Improved protein free energy calculation by more accurate treatment of nonbonded energy: Application to chymotrypsin inhibitor 2, V57A

Proteins: Structure, Function and Genetics

Volumn 30, Issue 4, 1998, Pages 388-400

  Sugita, Yuji ^b   Kitao, Akio ^a  

^a KYOTO UNIVERSITY   (Japan)

^b NONE

Author keywords

Cell multipole method; Chymotrypsin inhibitor 2; Component analysis; Free energy perturbation; Molecular dynamics; Nose Hoover equation; Spherical solvent boundary potential; Thermodynamics integration

Indexed keywords

ALANINE; ARGININE; CHYMOTRYPSIN INHIBITOR; LEUCINE; PHENYLALANINE; VALINE;

ALGORITHM; AMINO ACID SUBSTITUTION; ARTICLE; COMPUTER PROGRAM; CRYSTAL STRUCTURE; HYDROPHILICITY; HYDROPHOBICITY; MOLECULAR DYNAMICS; MUTATION; PRIORITY JOURNAL; PROTEIN DENATURATION; PROTEIN STRUCTURE; REACTION ANALYSIS; THERMODYNAMICS;

ALGORITHMS; COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PLANT PROTEINS; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 0032032108     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980301)30:4<388::AID-PROT6>3.0.CO;2-F     Document Type: Article

References (53)

1. Beveridge, B.L., DiCapua, F.M. Free energy via molecular simulation: Application to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-92, 1989.
2. van Gunsteren, W.F., Mark, A.E. On the interpretation of biochemical data by molecular dynamics computer simulation. Eur. J. Biochem. 204:947-961, 1992.
3. Straatsma, T.P., McCammon, J.A. Computational alchemy. Annu. Rev. Phys. Chem. 43:407-435, 1992.
4. Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 93:2395-2417, 1993.
5. Ewald, P. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 64:253-287, 1921.
6. Heyes, D.M. Electrostatic potentials and fields in infinite point charge lattices. J. Chem. Phys. 74:1924-1929, 1981.
7. York, D.M., Wlodawer, A., Pedersen, L.G., Darden, T.A. Atomic-level accuracy in simulations of large protein crystals. Proc. Natl. Acad. Sci. U.S.A. 91:8715-8718, 1994.
8. Beglov, D., Roux, B. Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations. J. Chem. Phys. 100:9050-9063, 1994.
9. Greengard, L., Rokhlin, V. On the evaluation of electrostatic interactions in molecular modeling. Chem. Scripta 29A:139-144, 1989.
10. Greengard, L. Fast algorithms for classical physics. Science 265:909-914, 1994.
11. Ding, H.-Q., Karasawa, N., Goddard III, W.A. Atomic level simulations on million particles: The cell multipole method for Coulomb and London nonbond interactions. J. Chem. Phys. 97:4309-4315, 1992.
12. Mathiowetz, A.M., Jain, A., Karasawa, N., Goddard III, W.A. Protein simulations using techniques suitable for very large systems: The cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics. Proteins 20:227-247, 1994.
13. Saito, M. Molecular dynamics simulations of proteins in water without the truncation of long-range coulomb interactions. Mol. Simul. 8:321-333, 1992.
14. Saito, M. Molecular dynamics simulations of proteins in solution: Artifacts caused by the cutoff approximation. J. Chem. Phys. 101:4055-4061, 1994.
15. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., DiNola A., Haak, J.R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690, 1984.
16. Hoover, W.G. Canonical dynamics: Equilibrium phase-space distributions. Phys. Rev. A31:1695-1697, 1985.
17. Nosé, S. A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52:255-268, 1984.
18. Mark, A.E., van Gunsteren, W.F. Decomposition of the free energy of a system in terms of specific interactions implications for theoretical and experimental studies. J. Mol. Biol. 240:167-176, 1994.
19. Smith, P.E., van Gunsteren, W.F. When are free energy components meaningful? J. Phys. Chem. 98:2366-2379, 1994.
20. Boresch, S., Archontis, G., Karplus, M. Free energy simulations: The meaning of the individual contributions from a component analysis. Proteins 20:25-33, 1994.
21. Boresch, S., Karplus, M. The meaning of component analysis: Decomposition of the free energy in terms of specific interaction. J. Mol. Biol. 254:801-807, 1995.
22. Zacharias, M., Straatsma, T.P. Path dependence of free energy components in thermodynamic integration. Mol. Simul. 14:417-423, 1995.
23. Brady, G.P., Sharp, K.A. Decomposition of interaction free energies in proteins and other complex systems. J. Mol. Biol. 254:77-85, 1995.
24. Brady, G.P., Szabo, A., Sharp, K.A. On the decomposition of free energies. J. Mol. Biol. 263:123-125, 1996.
25. Jackson, S.E., Fersht, A.R. Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition. Biochemistry 30:1428-1435, 1991.
26. Itzhaki, L.S., Otzen, D.E., Fersht, A.R. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254:260-288, 1995.
27. Otzen, D.E., Rheinnecker, M., Fersht, A.R. Structural factors contributing to the hydrophobic effect: The partly exposed hydrophobic minicore in chymotrypsin inhibitor 2. Biochemistry 34:13051-13058, 1995.
28. Otzen, D.E., Fersht, A.R. Side-chain determinants of beta-sheet stability. Biochemistry 34:5718-5724, 1995.
29. McPhalen, C.A., James, M.N.G. Structural Comparison of two serine proteinase-protein inhibitor complexes: Eglin-C-subtilisin Carlsberg and CI-2-subtilisin novo. Biochemisry 27:6582-6598, 1988.
30. Weiner, S.J., Kollman, P.A., Nguyen, D.T., Case, D.A. An all atom force field for simulations of proteins and nucleic acids. J. Comput. Chem. 7:230-252, 1986.
31. Gear, C.W. "Numerical Initial Value Problems in Ordinally Differential Equations." Englewood Cliffs, NJ: Prentice-Hall, 1971.
32. Tidor, B., Karplus, M. Simulation analysis of the stability mutant R96H of T4 lysozyme. Biochemistry 30:3217-3228, 1991.
33. Sneddon, S.F., Tobias, D.J. The role of packing interactions in stabilizing folded proteins. Biochemistry 31:2842-2846, 1992.
34. Yun-yu, S., Mark, A.E., Cun-xin, W., Fuhua, H., Berendsen, H.J.C., van Gunsteren, W.F. Can the stability of protein mutants be predicted by free energy calculations? Protein Eng. 6:289-295, 1993.
35. Saito, M., Taminura, R. Relative melting temperatures of RNase HI mutant proteins from MD simulation/free energy calculations. Chem. Phys. Lett. 236:156-161, 1995.
36. Tanimura, R., Saito, M. Molecular dynamics/free energy perturbation studies of the thermostable V74I mutant of ribonuclease HI. Mol. Simul. 16:75-85, 1996.
37. McPhalen, C.A., James, M.N.G. Crystal and molecular structure of the serine proteinase inhibitor CI-2 form barley seeds. Biochemistry 26:261-269, 1987.
38. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L. Comparison of simple poteintial funcitons for simulating liquid water. J. Chem. Phys. 79:926-935, 1983.
39. Reynolds, C.A., King, P.M., Richards, W.G. Free energy calculations in molecular biophysics. Mol. Phys. 76:251-275, 1992.
40. Severance, D.L., Essex, J.W., Jorgensen, W.L. Generalized alteration of structure and parameters: A new method for free-energy perturbations in systems containing flexible degrees of freedom. J. Comp. Chem. 16:311-327, 1994.
41. Morikami, K., Nakai, T., Kidera, A., Saito, M. PRESTO (PRotein Engineering SimulaTOr): A vectorized molecular mechanics program for biopolymers. Comput. Chem. 16: 243-248, 1992.
42. Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341, 1977.
43. Saito, M. Molecular dynamics/free energy study of a protein in solution with all degrees of freedom and long-range coulomb interactions. J. Phys. Chem. 99:17043-17048, 1995.
44. Kirkwood, J.G. The dielectric polarization of polar liquids. J. Chem. Phys. 7:911-919, 1939.
45. Straatsma, T.P., Berendsen, H.J.C. Free energy of ionic hydration: Analysis of a thermodynamic integration technique to evaluate free energy differences by molecular dynamics simulations. J. Chem. Phys. 89:5876-5886, 1988.
46. King, G., Warshel, A. A surface constrained all-atom solvent model for effective simulations of polar solutions. J. Chem. Phys. 91:3647-3661, 1989.
47. Nakamura, H. Roles of electrostatic interaction in proteins. Q. Rev. Biophys. 29:1-90, 1996.
48. Matthews, B.W. Structural and genetic analysis of protein stability. Annu. Rev. Biochem. 62:139-160, 1993.
49. Takano, K., Ogasahara, K., Kaneda, H., Yamagata, Y., Fjii, S., Kanaya, E., Kikuchi, M., Oobatake, M., Yutani, K. Contribution of hydrophobic residues to the stability of human lysozyme: Calorimetric studies and x-ray structural analysis of the five isoleucine to valine mutants. J. Mol. Biol. 254:62-76, 1995.
50. Funahashi, J., Takano, K., Ogasahara, K., Yamagata, Y., Yutani, K. The structure, stability, and folding process of amyloidogenic mutant human lysozyme. J. Biochem. 120: 1216-1223, 1996.
51. Takano, K., Yamagata, Y., Fujii, S., Yutani, K. Contribution of the hydrophobic effect to the stability of human lysozyme: Calorimetric studies and x-ray structural analyses of the nine valine to alanine mutants. Biochemistry 36:688-698, 1997.
52. Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
53. Merrit, E.A., Murphy, M.E.P. Raster3D Version 20. A program for photorealistic molecular graphics. Acta Crystallogr. D50:869-873, 1994.