The folding funnel landscape for the peptide Met-enkephalin

Proteins: Structure, Function and Genetics

Volumn 34, Issue 4, 1999, Pages 472-483

  Hansmann, Ulrich H E ^a   Okamoto, Yuko ^b   Onuchic, Jose N ^c  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Energy landscape theory; Generalized ensembles; Monte Carlo simulations; Protein folding

Indexed keywords

METENKEPHALIN; PEPTIDE;

ARTICLE; ENERGY; ENTROPY; PRIORITY JOURNAL; PROTEIN FOLDING; SIMULATION; SYSTEM ANALYSIS;

COMPUTER SIMULATION; ENKEPHALIN, METHIONINE; KINETICS; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN FOLDING; TEMPERATURE;

EID: 0033104745     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990301)34:4<472::AID-PROT7>3.0.CO;2-X     Document Type: Article

References (57)

1. Anfinsen CB. Principles that govern the folding of protein chains. Science 1973;181:223-230.
2. Dill KA, Chan HS. From Levinthal to pathways to funnels. Nat Struct Biol 1997;4:10-19.
3. Sali A, Shakhnovich EI, Karplus M. Kinetics of protein folding - A lattice model study of the requirements for folding to the native state. J Mol Biol 1994;235:1614-1636.
4. Guo Zh, Thirumalai D. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol 1996;236: 323-343.
5. Bryngelson JD, Wolynes PG. Spin glasses and the statistical mechanics of protein folding. Proc Natl Acad Sci USA 1987;84: 7524-7528.
6. Leopold PE, Montal M, Onuchic JN. Protein folding funnels: kinetic pathways through compact conformational space. Proc Natl Acad Sci USA 1992;89:8721-8725.
7. Onuchic JN, Luhey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem 1997;48:545-600.
8. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. Funnels, pathways and the energy landscape of protein folding: a synthesis. Proteins 1995;21:167-195.
9. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. Towards an outline of the topography of a realistic protein folding funnel. Proc Natl Acad Sci USA 1995;92:3626-3630.
10. Socci ND, Onuchic JN, Wolynes PG. Diffusive dynamics of the reaction coordinate for protein folding funnels. J Chem Phys 1996;104:5860-5871.
11. Guo Zh, Thirumalai D. Kinetics of protein folding - nucleation mechanism, time scales, and pathways. Biopolymers 36:103-116, 1995.
12. Mirny LA, Abkevich V, Shakhnovich EI. Universality and diversity of the protein folding scenarios: a comprehensive analysis with the aid of a lattice model. Fold Des 1996;1:103-116.
13. Friedrichs MS, Goldstein RA, Wolynes PG. Generalized protein tertiary structure recognition using associative memory hamiltonians. J Mol Biol 1991;222:1013-1034.
14. Guo Zh, Brooks III, CL. Thermodynamics of protein folding: a statistical mechanical study of a small all β protein. Biopolymers 1997;42:745-757.
15. Nymeyer H, García AE, Onuchic JN. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc Natl Acad Sci USA 1998;95:5921-5928.
16. Shea J-E, Nochomovitz YD, Guo Zh, Brooks III, CL. Exploring the space of protein folding hamiltonians: the balance of forces in a minimalist β-barrel model. J Chem Phys 1998;109:2895-2903.
17. Hardin C, Luthey-Schulten ZA, Wolynes PG. Backbone dynamics, fast folding, and secondary structure of helical proteins and peptides. Proteins 1998; in press.
18. Wolynes PG, Luthey-Schulten ZA, Onuchic JN. Fast-folding experiments and the topography of protein folding energy landscapes. Chem Biol 1996;3:425-432.
19. Vásquez M, Némethy G, Scheraga HA. Conformational energy calculations of polypeptides and proteins. Chem Rev 1994;94:2183-2239.
20. Hansmann UHE, Okamoto Y. The generalized-ensemble approach for protein folding simulations. In: Stauffer D, editor. Annual reviews in computational physics VI. Singapore: World Scientific; 1998, in press.
21. Berg BA, Neuhaus T. Multicanonical algorithms for first order phase transitions. Phys Lett 1991;267:249-253.
22. Lyubartsev AP, Martinovski AA, Shevkunov SV, Vorontsov-Velyaminov PN. New approach to Monte Carlo calculations of the free energy: method of expanded ensembles. J Chem Phys 1992;96: 1776-1783; Marinari E, Parisi G. Simulated tempering: a new Monte Carlo scheme. Europhys Lett 1992;19:451-458.
23. Lyubartsev AP, Martinovski AA, Shevkunov SV, Vorontsov-Velyaminov PN. New approach to Monte Carlo calculations of the free energy: method of expanded ensembles. J Chem Phys 1992;96: 1776-1783; Marinari E, Parisi G. Simulated tempering: a new Monte Carlo scheme. Europhys Lett 1992;19:451-458.
24. Hansmann UHE, Okamoto Y. Prediction of peptide conformation by multicanonical algorithm: a new approach to the multiple-minima problem. J Comp Chem 1993;14:1333-1338.
25. Okamoto Y, Hansmann UHE. Thermodynamics of helix - coil transitions studied by multicanonical algorithms. J Phys Chem 1995;99:11276-11287.
26. Hansmann UHE, Okamoto Y. Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations. J Chem Phys 1999; in press.
27. Hansmann UHE, Okamoto Y. Tertiary structure prediction of C-peptide of ribonuclease A by multicanonical algorithm. J Phys Chem 1998;102:653-656.
28. Hansmann UHE, Okamoto Y. Effects of side-chain charges on α-helix stability in C-peptide of ribonuclease A studied by multicanonical algorithm. J Phys Chem 1999; in press.
29. Hansmann UHE, Okamoto Y. Numerical comparisons of three recently proposed algorithms in the protein folding problem. J Comp Chem 1997;18:920-933.
30. Hansmann UHE, Masuya M, Okamoto Y. Characteristic temperatures of folding of a small peptide. Proc Natl Acad Sci USA 1997;94:10652-10656.
31. Boczko EM, Brooks CL III. First principles calculation of the folding free energy for a three helix bundle protein. Science 1995;269:393-396.
32. Aubry A, Birlirakis N, Sakarellos-Daitsiotis M, Sakarellos C. A crystal molecular conformation of leu-enkephalin related to the morphin molecule. Biopolymers 1989;28:27-40.
33. Behnam BA, Deber CM. Evidence for a folded conformation of methionine-and Leucine-Enkephalin in a Membrane Environment. J Biol Chem 1984;259:14939-14940.
34. 14N-NMR studies of leu-enkephalin and enkephalin related fragments in aqueous solution. Biopolymers 1990;29:423-439.
35. Li Z, Scheraga HA. Monte Carlo minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1984;84:6611-6615.
36. Freyberg B von, Braun W. Efficient search for all low energy conformations of polypeptides by Monte Carlo methods. J Comp Chem 1991;12:1065-1076.
37. Okamoto Y, Kikuchi T, Kawai H. Prediction of low-energy structures of met-enkephalin by Monte Carlo simulated annealing. Chem Lett 1992;1992:1275-1278.
38. Hansmann UHE, Okamoto Y. Comparative study of multicanonical and simulated annealing algorithms in the protein folding problem. Physica A 1994;212:415-437.
39. Montcalm T, Cui W, Zhao H, Guarnieri F, Wilson SR. Simulated annealing of met-enkephalin: low energy states and their relevance to membrane-bound, solution and solid-state conformations. J Mol Struct Theochem 1994;308:37-51.
40. Eisenmenger F, Hansmann UHE. Variation of the energy landscape of a small peptide under a change from the ECEPP/2 Force Field to ECEPP/3. J Phys Chem B 1997;101:3304-3310.
41. Hansmann UHE. Parallel tempering algorithm for conformational studies of biological molecules. Chem Phys Lett 1997;281: 140-150.
42. Mitsutake A, Hansmann UHE, Okamoto Y. in preparation.
43. Sippl MJ, Némethy G, Scheraga HA. Intermolecular potentials from crystal data. 6. Determination of empirical potentials for O-H ⋯ O = C hydrogen bonds from packing configurations. J Phys Chem 1994;88:6231-6233. (And references therein.)
44. Hansmann UHE. Simulated annealing with Tsallis weights - A numerical comparison. Physica A 1997;242:250-257.
45. Hansmann UHE, Okamoto Y. Generalized-ensemble Monte Carlo method for systems with rough energy landscape. Phys Rev E 1997;56:2228-2233.
46. Tsallis C. Possible generalization of Boltzmann-Gibbs statistics. J Stat Phys 1988;52:479-487.
47. Ferrenberg AM, Swendsen RH. Optimized Monte Carlo data analysis. Phys Rev Lett 1988;61:2635-2638. Phys Rev Lett 1989; 63:1658-1658(E). (And references given in the erratum.)
48. Ferrenberg AM, Swendsen RH. Optimized Monte Carlo data analysis. Phys Rev Lett 1988;61:2635-2638. Phys Rev Lett 1989; 63:1658-1658(E). (And references given in the erratum.)
49. Kawai H, Okamoto Y, Fukugita M, Nakazawa T, Kikuchi T. Prediction of α-helix folding of isolated C-peptide of ribonuclease A by Monte Carlo simulated annealing. Chem Lett 1991;213-216.
50. The program for the calculation of solvent excluded volume was written by M. Masuya and will be described in detail elsewhere.
51. Eisenhaber F, Lijnzaad P, Argos P, Sander C, Scharf M. 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 1995;16:273-284.
52. Socci ND, Onuchic JN, Wolynes PG. Protein folding mechanisms and the multidimensional folding funnel. Proteins 1998;32:136-158.
53. Scalley ML, Baker D. Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proc Natl Acad Sci USA 1997;44: 10636-10640.
54. Plotkin SS, Wolynes PG. Non-Markovian configurational diffusion and reaction coordinates in protein folding. Phys Rev Lett 1998;22: 5015-5018.
55. Camacho CJ, Thirumalai D. A criterion that determines fast folding of proteins: A model study. Proc Natl Acad Sci USA 1993;90:6369-6372.
56. Klimov DK, Thirumalai D. Factors governing the foldability of proteins. Proteins 1996;26:411-441.
57. Sayle RA, Milner-White EJ. RasMol: biomolecular graphics for all. TIBS 1995;20:374-376.