Protein folding simulations with genetic algorithms and a detailed molecular description

Journal of Molecular Biology

Volumn 269, Issue 2, 1997, Pages 240-259

  Pedersen, Jan T ^a   Moult, John ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

Genetic algorithms; Global energy function; Monte Carlo; Protein folding

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 0031556019     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1010     Document Type: Article

References (69)

1. Abagyan R., Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:1994;983-1002.
2. Allen M. P., Tildesley D. J. Computer Simulation of Liquids. 1989;Oxford Science Publications, Clarendon Press, Oxford.
3. Alonso D. O. V., Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding: characterization of partially unfolded states of ubiquitin in 60methanol and in water. J. Mol. Biol. 247:1995;501-520.
4. Anderson D. E., Becktel W. J., Dahlquist F. W. pH-induced denaturation of proteins: a salt bridge contributes 3-5 kcal/mol to the free energy of folding of T4 lysozyme. Biochemistry. 29:1990;2403-2408.
5. Åqvist J., Gunsteren V. W. F., Leijonmarck M., Tapia O. A molecular dynamics study of the C-terminal fragment of the l7/l12 ribosomal protein: secondary structure motion in a 150 picosecond trajectory. J. Mol. Biol. 183:1985;461-477.
6. Avbelj F. Use of a potential of mean force to analyse free energy contributions in protein folding. Biochemistry. 31:1992;6290-6297.
7. Avbelj F., Moult J. Determination of the conformations of folding initiation sites in proteins by computer simulation. Proteins: Struct. Funct. Genet. 23:1995a;129-141.
8. Avbelj F., Moult J. The role of electrostatic screening in determining protein main chain conformational preferences. Biochemistry. 34:1995b;755-764.
9. Baudet S., Janin J. Crystal structure of a barnase complex at 1.9 Å resolution. J. Mol. Biol. 219:1991;123-132.
10. Bernstein F., Koetzle T., Williams G. J. B., Meyer E., Brice M., Rodgers J., Kennard O., Shimanouchi T., Tasumi M. The protein databank: a computer based archival file for macromolecular structures. J. Mol. Biol. 112:1977;535-542.
11. Blanco F. J., Serrano L. Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur. J. Biochem. 230:1995;634-649.
12. Brandt D. T., Flory P. J. The role of dipole interactions in determining polypeptide conformation. J. Am. Chem. Soc. 87:1965;663-664.
13. Braxenthaler M., Pedersen J. T., Samudrala R., Lou R., Moult J. Carb biocomputing web pages, force field and parameters: http:/ /iris4.carb.nist.gov/WWW/moultgroups/potentials.html; pre-processed library of folds: http: / /prostar.carb.nist.gov:8000/PDec/PDecRetr . 1996.
14. Brooks B., Bruccoleri R., Olafson B., States D., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:1983;187-217.
15. Brooks C. L. I., Head-Gordon T. Virtual rigid body dynamics. Biopolymers. 31:1991;77-100.
16. Brooks C. L. I., Karplus M., Pettitt M. G. Nemethy on proteins: a theoretical perspective of dynamics structure and thermodynamics. Advan. Chem. Phys. Bull. Mathemat. Biol. 53:1991;313.
17. Brunne R. M., Berndt K. D., Guntert P., Wuthrich K., van Gunsteren W. F. Structure and internal dynamics of the bovine pancreatic trypsin inhibitor in aqueous solution from long-time molecular dynamics simulations. Proteins: Struct. Funct. Genet. 23:1995;49-62.
18. Chothia C. The principles that determine the structure of proteins. Annu. Rev. Biochem. 55:1984;537-572.
19. Creamer T. P., Rose G. D. Side-chain entropy opposes alpha-helix formation but rationalizes experimentally determined helix-forming propensities. Proc. Natl Acad. Sci. USA. 89:1992;5937-5941.
20. Dandekar T., Argos P. Potential of genetic algorithms in protein folding and protein engineering simulations. Protein Eng. 5:1992;637-645.
21. Dandekar T., Argos P. Folding the main-chain of small proteins with the genetic algorithm. J. Mol. Biol. 236:1994;844-861.
22. Dauber-Osguthorpe P., Roberts V. A., Osguthorpe D. J., Wolff J., Genest M., Hagler A. T. Structure and energetics of ligand binding to proteins:E. coli. Proteins: Struct. Funct. Genet. 4:1988;31-47.
23. DeBolt S. E., Skolnick J. Evaluation of atomic level mean force potentials via inverse folding and inverse refinement of protein structures: atomic burial position and pairwise non-bonded interactions. Protein Eng. 9:1996;637-655.
24. Dunbrack R., Karplus M. Conformational analysis of the backbone-dependent rotamer preferences of protein sidechains. Nature Struct. Biol. 1:1994;334-340.
25. Dyson H. J., Merutka G., Waltho J. P., Lerner R. A., Wright P. E. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Myohermerythrin. J. Mol. Biol. 226:1992a;795-817.
26. Dyson H. J., Sayre J. R., Merutka G., Shin H. C., Lerner R. A., Wright P. E. Folding of peptide fragments comprising the complete sequence of proteins. Models for initiation of protein folding. I. Plastocyanin. J. Mol. Biol. 226:1992b;819-835.
27. Elofsson A., LeGrand S., Eisenberg D. Local moves, an efficient method for protein folding simulations. Proteins: Struct. Funct. Genet. 23:1995;73-82.
28. Garnier J., Osguthorpe D. J., Robson B. Analysis of the accuracy and implications of simple models for predicting the secondary structure of globular proteins. J. Mol. Biol. 78:1978;97-120.
29. Geist A., Beguelin A., Dongarra J., Jiang W., Manchek R., Sinderam V. PVM 3 User's Guide and Reference Manual. 1993.
30. Gilbert G., Baleja J. Membrane-binding peptide from the C2 domain of factor VIII forms an amphiphatic structure as determined by NMR spectroscopy. Biochemistry. 34:1995;3022-3031.
31. Goldberg D. Genetic Algorithms in Search, Optimization, and Machine Learning. 1989;Addison-Wesley, San Mateo, CA.
32. Hagler A. T. The Peptides: Analysis, Synthesis, Biology. 1985;Academic Press, Orlando, FL.
33. Hao M.-H., Sheraga H. Monte Carlo simulation of a first-order transition for protein folding. J. Phys. Chem. 98:1994;4940-4948.
34. Holland J. Adaptation in Natural and Artificial Systems. 1975;University of Michigan Press, Ann Arbor, MI.
35. Holm L., Sander C. Protein-structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1994;123-138.
36. Horovitz A., Fersht A. R. Co-operative interactions during protein folding. J. Mol. Biol. 224:1992;733-740.
37. Huang E. S., Subbiah S., Tsai J., Levitt M. Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations. J. Mol. Biol. 257:1996;716-725.
38. Kabsch W., Sander C. Dictionary of protein secondary structure: recognition of hydrogen bonded and geometrical features. Biopolymers. 22:1983;2577-2637.
39. Kang Y. K., No K. T., Scheraga H. A. Intrinsic torsional potential parameters for conformational analysis of peptides and proteins. J. Phys. Chem. 100:1996;15588-15598.
40. Kitson D. H., Avbelj F., Moult J., Nguyen D. T., Mertz J. E., Hadzi D., Hagler A. T. On achieving better than 1 Å accuracy in a simulation of a large protein:Streptomyces griseus. Proc. Natl Acad. Sci. USA. 90:1993;8920-8924.
41. Kolinski A., Skolnick J. Monte Carlo simulations of protein-folding. 1. Lattice model and interaction scheme. Proteins: Struct. Funct. Genet. 18:1994;338-352.
42. Kuszewski J., Clore G. M., Gronenborn A. M. Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G. Protein Sci. 3:1994;1945-1952.
43. Laskowski R., MacArthur M., Moss D., Thornton J. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26:1993;283-290.
44. Lazaridis T., Archontis G., Karplus M. Enthalpic contribution to protein stability: insights from atom-based calculations and statistical mechanics. Advan. Protein Chem. 47:1995;231-306.
45. Lee B. K., Richards F. M. Interpretation of protein structure: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
46. Lee H., Darden T., Pedersen L. Accurate crystal molecular dynamics simulations using particle-mesh-Ewald: RNA dinucleotides ApU and GpC. Chem. Phys. Letters. 243:1995;229.
47. Maiorov V. N., Crippen G. M. Size-independent comparison of protein three-dimensional structures. Proteins: Struct. Funct. Genet. 22:1995;273-283.
48. 2. J. Mol. Biol. 224:1992;837-845.
49. Metropolis N., Rosenbluth A., Rosenbluth M., Teller A., Teller E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1953;1087-1091.
50. Moult J., Unger R. An analysis of protein folding pathways. Biochemistry. 30:1991;3816-3824.
51. Mounge A., Lathrop E. J. P., Gunn J. R., Shenkin P. S., Friesner R. A. Computer modelling of protein folding: conformational and energetic analysis of reduced and detailed protein models. J. Mol. Biol. 247:1995;995-1012.
52. Park B., Levitt M. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258:1996;367-392.
53. Pedersen J. T., Moult J. Ab initio. Proteins: Struct. Funct. Genet. 23:1995;454-460.
54. Pedersen J. T., Moult J. Genetic algorithms for protein structure prediction. Curr. Opin. Struct. Biol. 6:1996;227-231.
55. Rice L. M., Brünger A. T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins: Struct. Funct. Genet. 19:1994;277-290.
56. Rooman M., Kocher J.-P., Wodak S. Prediction of protein backbone conformation based on seven structural assignments. J. Mol. Biol. 221:1991;961-979.
57. Sancho J., Neira J., Fersht A. An N-terminal fragment of Barnase has residual helical structure similar to that of a refolding intermediate. J. Mol. Biol. 224:1992;749-758.
58. Scheraga H. A. Recent developments in the theory of protein folding: searching for the global energy minimum. Biophys. Chem. 59:1996;329.
59. Sharp K. A., Nicholls A., Friedmann R., Honig B. Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models. Biochemistry. 30:1991;9686-9697.
60. Shirley B. A., Stanssens P., Hahn U., Pace C. N. Contribution of hydrogen bonding to the conformational stability of ribonuclease T1. Biochemistry. 31:1992;725-732.
61. Shrake A., Rupley J. Environment and exposure to solvent of protein atoms. J. Mol. Biol. 79:1973;351-371.
62. Srinivasan R., Rose G. D. LINUS: a hierarchic procedure to predict the fold of a protein. Proteins: Struct. Funct. Genet. 22:1995;81-99.
63. Sun S. Reduced representation of protein structure prediction: statistical potential and genetic algorithms. Protein Sci. 2:1993;762-785.
64. Sun S., Thomas P. D., Dill K. A. Simple protein folding algorithm using a binary code and secondary structure constraints. Protein Eng. 8:1995;769-778.
65. Unger R., Moult J. Effect of mutations on the performance of genetic algorithms suitable for protein folding simulations, in computer aided innovation of new materials. Comput.-Aided Innovat. New Mater. 2:1993a;1283-1286.
66. Unger R., Moult J. Genetic algorithms for protein folding simulations. J. Mol. Biol. 231:1993b;75-81.
67. Weiner S., Kollman P., Case D., Singh U., Ghio C., Alagona G., Profeta S., Weiner P. A new force field for molecular mechanics simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:1984;765-783.
68. Wetlaufer D. Nucleation, rapid folding, and globular interchain regions in proteins. Proc. Natl Acad. Sci. USA. 70:1973;697-701.
69. Williams S., Causgrove T. P., Gilmanshin R., Fang K. S., Callender R. H., Woodruff W. H., Dyer R. Fast events in protein folding: helix melting and formation in a small peptide. Biochemistry. 35:1996;691-697.