protein folding. , 1993, Journal of molecular biology.

[70]  J. Janin,et al.  Rigid‐body docking with mutant constraints of influenza hemagglutinin with antibody HC19 , 1994, Proteins.

[71]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[72]  Pedro M. Alzari,et al.  A potent new mode of β-lactamase inhibition revealed by the 1.7 Å X-ray crystallographic structure of the TEM-1–BLIP complex , 1996, Nature Structural Biology.

[73]  L. Pauling,et al.  THE NATURE OF THE INTERMOLECULAR FORCES OPERATIVE IN BIOLOGICAL PROCESSES. , 1940, Science.

[74]  A V Finkelstein,et al.  The price of lost freedom: entropy of bimolecular complex formation. , 1989, Protein engineering.

[75]  Steven Hahn,et al.  Crystal structure of a yeast TBP/TATA-box complex , 1993, Nature.

[76]  P. Privalov,et al.  Heat capacity of proteins. I. Partial molar heat capacity of individual amino acid residues in aqueous solution: hydration effect. , 1990, Journal of molecular biology.

[77]  R. Willson,et al.  Isothermal titration calorimetric study of the association of hen egg lysozyme and the anti-lysozyme antibody HyHEL-5. , 1994, Biochemistry.

[78]  K. P. Murphy,et al.  Entropy in biological binding processes: Estimation of translational entropy loss , 1994, Proteins.

[79]  M J Sternberg,et al.  A continuum model for protein-protein interactions: application to the docking problem. , 1995, Journal of molecular biology.

[80]  Djordje Musil,et al.  The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis Structural analysis, subtilisin structure and interface geometry , 1987 .

[81]  C. Betzel,et al.  Molecular structure of the acyl-enzyme intermediate in β-lactam hydrolysis at 1.7 Å resolution , 1992, Nature.

[82]  C. Aflalo,et al.  Hydrophobic docking: A proposed enhancement to molecular recognition techniques , 1994, Proteins.

[83]  Brian K. Shoichet,et al.  Molecular docking using shape descriptors , 1992 .

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

[85]  I. Kuntz,et al.  Protein docking and complementarity. , 1991, Journal of molecular biology.

[86]  I. Kuntz,et al.  Automated docking with grid‐based energy evaluation , 1992 .

[87]  R. Bruccoleri,et al.  On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. , 1989, Biochemistry.

[88]  V. Guillet,et al.  Recognition between a bacterial ribonuclease, barnase, and its natural inhibitor, barstar. , 1993, Structure.

[89]  J F Brandts,et al.  Rapid measurement of binding constants and heats of binding using a new titration calorimeter. , 1989, Analytical biochemistry.

[90]  A. D. McLachlan,et al.  Solvation energy in protein folding and binding , 1986, Nature.

[91]  M. Lawrence,et al.  Shape complementarity at protein/protein interfaces. , 1993, Journal of molecular biology.

[92]  K. P. Murphy,et al.  Structural energetics of peptide recognition: Angiotensin II/antibody binding , 1993, Proteins.

[93]  I. Vakser.  Protein docking for low-resolution structures. , 1995, Protein engineering.