Implementation and application of helix-helix distance and crossing angle restraint potentials

Journal of Computational Chemistry

Volumn 28, Issue 3, 2007, Pages 669-680

  Lee, Jinhyuk ^a   Im, Wonpil ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

Molecular dynamics; MS1; Potential of mean force; Transmembrane helix

Indexed keywords

HELICAL PRINCIPAL AXES; MS1; POTENTIAL OF MEAN FORCE; TRANSMEMBRANE HELIX;

AMINO ACIDS; ATOMS; COMPUTER SIMULATION; MODELS; POTENTIAL ENERGY;

MOLECULAR DYNAMICS;

PEPTIDE;

CHEMICAL STRUCTURE; CHEMISTRY; MOLECULAR DYNAMICS; PROTEIN SECONDARY STRUCTURE;

MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PEPTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 33847678434     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20614     Document Type: Article

References (48)

1. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
2. White, S. http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html, 2003.
3. Hessa,T.; Kim, H.; Bihlmaier, K.; Lundin,C.; Boekel, J.; Andersson, H.; Nilsson, I.; White, S. H.; von Heijne, G. Nature 2005, 433, 377.
4. MacKenzie, K.; Prestegard, J.; Engelman, D. Science 1997, 276, 131.
5. Popot, J. L. and Engelman, D. M. Annu Rev Biochem 2000, 69, 881.
6. Smith, S.; Song, D.; Shekar, S.; Groesbeek, M.; Ziliox, M.; Aimoto, S. Biochemistry 2001, 40, 6553.
7. Degrado, W. F.; Gratkowski, H.; Lear, J. D. Protein Sci 2003, 12, 647.
8. Fleming, K. G. and Engelman, D. M. Proc Natl Acad Sci USA 2001, 98, 14340.
9. Choma, C.; Gratkowski, H.; Lear, J. D.; DeGrado, W. F. Nat Struct Biol 2000, 7, 161.
10. Zhou, F. X.; Cocco, M. J.; Russ, W. P.; Brunger, A. T.; Engelman, D. M. Nat Struct Biol 2000, 7, 154.
11. Popot, J.-L.; Engelman, D. M. Biochemistry 1990, 29, 4031.
12. Schneider, D.; Engelman, D. M. J Mol Biol 2004, 343, 799.
13. Curran, A. R.; Engelman, D. M. Curr Opin Struct Biol 2003, 13, 412.
14. Senes, A.; Engel, D. E.; DeGrado, W. F. Curr Opin Struct Biol 2004, 14, 465.
15. Hill, R. B.; Raleigh, D. P.; Lombardi, A.; Degrado, W. F. Acc Chem Res 2000, 33, 745.
16. Senes, A.; Gerstein, M.; Engelman, D. M. J Mol Biol 1999, 296, 921.
17. Senes, A.; Ubarretxena-Belandia, I.; Engelman, D. M. Proc Natl Acad Sci USA 2001, 98, 9056.
18. Zhou, F. X.; Merianos, H. J.; Brunger, A. T.; Engelman, D. M. Proc Natl Acad Sci USA 2001, 98, 2250.
19. Li, W.; Zhang, Y.; Skolnick, J. Biophys J 2004, 87, 1241.
20. Kukol, A.; Adams, P. D.; Rice, L. M.; Brunger, A. T.; Arkin, I. T. J Mol Biol 1999, 286, 951.
21. Woolf, T. B.; Roux, B. Proc Natl Acad Sci USA 1994, 91, 11631.
22. Wang, J.; Kim, S.; Kovacs, F.; Cross, T. A. Protein Sci 2001, 10, 2241.
23. Kovacs, F. A.; Cross, T. A. Biophys J 1997, 73, 2511.
24. Bu, L.; Im, W.; Brooks, C. L. III. Biophys J (in press).
25. Gratkowski, H.; Lear, J. D.; DeGrado, W. F. Proc Natl Acad Sci USA 2001, 98, 880.
26. Stockner, T.; Ash, W. L.; MacCallum, J. L.; Tieleman, D. P. Biophys J 2004, 87, 1650.
27. Lague, P.; Zuckermann, M. J.; Roux, B. Biophys J 2001, 81, 276.
28. Chothia, C.; Levitt, M.; Richardson, D. J Mol Biol 1981, 145, 215.
29. Bansal, M.; Kumar, S.; Velavan, R. J Biomol Struct Dyna 2000, 17, 811.
30. Dalton, J. A. R.; Michalopoulos, I.; Westhead, D. R. Bioinformatics 2003, 19, 1298.
31. Walther, D.; Springer, C.; Cohen, F. E. Proteins 1998, 33, 457.
32. Hutchinson, E. G.; Thornton, J. M. Protein Sci 1996, 5, 212.
33. Aqvist, J. Comput Chem 1986, 10, 97.
34. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
35. Im, W.; Lee, M. S.; Brooks, C. L. III. J Comput Chem 2003, 24, 1691.
36. Im, W.; Feig, M.; Brooks, C. L. III. Biophys J 2003, 85, 2900.
37. Lee, M. S.; Salsbury, F. R. Jr.: Brooks, C. L. III. J Chem Phys 2002, 116, 10606.
38. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J Comput Chem 1977, 23, 327.
39. Chen, J.; Im, W.; Brooks, C. L. III. J Comput Chem 2005, 26, 1565.
40. Kraulis, P. J. J Appl Cryst 1991, 24, 946.
41. Roux, B. Comput Phys Comm 1995, 91, 275.
42. Kumar, S.; Bouzida, D.; Swendsen, R.; Kollman, P.; Rosenberg, J. J Comput Chem 1992, 13, 1011.
43. Marti, D. N.; Bjelic, S.; Lu, M.; Bosshard, H. R.; Jelesarov, I. J Mol Biol 2004, 336, 118.
44. Chan, D. C.; Fass, D.; Berger, J. M.; Kim, P. S. Cell 1997, 89, 263.
45. Han, X.; Bushweller, J. H.; Cafiso, D. S.: Tamm, L. K. Nat Struct Biol 2001, 8, 715.
46. Cushley, R. J.; Okon, M. Annu Rev Biophys Biomol Struct 2002, 31, 177.
47. Ajees, A. A.; Anantharamaiah, G. M.; Mishra, V. K.; Hussain, M. M.; Murthy, H. M. K. Proc Natl Acad Sci USA 2006, 103, 2126.
48. Johnson, B. G.; Gill, P. M. W.; Pople, J. A. Chem Phys Lett 1994, 220, 337.