Analytical rebridging Monte Carlo: Application to cis/trans isomerization in proline-containing, cyclic peptides

Journal of Chemical Physics

Volumn 111, Issue 14, 1999, Pages 6625-6632

  Wu, Minghong G ^a   Deem, Michael W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000484448     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.479952     Document Type: Article

References (44)

1. S. Jackson, W. Degrado, A. Dwivedi, A. Parthasarathy, A. Higley, J. Krywko, A. Rockwell, J. Markwalder, G. Wells, R. Wexler, S. Mousa, and R. Harlow, J. Am. Chem. Soc. 116, 3220 (1994).
2. C. Bisang, L. Jiang, E. Freund, F. Emery, C. Bauch, H. Matile, G. Pluschke, and J. A. Robinson, J. Am. Chem. Soc. 120, 7439 (1998).
3. R. Haubner, R. Gratias, B. Diefenbach, S. L. Goodman, A. Jonczyk, and H. Kessler, J. Am. Chem. Soc. 118, 7461 (1996).
4. Z. Huang, A. Pröbstl, J. R. Spencer, T. Yamazaki, and M. Goodman, Int. J. Pept. Protein Res. 42, 352 (1993).
5. K. T. O'Neil, R. H. Hoess, S. A. Jackson, N. Ramachandran, S. A. Mousa, and W. F. DeGrado, Proteins: Struct., Funct., Genet. 14, 509 (1992).
6. L. Stryer, Biochemistry, 3rd ed. (W. H. Freeman, New York, 1988).
7. K. A. Higgins, D. J. Craik, J. G. Hall, and P. R. Andrews, Drug Design Deliv. 3, 159 (1988).
8. H. Weißhoff, T. Wieprecht, P. Henklein, C. Frömmel, C. Antz, and C. Mügge, Fed. Euro. Bioc. Soc. Lett. 387, 201 (1996).
9. R. L. Stein, Adv. Quantum Chem. 11, 1 (1993).
10. G. Scherer, M. L. Kramer, M. Schutkowski, and G. Fischer, J. Am. Chem. Soc. 120, 5568 (1998).
11. F. X. Schmid, L. M. Mayr, M. Mueche, and E. R. Schoenbrunner, Adv. Quantum Chem. 11, 25 (1993).
12. L. R. Dodd, T. D. Boone, and D. N. Theodorou, Mol. Phys. 78, 961 (1993).
13. D. Frenkel and B. Smit, Mol. Phys. 75, 983 (1992).
14. J. J. de Pablo, M. Laso, and U. W. Suter, J. Chem. Phys. 96, 6157 (1992).
15. M. G. Wu and M. W. Deem, Mol. Phys. 97, 559 (1999).
16. D. Manocha and J. F. Canny, IEEE Trans. Rob. Autom. 10, 648 (1994).
17. M. W. Deem and J. S. Bader, Mol. Phys. 87, 1245 (1996).
18. The analytical rebridging equations are singular for the geometry which allows for an infinite number of "crankshaft-type" solutions. This geometry occurs with probability zero in the general case.
19. W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C, 2nd ed. (Cambridge, New York, 1992).
20. D. Frenkel and B. Smit, Understanding Molecular Simulation (Academic, San Diego, 1996).
21. C. J. Geyer, Computing Science and Statistics (American Statistical Association, New York, 1991), pp. 156-163.
22. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
23. E. Marinari, G. Parisi, and J. Ruiz-Lorenzo, in Spin Glasses and Random Fields, Vol. 12 of Directions in Condensed Matter Physics, edited by A. Young (World Scientific, Singapore, 1998).
24. M. C. Tesi, E. J. Janse van Rensburg, E. Orlandini, and S. G. Whittington, J. Stat. Phys. 82, 155 (1996).
25. G. Boyd, Nucl. Phys. B (Proc. Suppl.) 60A, 341 (1998).
26. M. Falcioni and M. W. Deem, J. Chem. Phys. 110, 1754 (1999).
27. S. J. Weiner, P. A. Kollman, D. T. Nguyen, and D. A. Case, J. Comput. Chem. 7, 230 (1986).
28. P. E. Smith, B. M. Pettitt, and M. Karplus, J. Phys. Chem. 97, 6907 (1993).
29. D. F. Veber, in Peptides, Synthesis, Structure and Function, Proceedings of the Seventh American Peptide Symposium, edited by D. H. Rich and V. J. Gross (Pierce Chemical Co., Rockford, IL, 1981), p. 685.
30. H. Kessler, M. Klein, A. Müller, K. Wagner, J. W. Bats, K. Ziegler, and M. Frimmer, Angew. Chem. Int. Ed. Engl. 25, 997 (1986).
31. G. Zanotti, M. Saviano, G. Saviano, T. Tancredi, F. Rossi, C. Pedone, and E. Benedetti, J. Peptide Research 51, 460 (1998).
32. I. McEwen, Biopolymers 33, 693 (1993).
33. G. Müller, M. Gurrath, M. Kurz, and M. Kessler, Proteins: Struct., Funct., Genet. 15, 235 (1993).
34. E. Pinet, J. M. Neumann, I. Dahse, G. Girault, and F. André, Biopolymers 36, 135 (1995).
35. CRC Handbook of Chemistry and Physics, 68th ed., edited by R. C. Weast, M. J. Astle, and W. H. Beyer (CRC, Boca Raton, FL, 1987), p. E-50.
36. The Merck Index, 10th ed., edited by M. Windholz, S. Budavari, R. F. Blumetti, and E. S. Otterbein (Merck & Co. Inc., New Jersey, 1983), p. 475.
37. H. S. Ashbaugh and M. E. Paulaitis, J. Phys. Chem. B 102, 5029 (1998).
38. M. E. Paulaitis, Curr. Opin. Colloid Interface Sci. 2, 315 (1997).
39. B. Smit, S. Karaborni, and J. Siepmann, J. Chem. Phys. 102, 2126 (1995).
40. S. K. Nath, F. A. Escobedo, and J. J. de Pablo, J. Chem. Phys. 108, 9905 (1998).
41. E. J. F. Primrose, Mech. Mach. Theory 21, 509 (1986).
42. H.-Y. Lee and C.-G. Liang, Mech. Mach. Theory 23, 209 (1988).
43. H.-Y. Lee and C.-G. Liang, Mech. Mach. Theory 23, 219 (1988).
44. M. Raghavan and B. Roth, Trans. ASME, J. Mech. Design 115, 502 (1993).