On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions

Protein Science

Volumn 6, Issue 6, 1997, Pages 1293-1301

  Froloff, Nicolas ^a,b   Windemuth, Andreas ^a   Honig, Barry ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

^b INSERM   (France)

Author keywords

Binding free energy; Hydrophobic effect; Major Histocompatibility Complex; Poisson Boltzmann electrostatics; Protein peptide interactions; Solvation free energy

Indexed keywords

MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1;

ARTICLE; CALCULATION; ELECTRICITY; ENERGY TRANSFER; HLA SYSTEM; HYDROPHOBICITY; MAJOR HISTOCOMPATIBILITY COMPLEX; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION;

MURINAE;

EID: 0031008575     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560060617     Document Type: Article

References (73)

1. Ajay, Murcko MA. 1995. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem 38:4953-4967.
2. Altuvia Y, Schueler O, Margalit H. 1995. Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 249:244-250.
3. Andrews PR, Craik DJ, Martin JL. 1984. Functional group contributions to drug-receptor interactions. J Med Chem 27:1648-1657.
4. Bash PA, Singh UC, Brown FK, Langridge R, Kollman PA. 1987. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 235:574-576.
5. Ben-Tal N, Sitkoff D, Topol IA, Yang AS, Burt SK, Honig B. 1997. Free energy of amide hydrogen bond formation in vacuum, in water and in liquid alkane solution. J Phys Chem B 101:450-457.
6. Bernstein FC, Koetzle TF, Williams GJ, Meyer EE Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. 1977. The Protein Data Bank: A computer-based archival file for macromolecular structures. J Mol Biol 112:535-542.
7. Beveridge DL, DiCapua FM. 1989. Free energy via molecular simulation: Applications to chemical and biomolecular systems. Annu Rev Biophys Biophys Chem 18:431-492.
8. Bluestone JA, Jameson S, Miller S, Dick R II 1992. Peptide-induced conformational changes in class I heavy chains alter major histocompatibility complex recognition. J Exp Med 176:1757-1761.
9. Bluestone JA, Kaliyaperumal A, Jameson S, Miller S, Dick R II 1993. Peptide-induced changes in class I heavy chains alter allorecognition. J Immunol 151:3943-3953.
10. Board JA Jr, Causey JW, Leathrum JF Jr, Windemuth A, Schulten K. 1992. Accelerated molecular dynamics simulation with the parallel fast multipole algorithm. Chem Phys Lett 198:89-94.
11. Böhm HJ. 1994. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput-Aided Mol Des 8:243-256.
12. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4:187-217.
13. Brünger AT. 1992. Free R value: A novel statistical quantity for assessing the accuracy of crystal structures. Nature 355:472-475.
14. Brünger AT. 1995. X-PLOR, Version 3.1. New Haven, Connecticut: Yale University.
15. Brünger AT, Karplus M. 1988. Polar hydrogen positions in proteins: Empirical energy placement and neutron diffraction comparison. Proteins Struct Funct Genet 4:148-156.
16. Catipovic B, Dal Porto J, Mage M, Johansen TE, Schneck JP. 1992. Major histocompatibility complex conformational epitopes are peptide specific. J Exp Med 176:1611-1618.
17. Catipovic B, Talluri G, Oh J, Wei T, Su XM, Johansen TE, Edidin M, Schneck JP. 1994. Analysis of the structure of empty and peptide-loaded major histocompatibility complex molecules at the cell surface. J Exp Med 180:1753-1761.
18. Doig AJ, Sternberg MJE. 1995. Side-chain conformational entropy in protein folding. Protein Sci 4:2247-2251.
19. Elliott T, Cerundolo V, Elvin J, Townsend A. 1991. Peptide-induced conformational change of the class I heavy chain. Nature 351:402-406.
20. Erickson HP. 1989. Co-operativity in protein-protein association. The structure and stability of the actin filament. J Mol Biol 206:465-474.
21. Finkelstein AV, Janin J. 1989. The price of lost freedom: Entropy of bimolecular complex formation. Protein Eng 3:1-3.
22. b. Science 257:919-927.
23. b-ovalbumin peptide complex reveals the interplay of primary and secondary anchor positions in the major histocompatibility complex binding groove. Proc Natl Acad Sci USA 92:2479-2483.
24. Friedman RA, Honig B. 1995. A free energy analysis of nucleic acid base stacking in aqueous solution. Biophys J 69:1528-1535.
25. Froloff N, Honig B. 1995. Evaluation of binding free energies of MHC class I protein-peptide complexes. Biophys J 68:A404.
26. Gilson MK, Given JA, Bush BL, McCammon JA. 1997. The statistical thermodynamic basis for computation of binding affinities: A critical review. Biophys J 72:1047-1069.
27. Gilson MK, Honig B. 1988. Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis. Proteins Struct Funct Genet 4:7-18.
28. Honig B, Yang AS. 1995. Free energy balance in protein folding. Adv Protein Chem 46:27-58.
29. Ippolito JA, Alexander RS, Christianson DW. 1990. Hydrogen bond stereochemistry in protein structure and function. J Mol Biol 215:457-471.
30. Jackson RM, Sternberg MJE. 1995. A continuum model for protein-protein interactions: Application to the docking problem. J Mol Biol 250:258-275.
31. Janin J. 1995. Elusive affinities. Proteins Struct Funct Genet 21:30-39.
32. Kollman PA. 1993. Free energy calculations: Applications to chemical and biochemical phenomena. Chem Rev 93:2395-2417.
33. Kollman PA. 1994. Theory of macromolecule-ligand interactions. Curr Opin Struct Biol 4:240-245.
34. Lee B, Richards FM. 1971. The interpretation of protein structures: Estimation of static accessibility. J Mol Biol 55:379-400.
35. Luzzati V. 1952. Traitement statistique des erreurs dans la détermination des structures cristallines. Acta Cryst 5:802-810.
36. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Nguyen DT, Ngo T, Prodhom B, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Wiorkiewicz-Kuczera J, Karplus M. 1992. Self-consistent parameterization of biomolecules for molecular modeling and condensed phase simulations. Biophys J 61:A143.
37. Madden DR, Garboczi DN, Wiley DC. 1993. The antigenic identity of peptide-MHC complexes: A comparison of the conformations of five viral peptides presented by HLA-A2. Cell 75:693-708.
38. Matsumura M, Saito Y, Jackson MR, Song ES, Peterson PA. 1992. In vitro peptide binding to soluble empty class I major histocompatibility complex molecules isolated from transfected Drosophila melanogaster cells. J Biol Chem 267:23589-23595.
39. McCammon JA. 1987. Computer-aided molecular design. Science 238:486-491.
40. Miyamoto S, Kollman PA. 1993. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins Struct Funct Genet 16:226-245.
41. Myers JK, Pace CN. 1996. Hydrogen bonding stabilizes globular proteins. Biophys J 71:2033-2039.
42. Nicholls A, Honig B. 1991. A rapid finite difference algorithm utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem 12:435-445.
43. Nicholls A, Sharp KA, Honig B. 1991. Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct Funct Genet 11:281-296.
44. Novotny J, Bruccoleri RE, Saul FA. 1989. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry 28:4735-4749.
45. Page MI, Jencks WP. 1971. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc Natl Acad Sci USA 68:1678-1683.
46. Pickett SD, Sternberg MJE. 1993. Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 231:825-839.
47. Richards FM. 1977. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 6:151-176.
48. Rohren EM, McCormick DJ, Pease LR. 1994. Peptide-induced conformational changes in class I molecules. Direct detection by flow cytometry. J Immunol 152: 5337-5343.
49. Ruppert J, Sidney J, Celis E, Kubo RT, Grey HM, Sette A. 1993. Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell 74:929-937.
50. Searle MS, Williams DH, Gerhard U. 1992. Partitioning of free energy contributions in the estimation of binding constants. Residual motions and consequences for amide-amide hydrogen bond strengths. J Am Chem Soc 114:10697-10704.
51. Sharp KA, Honig B. 1990. Electrostatic interactions in macromolecules. Annu Rev Biophys Biophys Chem 19:301-332.
52. Sharp KA, Nicholls A, Fine RF, Honig B. 1991. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 252:106-109.
53. Shen J, Quiocho FA. 1995. Calculation of binding energy differences for receptor-ligand systems using the Poisson-Boltzmann method. J Comput Chem 16:445-448.
54. Shen J, Wendoloski J. 1995. Binding of phosphorus-containing inhibitors to thermolysin studied by the Poisson-Boltzmann method. Protein Sci 4:373-381.
55. Sherman LA, Chattopadhyay S, Biggs JA, Dick RF, Bluestone JA. 1993. Alloantibodies can discriminate class I major histocompatibility complex molecules associated with various endogenous peptides. Proc Natl Acad Sci USA 90:6949-6951.
56. Sitkoff D, Sharp KA, Honig B. 1994. Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978-1988.
57. Smith KC, Honig B. 1994. Evaluation of the conformational free energies of loops in proteins. Proteins Struct Funct Genet 18:119-132.
58. Sridharan S, Nicholls A, Honig B. 1992. A new vertex algorithm to calculate solvent accessible surface areas. Biophys J 61:A174.
59. Sridharan S, Nicholls A, Honig B. 1997. A fast algorithm for molecular surface generation with applications to finite-difference electrostatic calculations. (Manuscript in preparation).
60. Stanfield RL, Wilson IA. 1995. Protein-peptide interactions. Curr Opin Struct Biol 5:103-113.
61. Steinberg IZ, Sheraga HA. 1963. Entropy changes accompanying association reactions of proteins. J Biol Chem 238:172-181.
62. Straatsma TP, McCammon JA. 1991. Theoretical calculations of relative affinities of binding. Methods Enzymol 202:497-511.
63. Tidor B, Karplus M. 1994. The contribution of vibrational entropy to molecular association. The dimerization of insulin. J Mol Biol 238:405-414.
64. Vajda S, Weng Z, Rosenfeld R, DeLisi C. 1994. Effect of conformational flexibility and solvation on receptor-ligand binding free energies. Biochemistry 33:13977-13988.
65. Warwicker J, Watson HC. 1982. Calculation of the electric potential in the active site cleft due to alpha-helix dipoles. J Mol Biol 157:671-679.
66. Wendoloski JJ, Shen J, Oliva MT, Weber PC. 1993. Biophysical tools for structure-based drug design. Pharmacol Ther 60:169-183.
67. Williams DH, Cox JPL, Doig AJ, Gardner M, Gerhard U, Kaye PT, Lal AR, Nicholls IA, Salter CJ, Mitchell RC. 1991. Toward the semiquantitative estimation of binding constants. Guides for peptide-peptide binding in aqueous solution. J Am Chem Soc 113:7020-7030.
68. Williams DH, Searle MS, Mackay JP, Gerhard U, Maplestone RA. 1993. Toward an estimation of binding constants in aqueous solution: Studies of associations of vancomycin group antibiotics. Proc Natl Acad Sci USA 90:1172-1178.
69. Windemuth A. 1995. Advanced algorithms for molecular dynamics simulation: The program PMD. In: Mattson TG, ed. Parallel Computing in Computational Chemistry. ACS Symposium Series 592. Washington, D.C.: American Chemical Society. pp 151-169.
70. Windemuth A, Schulten K. 1991. Molecular dynamics on the Connection Machine. Mol Simul 5:353-361.
71. Yang AS, Honig B. 1995a. Free energy determinants of secondary structure formation: I. α-Helices. J Mol Biol 252:351-365.
72. Yang AS, Honig B. 1995b. Free energy determinants of secondary structure formation: II. Antiparallel β-sheets. J Mol Biol 252:366-376.
73. Zhang T, Koshland DE Jr. 1996. Computational method for relative binding energies of enzyme-substrate complexes. Protein Sci 5:348-356.