Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking

Bioinformatics

Volumn 32, Issue 16, 2016, Pages 2451-2456

  Kuroda, Daisuke ^a,b   Gray, Jeffrey J ^a,c  

^a Johns Hopkins University   (United States)

^b SHOWA UNIVERSITY   (Japan)

^c JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; HYDROGEN; PROTEIN; PROTEIN BINDING;

ALGORITHM; BIOLOGY; HYDROGEN BOND; MOLECULAR MODEL; PROCEDURES; PROTEIN ANALYSIS; PROTEIN CONFORMATION;

ALGORITHMS; ANTIBODIES; COMPUTATIONAL BIOLOGY; HYDROGEN; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 84983371891     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btw197     Document Type: Article

References (47)

1. Abhinandan, K.R. and Martin, A.C. (2010) Analysis and prediction of VH/VL packing in antibodies. Protein Eng. Des. Sel., 23, 689-697.
2. Ahmad, M. et al. (2011) Adhesive water networks facilitate binding of protein interfaces. Nat. Commun., 2, 261.
3. Almagro, J.C. et al. (2011) Antibody modeling assessment. Proteins, 79, 3050-3066.
4. Bahadur, R.P. et al. (2004) A dissection of specific and non-specific proteinprotein interfaces. J. Mol. Biol., 336, 943-955.
5. Bates, P.A. et al. (1998) Conformational analysis of the first observed non-proline cis-peptide bond occurring within the complementarity determining region (CDR) of an antibody. J. Mol. Biol., 284, 549-555.
6. Chailyan, A. et al. (2011) The association of heavy and light chain variable domains in antibodies: implications for antigen specificity. FEBS J., 278, 2858-2866.
7. Cohen, G.H. et al. (2005) Water molecules in the antibody-antigen interface of the structure of the Fab HyHEL-5-lysozyme complex at 1.7 A resolution: comparison with results from isothermal titration calorimetry. Acta Crystallogr. D Biol. Crystallogr., 61, 628-633.
8. Dalkas, G.A. et al. (2014) Cation-pi, amino-pi, pi-pi, and H-bond interactions stabilize antigen-antibody interfaces. Proteins, 82, 1734-1746.
9. De, S. et al. (2005) Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different. BMC Struct. Biol., 5, 15.
10. de Wildt, R.M. et al. (1999) Analysis of heavy and light chain pairings indicates that receptor editing shapes the human antibody repertoire. J. Mol. Biol., 285, 895-901.
11. Dunbar, J. et al. (2013) ABangle: characterising the VH-VL orientation in antibodies. Protein Eng. Des. Sel., 26, 611-620.
12. Dunbar, J. et al. (2014) SAbDab: the structural antibody database. Nucleic Acids Res., 42(Database issue), D1140-D1146.
13. Fernandez, A. and Scheraga, H.A. (2003) Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl. Acad. Sci. USA, 100, 113-118.
14. Jackson, R.M. (1999) Comparison of protein-protein interactions in serine protease-inhibitor and antibody-antigen complexes: implications for the protein docking problem. Protein Sci., 8, 603-613.
15. Janin, J. et al. (2008) Protein-protein interaction and quaternary structure. Quart. Rev. Biophys., 41, 133-180.
16. Jemmerson, R. (1987) Antigenicity and native structure of globular proteins: low frequency of peptide reactive antibodies. Proc. Natl. Acad Sci. USA, 84, 9180-9184.
17. Jones, S. (2012) Computational and structural characterisation of protein associations. Advances in Exp. Med. Biol., 747, 42-54.
18. Keskin, O. et al. (2008) Principles of protein-protein interactions: what are the preferred ways for proteins to interact? Chem. Rev., 108, 1225-1244.
19. Kinjo, A.R. and Nakamura, H. (2010) Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: an exhaustive structural classification study. J. Mol. Biol., 399, 526-540.
20. Kortemme, T. et al. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and proteinprotein complexes. J. Mol. Biol., 326, 1239-1259.
21. Kuroda, D. et al. (2008) Structural classification of CDR-H3 revisited: a lesson in antibody modeling. Proteins, 73, 608-620.
22. Laskowski, R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph., 13, 323-330. 307-328.
23. Lawrence, M.C. and Colman, P.M. (1993) Shape complementarity at protein/protein interfaces. J. Mol. Biol., 234, 946-950.
24. Leaver-Fay, A. et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol., 487, 545-574.
25. Lee, M. et al. (2006) Shapes of antibody binding sites: qualitative and quantitative analyses based on a geomorphic classification scheme. J. Org. Chem., 71, 5082-5092.
26. Levy, E.D. et al. (2006) 3D complex: a structural classification of protein complexes. PLoS Comput. Biol., 2, e155.
27. Li, Y. et al. (2003) X-ray snapshots of the maturation of an antibody response to a protein antigen. Nat. Struct. Biol., 10, 482-488.
28. Lo Conte, L. et al. (1999) The atomic structure of protein-protein recognition sites. J. Mol. Biol., 285, 2177-2198.
29. Luo, Q. et al. (2013) Local network patterns in protein-protein interfaces. PloS One, 8, e57031.
30. MacCallum, R.M. et al. (1996) Antibody-antigen interactions: contact analysis and binding site topography. J. Mol. Biol., 262, 732-745.
31. McDonald, I.K. and Thornton, J.M. (1994) Satisfying hydrogen bonding potential in proteins. J. Mol. Biol., 238, 777-793.
32. Mintseris, J. and Weng, Z. (2005) Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl. Acad. Sci. USA, 102, 10930-10935.
33. Moreira, I.S. et al. (2007) Hot spots-a review of the protein-protein interface determinant amino-acid residues. Proteins, 68, 803-812.
34. Narayanan, A. et al. (2009) Energy-based analysis and prediction of the orientation between light-and heavy-chain antibody variable domains. J. Mol. Biol., 388, 941-953.
35. Ofran, Y. and Rost, B. (2003) Analysing six types of protein-protein interfaces. J. Mol. Biol., 325, 377-387.
36. Pauling, L. and Corey, R.B. (1951) Atomic coordinates and structure factors for two helical configurations of polypeptide chains. Proc. Natl. Acad. Sci. USA, 37, 235-240.
37. Peng, H.P. et al. (2014) Origins of specificity and affinity in antibody-protein interactions. Proc. Natl. Acad. Sci. USA, 111, E2656-E2665.
38. Ramaraj, T. et al. (2012) Antigen-antibody interface properties: composition, residue interactions, and features of 53 non-redundant structures. Biochim. Biophys. Acta, 1824, 520-532.
39. Rodier, F. et al. (2005) Hydration of protein-protein interfaces. Proteins, 60, 36-45.
40. Russell, R.B. and Aloy, P. (2008) Targeting and tinkering with interaction networks. Nat. Chem. Biol., 4, 666-673.
41. Stranges, P.B. and Kuhlman, B. (2013) A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds. Prot. Sci., 22, 74-82.
42. Tan, P.H. et al. (1998) Contributions of a highly conserved VH/VL hydrogen bonding interaction to scFv folding stability and refolding efficiency. Biophys. J., 75, 1473-1482.
43. Tsuchiya, Y. et al. (2006) Analyses of homo-oligomer interfaces of proteins from the complementarity of molecular surface, electrostatic potential and hydrophobicity. Protein Eng., Des. Sel., 19, 421-429.
44. Vreven, T. et al. (2015) Updates to the integrated protein-protein interaction benchmarks: docking benchmark version 5 and affinity benchmark version 2. J.Mol. Biol., 427, 3031-3041.
45. Weitzner, B.D. et al. (2015) The origin of CDR H3 structural diversity. Structure, 23, 302-311.
46. Xu, D. et al. (1997) Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng., 10, 999-1012.
47. Ye, J. et al. (2013) IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Res., 41(Web Server issue), W34-W40.