New developments of the electrostatically driven monte carlo method: test on the membrane-bound portion of melittin

Biopolymers

Volumn 46, Issue 2, 1998, Pages 117-126

  Ripoll, Daniel R ^a   Liwo, Adam ^a,b   Scheraga, Harold A ^a  

^a Department of Obstetrics Gynecology   (United States)

^b UNIVERSITY OF GDA SK   (Poland)

Author keywords

Cluster analysis; Conformational space; Electrostatically driven monte carlo method; Global energy minimum; Lowest energy conformations; Melittin, membrane bound portion; Perturbed conformations; Polypeptide chain

Indexed keywords

ALGORITHMS; CONFORMATIONS; MOLECULAR STRUCTURE; POLYPEPTIDES;

ELECTROSTATICALLY DRIVEN MONTE CARLO; GLOBAL ENERGY MINIMUM; LOW ENERGY CONFORMATION; MELITTIN;

MONTE CARLO METHODS;

MELITTIN; MEMBRANE PROTEIN; TRIPEPTIDE;

ARTICLE; CLUSTER ANALYSIS; ELECTRICITY; ENERGY; PROTEIN CONFORMATION; SYSTEM ANALYSIS;

AMINO ACID SEQUENCE; ELECTROSTATICS; MELITTEN; MEMBRANES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PEPTIDE FRAGMENTS; PROTEIN BINDING; PROTEIN CONFORMATION; THERMODYNAMICS;

EID: 0032146488     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0282(199808)46:2<117::AID-BIP6>3.0.CO;2-P     Document Type: Article

References (44)

1. Terwilliger, T. C., Weissman, L. & Eisenberg, D. (1982) Biophys. J. 37, 353-361.
2. Terwilliger, T. C. & Eisenberg, D. (1982) J. Biol. Chem. 257, 6010-6015.
3. Terwilliger, T. C. & Eisenberg, D. (1982) J. Biol. Chem, 257, 6016-6022.
4. Lauterwein, J., Brown, L. R. & Wüthrich, K. (1980) Biochim. Biophys. Acta 622, 219-230.
5. Brown, L. R., Lauterwein, J. & Wüthrich, K. (1980) Biochim. Biophys. Acta 622, 231-244.
6. Brown, L. R. & Wüthrich, K. (1981) Biochim. Biophys. Acta 647, 95-111.
7. Brown, L. R., Braun, W., Kumar, A. & Wüthrich, K. (1982) Biophys. J. 37, 319-328.
8. Stanislawski, B. & Rüterjans, H. (1987) Eur. Biophys. J. 15, 1-12.
9. Bazzo, R., Tappin, M. J., Pastore, A., Harvey, T. S., Carver, J. A. & Campbell, I. D. (1988) Eur. J. Biochem. 173, 139-146.
10. Inagaki, F., Shimada, I., Kawaguchi, K., Hirano, M., Terasawa, I., Ikura, T. & Go, N. (1989) Biochemistry 28, 5985-5991.
11. Ikura, T., Go, N. & Inagaki, F. (1991) Proteins Struct. Funct. Genet. 9, 81-89.
12. Altenbach, C. & Hubbell, W. L. (1988) Proteins Struct. Funct. Genet 3, 230-242.
13. Momany, F. A., McGuire, R. F., Burgess, A. W. & Scheraga, H. A. (1975) J. Phys. Chem. 79, 2361-2381.
14. Némethy, G., Pottle, M. S. & Scheraga, H. A. (1983) J. Phys. Chem. 87, 1883-1887.
15. Sippl, M. J., Némethy, G. & Scheraga, H. A. (1984) J. Phys. Chem. 88, 6231-6233.
16. Némethy, G., Gibson, K. D., Palmer, K. A., Yoon, C. N., Paterlini, G., Zagari, A., Rumsey, S. & Scheraga, H. A. (1992) J. Phys. Chem. 96, 6472-6484.
17. Pincus, M. R., Klausner, R. D. & Scheraga, H. A. (1982) Proc. Natl. Acad. Sci. USA 79, 5107-5110.
18. Ripoll, D. R. & Scheraga, H. A. (1990) Biopolymers 30, 165-176.
19. Olszewski, K. A., Piela, L. & Scheraga, H. A. (1993) J. Phys. Chem. 97, 267-270.
20. Lee, J., Scheraga, H. A. & Rackovsky, S. (1998) Biopolymers 46, 103-115.
21. Crippen, G. M. & Snow, M. E. (1990) Biopolymers 29, 1479-1489.
22. Li, Z. & Scheraga, H. A. (1987) Proc. Natl. Acad. Sci USA 84,6611-6615.
23. Li, Z. & Scheraga, H. A. (1988) J. Mol. Struct. (Theochem.) 179, 333-352.
24. Purisima, E. O. & Scheraga, H. A. (1987) J. Mol. Biol. 196, 697-709.
25. Ripoll, D. R. & Scheraga, H. A. (1989) J. Prot. Chem. 8, 263-287.
26. Olszewski, K. A., Piela, L. & Scheraga, H. A. (1992) J. Phys. Chem. 96, 4672-4676.
27. Lee, J., Scheraga, H. A. & Rackovsky, S. (1997) J. Comp. Chem. 18, 1222-1232.
28. Ripoll, D. R. & Scheraga, H. A. (1988) Biopolymers 27, 1283-1303.
29. Ripoll, D. R. & Thomas, S. J. (1992) J. Supercomput. 6, 163-185.
30. O'Donnell, T. J., Hotovy, S. G., Pottle, M. S., Ripoll, D. R. & Scheraga, H. A. (1996) in Lecture Notes in Computer Science, Vol. 1067: High Performance Computing and Networking, Liddell, H., Colbrook, A., Hertzberger, B. & Sloot, P. eds., Springer-Verlag, Berlin, Heidelberg, New York, pp. 365-372.
31. Piela, L. & Scheraga, H. A. (1987) Biopolymers 26, S33-S58.
32. Zimmerman, S. S., Pottle, M. S., Némethy, G. & Scheraga, H. A. (1977) Macromolecules 10, 1-9.
33. Gay, D. M. (1983) ACM Trans. Math. Software 9, 503-524.
34. Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. (1953) J. Chem. Phys. 21, 1087-1092.
35. Kirkpatrkk, S., Gelatt, Jr., C. D. & Vecchi, M. P. (1983) Science 220, 671-680.
36. Späth, H. (1980) Cluster Analysis Algorithms, Halsted Press, New York, pp. 170-194.
37. Gordon, H. L. & Somorjai, R. L. (1992) Proteins Struct. Funct. Genet. 14, 249-264.
38. Karpen, M. E., Tobias, D. J. & Brooks, C. L., III (1993) Biochemistry 32, 412-420.
39. Vásquez, M., Némethy, G. & Scheraga, H. A. (1983) Macromolecules 16, 1043-1049.
40. Zimmerman, S. S. & Scheraga, H. A. (1977) Biopolymers 16, 811-843.
41. Go, N. & Scheraga, H. A. (1969) J. Chem. Phys. 51, 4751-4767.
42. Anfinsen, C. B. (1973) Science 181, 223-230.
43. Ripoll, D. R., Vorobjev, Y. N., Liwo, A., Vila, J. A. & Scheraga, H. A. (1996) J. Mol. Biol. 264, 770-783.
44. Vorobjev, Y. N. & Scheraga, H. A. (1997) J. Comput. Chem. 18, 569-583.