Predicting solvated peptide conformations via global minimization of energetic atom-to-atom interactions

Computers and Chemical Engineering

Volumn 22, Issue 6, 1998, Pages 765-788

  Klepeis, J L ^a   Androulakis, I P ^a   Ierapetritou, M G ^a   Floudas, C A ^a  

^a Princeton University   (United States)

Author keywords

Global optimization; Protein folding; Solvation

Indexed keywords

EID: 0001352857     PISSN: 00981354     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0098-1354(97)00258-5     Document Type: Article

References (58)

1. Adjiman, C.S., Androulakis, I.P. and Floudas, C.A. (1997) Global optimization of MINLP problems in process synthesis and design. Comput. Chem. Engng 21, S445-S450.
2. Adjiman, C.S., Androulakis, I.P. and Floudas, C.A. (1998a) A global optimization method, αBB, for general twice-differentiable NLPs-II. Implementation and computational results. Comput. Chem. Engng, in press.
3. Adjiman, C.S., Androulakis, I.P., Maranas, C.D. and Floudas, C.A. (1996) A global optimization method, αBB, for process design. Comput. Chem. Engng 20, S419-S424.
4. Adjiman, C.S., Dallwig, S., Floudas, C.A. and Neumaier, A. (1998b) A global optimization method, αBB, for general twice-differentiable NLPs-I. Theoretical advances. Comput. Chem. Engng, in press.
5. Adjiman, C.S. and Floudas, C.A. (1996) Rigorous convex underestimators for general twice-differentiable problems. J. Glob. Opt. 9, 23-40.
6. Allinger, N.L., Yuh, Y.H. and Lii, J.H. (1989) Molecular mechanics. The MM3 force field for hydrocarbons. J. Am. Chem. Soc. 111, 8551-8565.
7. Androulakis, I.P., Maranas, C.D. and Floudas, C.A. (1995) αBB: A global optimization method for general constrained nonconvex problems. J. Glob. Opt. 7, 337-363.
8. Androulakis, I.P., Maranas, C.D. and Floudas, C.A. (1997) Global minimum potential energy conformation of oligopeptides. J. Glob. Opt. 11, 1-34.
9. Anfinsen, C.B., Haber, E., Sela, M. and White, F.H. (1961) The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. J. Proc. Nat. Acad. Sci. USA 47, 1309-1314.
10. Augspurger, J.D. and Scheraga, H.A. (1996) An efficient, differentiable hydration potential for peptides and proteins. J. Comp. Chem. 17, 1549-1558.
11. Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S. and Karplus, M. (1983) Charmm: A program for macromolecular energy minimization and dynamics calculations. J. Comp, Chem. 4, 187-217.
12. Burley, S.K. and Petsko, G.A. (1985) Aromatic-aromatic interaction: A mechanism of protein structure stabilization. Science 229, 23-28.
13. Camerman, A., Mastropaolo, D., Karle, I., Karle, J. and Camerman, N. (1983) Crystal structure of leucine-enkephalin. Nature 306, 447-450.
14. Connolly, M.L. (1983) Analytical molecular surface calculations. J. Appl. Cryst. 16, 548-558.
15. Dauber-Osguthorpe, P., Roberts, V.A., Osguthorpe, D.J., Wolff, J., Genest, M. and Hagler, A.T. (1988) Structure and energetics of ligand binding to peptides: Escherichia coli dihydrofolate reductase-trimethoprim, a drug receptor system. Proteins 4, 31-47.
16. Dejaegere, A. and Karplus, M. (1996) Analysis of coupling schemes in free energy simulations: A unified description of nonbonded contributions to solvation free energies. J. Phys. Chem, 100, 11148-11164.
17. Eisenhaber, F. and Argos, P. (1993) Improved strategy in analytic surface calculation for molecular systems: Handling of singularities and computational efficiency. J. Comp. Chem. 14, 1272-1280.
18. Eisenhaber, F., Lijnzaad, P., Argos, P., Sander, C. and Scharf, M. (1995) The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comp. Chem. 16, 273-284.
19. Floudas, C. (1997) Deterministic global optimization in design, control, and computational chemistry, in Large Scale Optimization with Applications, Part II: Optimal Design and Control, (Edited by L. Biegler, T. Coleman, A. Conn, and F. Santosa), Vol. pp. 129-184. 93IMA Volumes in Mathematics and its Applications, Springer-Verlag.
20. Gill, P.E., Murray, W., Saunders, M.A. and Wright, M. H. (1986) NPSOL 4.0 User's Guide, Systems Optimization Laboratory, Dept. of Operations Research, Stanford University, CA.
21. Graham, W.H., Carter II, E.S. and Hicks, R.P. (1992) Conformational analysis of met-enkephalin in both aqueous solution and in the presence of sodium dodecyl sulfate micelles using multi-dimensional nmr and molecular modeling. Biopolymers 32, 1755-1764.
22. Honig, B., Sharp, K. and Yang, A. (1993) Macroscopic models of aqueous solutions: Biological and chemical applications. J. Phys. Chem. 97, 1101-1109.
23. Kitao, A., Hirata, F. and Go, N. (1993) Effects of solvent on the conformation and the collective motions of a protein, 2. structure of hydration in melittin. J. Phys. Chem. 97, 10223-10230.
24. Kollman, P. (1993) Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 93, 2395-2417.
25. Lambert, M.H. and Scheraga, H.A. (1989) Pattern recognition in the prediction of protein structure. I. Tripeptide conformational probabilities calculated from the amino acid sequence. J. Comp. Chem. 10, 770-797.
26. Levitt, M. (1983) Protein folding by restrained energy minimization and molecular dynamics. J. Mol. Biol. 170, 723-764.
27. Li, Z. and Scheraga, H.A. (1988) Structure and free energy of complex thermodynamic systems. J. Mol. Struct. (Theochem.) 179, 333-352.
28. Madison, V. and Kopple, K.D. (1980) Solvent-dependent conformational distributions of some dipeptides. J. Am. Chem. Soc. 102, 4855-4863.
29. Maranas, C.D., Androulakis, I.P., Floudas, C.A. (1996) A deterministic global optimization approach for the protein folding problem, In DIMACS Series in Discrete Mathematics and Theoretical Computer Science, Vol. 23, pp. 133-150. American Mathematical Society.
30. Maranas, C.D. and Floudas, C. A. (1992) A global optimization approach for lennard-jones microclusters. J. Chem. Phys. 97, 7667-7677.
31. Maranas, C.D. and Floudas, C.A. (1993) Global optimization for molecular conformation problems. Annals Operations Res. 42, 85-117.
32. Maranas, C.D. and Floudas, C.A. (1994a) A deterministic global optimization approach for molecular structure determination. J. Chem. Phys. 100, 1247-1261.
33. Maranas, C.D. and Floudas, C.A. (1994b) Global minimum potential energy conformations of small molecules. J. Glob. Opt. 4, 135-170.
34. Meirovitch, H. and Meirovitch, E. (1996) New theoretical methodology for elucidating the solution structure of peptides from nmr data, 3. solvation effects. J. Phys. Chem. 100, 5123-5133.
35. Momany, F.A., Carruthers, L.M., McGuire, R.F. and Scheraga, H.A. (1974a) Intermolecular potential from crystal data. III. J. Phys. Chem. 78, 1595-1620.
36. Momany, F.A., Carruthers, L.M. and Scheraga, H.A. (1974b) Intermolecular potential from crystal data. IV. J. Phys. Chem. 78, 1621-1630.
37. Momany, F.A., McGuire, R.F., Burgess, A.W. and Scheraga, H.A. (1975) Energy parameters in poly-peptides. VII. J. Phys. Chem. 79, 2361-2381.
38. Némethy, G., Gibson, K.D., Palmer, K.A., Yoon, C.N., Paterlini, G., Zagari, A., Rumsey, S. and Scheraga, H.A. (1992) Energy parameters in polypeptides, 10. J. Phys. Chem. 96, 6472-6484.
39. Némethy, G., Pottle, M.S. and Scheraga, H.A. (1983) Energy parameters in polypeptides, 9. J. Phys Chem. 87, 1883-1887.
40. Neumaier, A. (1997) Molecular modeling of proteins and mathematical prediction of protein structure. SIAM Rev., accepted for publication.
41. Noguti, T. and Go, N. (1983) A method of rapid calculation of a second derivative matrix of conformational energy for large molecules. J. Phys. Soc. Jpn 52, 3685-3690.
42. Pardalos, P.M., Shalloway, D. and Xue, G. (Eds.) (1996) Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding, Vol. 23, of DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society.
43. Perrot, G., Cheng, B., Gibson, K.D.J., Vila, K.A.P., Nayeem, A., Maigret, B. and Scheraga, H.A. (1992) MSEED: a program for the rapid analytical determination of accessible surface areas and their derivatives. J. Comp. Chem. 13, 1-11.
44. Ramachandran, G.N. and Saisekharan, V. (1968) Conformation of polypeptides and proteins. Adv. Protein Chem. 23, 283-437.
45. Ripoll, D.R., Vásquez, M.J. and Scheraga, H.A. (1991) The electrostatically driven monte carlo method: application to conformational analysis of decaglycine. Biopolymers 31, 319-330.
46. Scheraga, H. (1996) PACK: Programs for Packing Polypeptide Chains, online documentation.
47. Scheraga, H.A. (1992) Predicting three-dimensional structures of oligopeptides, in Reviews in Computational Chemistry (Edited by K.B. Lipkowitz, and D.B. Boyd), Vol 3, pp. 73-142. VCH Publishers.
48. Straatsma, T.P. and McCammon, J.A. (1992) Computational alchemy. Annu. Rev. Phys. Chem. 43, 407-435.
49. van Groningen, W.F. and Berendsen, H.J.C. (1987) GROMOS, Groningen Molecular Simulation, Groningen, The Netherlands.
50. Vásquez, M., Némethy, G. and Scheraga, H.A. (1983) Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residue α-aminobutyric acid. Macromolecules 16, 1043-1049.
51. Vásquez, M., Némethy, G. and Scheraga, H.A. (1994) Conformational energy calculations on polypeptides and proteins. Chem. Rev. 94, 2183-2239.
52. Vila, J., Williams, R.L., Vásquez, M. and Scheraga, H.A. (1991) Empirical solvation models can be used to differentiate native from non-native conformations of bovine pancreatic trypsin inhibitor. Proteins 10, 199-218.
53. von Freyberg, B. and Braun, W. (1993) Minimization of empirical energy functions in proteins including hydrophobic surface area effects. J. Comp. Chem. 14, 510-521.
54. Wawak, R.J., Gibson, K.D. and Scheraga, H. A. (1994) Gradient discontinuities in calculations involving molecular surface area. J. Math. Chem. 15, 207-232.
55. Weiner, S., Kollman, P., Case, D., Singh, U., Ghio, C., Alagona, G., Profeta, S. and Weiner, P. (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106, 765-784.
56. Weiner, S., Kollman, P., Nguyen, D. and Case, D. (1986) An all atom force field for simulations of proteins and nucleic acids. J. Comp. Chem. 7, 230-252.
57. Williams, R.L., Vila, J., Perrot, G. and Scheraga, H.A. (1992) Empirical solvation models in the context of conformational energy searches: Application to bovine pancreatic trypsin inhibitor. Proteins 14, 110-119.
58. Zimmerman, S.S., Pottle, M.S., Némethy, G. and Scheraga, H.A. (1977) Conformational analysis of the 20 naturally occurring amino acid residues using Ecepp. Macromolecules 10, 1-9.