Predicting kinetic constants of protein-protein interactions based on structural properties

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 3, 2011, Pages 720-734

  Bai, Hongjun ^a,b   Yang, Kun ^a,b   Yu, Daqi ^a,b   Zhang, Changsheng ^a,b   Chen, Fangjin ^a,b   Lai, Luhua ^a,b  

^a PEKING UNIVERSITY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

Affinity dissociation constant, K d; Association rate constant, k on; Bayesian information criteria; Dissociation rate constant, k off; Protein complex structures; Protein protein interaction design; Systems biology

Indexed keywords

ARTICLE; CORRELATION COEFFICIENT; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; STATIC ELECTRICITY;

KINETICS; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEINS; STATIC ELECTRICITY;

EID: 79551482915     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22904     Document Type: Article

References (71)

1. Stein M, Gabdoulline RR, Wade RC. Bridging from molecular simulation to biochemical networks. Curr Opin Struct Biol 2007; 17: 166-172.
2. Dell'Orco D. Fast predictions of thermodynamics and kinetics of protein-protein recognition from structures: from molecular design to systems biology. Mol Biosyst 2009; 5: 323-334.
3. Keskin O, Ma BY, Rogale K, Gunasekaran K, Nussinov R. Protein-protein interactions: organization, cooperativity and mapping in a bottom-up systems biology approach. Phys Biol 2005; 2: S24-S35.
4. Camacho CJ, Vajda S. Protein-protein association kinetics and protein docking. Curr Opin Struct Biol 2002; 12: 36-40.
5. Kiel C, Selzer T, Shaul Y, Schreiber G, Herrmann C. Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex. Proc Natl Acad Sci USA 2004; 101: 9223-9228.
6. Selzer T, Albeck S, Schreiber G. Rational design of faster associating and tighter binding protein complexes. Nat Struct Biol 2000; 7: 537-541.
7. Schreiber G, Haran G, Zhou HX. Fundamental aspects of protein-protein association kinetics. Chem Rev 2009; 109: 839-860.
8. Schreiber G. Kinetic studies of protein-protein interactions. Curr Opin Struct Biol 2002; 12: 41-47.
9. Alsallaq R, Zhou HX. Energy landscape and transition state of protein-protein association. Biophys J 2007; 92: 1486-1502.
10. Alsallaq R, Zhou HX. Prediction of protein-protein association rates from a transition-state theory. Structure 2007; 15: 215-224.
11. Alsallaq R, Zhou HX. Electrostatic rate enhancement and transient complex of protein-protein association. Proteins 2008; 71: 320-335.
12. Schlosshauer M, Baker D. Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein Sci 2004; 13: 1660-1669.
13. Schlosshauer M, Baker D. A general expression for bimolecular association rates with orientational constraints. J Phys Chem B 2002; 106: 12079-12083.
14. Gabdoulline RR, Wade RC. Biomolecular diffusional association. Curr Opin Struct Biol 2002; 12: 204-213.
15. Haddadian EJ, Gross EL. A Brownian dynamics study of the effects of cytochrome f structure and deletion of its small domain in interactions with cytochrome c6 and plastocyanin in Chlamydomonas reinhardtii. Biophys J 2006; 90: 566-577.
16. Haddadian EJ, Gross EL. A Brownian dynamics study of the interactions of the luminal domains of the cytochrome b6f complex with plastocyanin and cytochrome c6: the effects of the Rieske FeS protein on the interactions. Biophys J 2006; 91: 2589-2600.
17. Spaar A, Dammer C, Gabdoulline RR, Wade RC, Helms V. Diffusional encounter of barnase and barstar. Biophys J 2006; 90: 1913-1924.
18. Rienzo FD, Gabdoulline RR, Menziani MC, Benedetti PGD, Wade RC. Electrostatic analysis and Brownian dynamics simulation of the association of plastocyanin and cytochrome f. Biophys J 2001; 81: 3090-3104.
19. Gabdoulline RR, Wade RC. Protein-protein association: investigation of factors influencing association rates by brownian dynamics simulations. J Mol Biol 2001; 306: 1139-1155.
20. Zou G, Skeel RD. Robust biased Brownian dynamics for rate constant calculation. Biophys J 2003; 85: 2147-2157.
21. Allison SA, Northrup SH, McCammon JA. Simulation of biomolecular diffusion and complex formation. Biophys J 1986; 49: 167-175.
22. Lin JP, Beratan DN. Simulation of electron transfer between cytochrome C2 and the bacterial photosynthetic reaction center: Brownian dynamics analysis of the native proteins and double mutants. J Phys Chem B 2005; 109: 7529-7534.
23. Gabdoulline RR, Wade RC. Simulation of the diffusional association of barnase and barstar. Biophys J 1997; 72: 1917-1929.
24. Gabdoulline RR, Stein M, Wade RC. qPIPSA: relating enzymatic kinetic parameters and interaction fields. BMC Bioinformatics 2007; 8: 373.
25. Pearce KH, Jr, Cunningham BC, Fuh G, Teeri T, Wells JA. Growth hormone binding affinity for its receptor surpasses the requirements for cellular activity. Biochemistry 1999; 38: 81-89.
26. Kumar P, Han BC, Shi Z, Jia J, Wang YP, Zhang YT, Liang L, Liu QF, Ji ZL, Chen YZ. Update of KDBI: kinetic data of bio-molecular interaction database. Nucleic Acids Res 2009; 37 (Database issue): D636-D641.
27. Zhou HX. Association and dissociation kinetics of colicin E3 and immunity protein 3: convergence of theory and experiment. Protein Sci 2003; 12: 2379-2382.
28. Shaul Y, Schreiber G. Exploring the charge space of protein-protein association: a proteomic study. Proteins 2005; 60: 341-352.
29. Reynolds C, Damerell D, Jones S. ProtorP: a protein-protein interaction analysis server. Bioinformatics 2009; 25: 413-414.
30. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-242.
31. Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997; 2: 173-181.
32. Haliloglu T, Bahar I, Erman B. Gaussian dynamics of folded proteins. Phys Rev Lett 1997; 79: 3090-3093.
33. Bai HJ, Ma WZ, Liu SY, Lai LH. Dynamic property is a key determinant for protein-protein interactions. Proteins 2008; 70: 1323-1331.
34. Flory PJ, Gordon M, McCrum NG. Statistical thermodynamics of random networks. Proc R Soc Lond A Math Phys Sci 1976; 351: 351-380.
35. Kloczkowski A, Mark JE, Erman B. chain dimensions and fluctuations in random elastomeric networks 1. Phantom Guassian network in the undeformed state. Macromolecules 1989; 22: 1423-1432.
36. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983; 22: 2577-2637.
37. Hubbard SJ, Thornton JM. NACCESS. London: Department of Biochemistry and Molecular Biology, University College London; 1993.
38. Sanner MF, Olson AJ, Spehner JC. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 1996; 38: 305-320.
39. Laskowski RA. SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J Mol Graph 1995; 13: 323-330.
40. Jones S, Thornton JM. Principles of protein-protein interactions. Proc Natl Acad Sci USA 1996; 93: 13-20.
41. Mitchell JC, Kerr R, Ten Eyck LF. Rapid atomic density methods for molecular shape characterization. J Mol Graph Model 2001; 19: 325-330.
42. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983; 4: 187-217.
43. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 1998; 102: 3586-3616.
44. Im W, Beglov D, Roux B. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput Phys Commun 1998; 111: 59-75.
45. Warme PK, Morgan RS. A survey of atomic interactions in 21 proteins. J Mol Biol 1978; 118: 273-287.
46. Jones S, Thornton JM. Protein-protein interactions: a review of protein dimer structures. Prog Biophys Mol Biol 1995; 63: 31-65.
47. Sanner MF. Python: a programming language for software integration and development. J Mol Graph Model 1999; 17: 57-61.
48. Hoeting JA, Madigan D, Raftery AE, Volinsky CT. Bayesian model averaging: a tutorial. Stat Sci 1999; 14: 382-401.
49. Wasserman L. Bayesian model selection and model averaging. J Math Psychol 2000; 44: 92-107.
50. Villa Braslavsky CI, Nowak C, Gorlich D, Wittinghofer A, Kuhlmann J. Different structural and kinetic requirements for the interaction of Ran with the Ran-binding domains from RanBP2 and importin-beta. Biochemistry (Mosc) 2000; 39: 11629-11639.
51. Albeck S, Schreiber G. Biophysical characterization of the interaction of the beta-lactamase TEM-1 with its protein inhibitor BLIP. Biochemistry (Mosc) 1999; 38: 11-21.
52. Miller S, Lesk AM, Janin J, Chothia C. The accessible surface area and stability of oligomeric proteins. Nature 1987; 328: 834-836.
53. Janin J, Miller S, Chothia C. Surface, subunit interfaces and interior of oligomeric proteins. J Mol Biol 1988; 204: 155-164.
54. Ponstingl H, Henrick K, Thornton JM. Discriminating between homodimeric and monomeric proteins in the crystalline state. Proteins 2000; 41: 47-57.
55. Bahadur RP, Chakrabarti P, Rodier F, Janin J. A dissection of specific and non-specific protein-protein interfaces. J Mol Biol 2004; 336: 943-955.
56. Argos P. An investigation of protein subunit and domain interfaces. Protein Eng 1988; 2: 101-113.
57. Dell'Orco D, De Benedetti PG, Fanelli F. In silico screening of mutational effects on enzyme-proteic inhibitor affinity: a docking-based approach. BMC Struct Biol 2007; 7: 37.
58. Zhou HX. Disparate ionic-strength dependencies of on and off rates in protein-protein association. Biopolymers 2001; 59: 427-433.
59. Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003; 326: 1239-1259.
60. Pokala N, Handel TM. Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity. J Mol Biol 2005; 347: 203-227.
61. Liang S, Li L, Hsu WL, Pilcher MN, Uversky V, Zhou Y, Dunker AK, Meroueh SO. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry 2009; 48: 399-414.
62. Liu S, Liu SY, Zhu XL, Liang HH, Cao AN, Chang ZJ, Lai LH. Nonnatural protein-protein interaction-pair design by key residues grafting. Proc Natl Acad Sci USA 2007; 104: 5330-5335.
63. Liang SD, Li WZ, Xiao L, Wang JS, Lai LH. Grafting of protein-protein interaction epitope. J Biomol Struct Dyn 2000; 17: 821-828.
64. Liang SD, Liu ZJ, Li WZ, Ni LS, Lai LH. Construction of proteinbinding sites in scaffold structures. Biopolymers 2000; 54: 515-523.
65. Bogan AA, Thorn KS. Anatomy of hot spots in protein interfaces. J Mol Biol 1998; 280: 1-9.
66. Reichmann D, Cohen M, Abramovich R, Dym O, Lim D, Strynadka NC, Schreiber G. Binding hot spots in the TEM1-BLIP interface in light of its modular architecture. J Mol Biol 2007; 365: 663-679.
67. Reichmann D, Rahat O, Albeck S, Meged R, Dym O, Schreiber G. The modular architecture of protein-protein binding interfaces. Proc Natl Acad Sci USA 2005; 102: 57-62.
68. Reichmann D, Rahat O, Cohen M, Neuvirth H, Schreiber G. The molecular architecture of protein-protein binding sites. Curr Opin Struct Biol 2007; 17: 67-76.
69. Potapov V, Reichmann D, Abramovich R, Filchtinski D, Zohar N, Ben Halevy D, Edelman M, Sobolev V, Schreiber G. Computational redesign of a protein-protein interface for high affinity and binding specificity using modular architecture and naturally occurring template fragments. J Mol Biol 2008; 384: 109-119.
70. Beltrao P, Kiel C, Serrano L. Structures in systems biology. Curr Opin Struct Biol 2007; 17: 378-384.
71. Aloy P, Russell RB. Structural systems biology: modelling protein interactions. Nat Rev Mol Cell Biol 2006; 7: 188-197.