Motion and conformation of side chains in peptides. A comparison of 2D umbrella-sampling molecular dynamics and NMR Results

Journal of Physical Chemistry

Volumn 100, Issue 7, 1996, Pages 2637-2645

  Beutler, Thomas C ^a   Bremi, Tobias ^a   Ernst, Richard R ^a   Van Gunsteren, Wilfred F ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000071835     PISSN: 00223654     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp951713k     Document Type: Article

References (43)

1. Frauenfelder, H.; Sligar, S.G.; Wolynes, P.G. Science 1991, 254, 1598.
2. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A theoretical perspective of dynamics, structures, and thermodynamics; John Wiley and Sons: New York, 1987.
3. van Gunsteren, W. F.; Berendsen, H. J. C. Angew. Chem., Int. Ed. Engl. 1990, 29, 992.
4. Tycko, R., Ed. Nuclear magnetic resonance probes of molecular dynamics; Kluwer Academic Publishers: Amsterdam, 1994.
5. Debrunner, P. G.; Frauenfelder, H. Annu. Rev. Phys. Chem. 1982, 33, 283.
6. Janin, J.; Wodak, S. J. Prog. Biophys. Mol. Biol. 1983, 42, 21.
7. Ringe, D.; Petsko, G. Prog. Biophys. Mol. Biol. 1985, 45, 197.
8. Janin, J.; Wodak, S. J.; Levitt, M.; Maigret, B. J. Mol. Biol. 1987, 125, 357.
9. Dunbrack, R. L.; Karplus, M. J. Mol. Biol. 1993, 230, 543.
10. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187.
11. van Gunsteren, W. F. Computer simulation of biomolecular systems: Overview of time-saving techniques. Advances in Biomolecular Simulations, American Institute of Physics (A.I.P.) Conference Proceedings Obernai (France); Lavery, R., Rivail, J.-L., Smith, J., Eds.; New York, 1991; Vol. 239, p 131.
12. Hill, T. L. Statistical Mechanics; McGraw-Hill: New York, 1956.
13. van Gunsteren, W. F.; Berendsen, H. J. C. Mol. Sim. 1988, 1, 173.
14. McQuarry, D. A. Statistical Mechanics; Harper and Row: New York, 1976.
15. Shi, Y. Y.; Wang, L.; van Gunsteren, W. F. Mol. Sim. 1988, 1, 369.
16. Kessler, K.; Griesinger, C.; Wagner, K. J. Am. Chem. Soc. 1987, 109, 6927.
17. Schmidt, J. M. To appear in Supramol. Struct. Funct.
18. Mádi, Z. L.; Griesinger, C.; Ernst, R. R. J. Am. Chem. Soc. 1990, 112, 2908.
19. Brüschweiler, R.; Roux, B.; Blackledse, M.; Griesinger, C.; Karplus, M.; Ernst, R. R. J. Am. Chem. Soc. 1992, 114, 2285.
20. Brüschweiler, R.; Blackledge, M.; Ernst, R. R. J. Biomol. NMR 1991, 1, 3.
21. Blackledge, M. J.; Brüschweiler, R.; Griesinger, C.; Schmidt, J. M.; Xu, P.; Ernst, R. R. Biochemistry 1993, 32, 10960.
22. Brunne, R. M.; van Gunsteren, W. F.; Brüschweiler, R.; Ernst, R. R. J. Am. Chem. Soc. 1993, 115, 4764.
23. Schmidt, J. M.; Brüschweiler, R.; Ernst, R. R.; Dunbrack, R. L., Jr.; Joseph, D.; Karplus, M. J. Am. Chem. Soc. 1993, 115, 8747.
24. Bremi, T.; Ernst, M.; Ernst, R. R. J. Phys. Chem. 1994, 98, 9322.
25. Gelin, B. R.; Karplus, M. Biochemistry 1979, 18, 1256.
26. Hermans, J.; Yun, R. H.; Anderson, A. G. J. Comput. Chem. 1992, 13, 429.
27. Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 101, 5032.
28. Hooft, R. W. W.; van Eijck, B. P.; Kroon, J. J. Chem. Phys. 1992, 97, 6690.
29. Karplus, M. J. Chem. Phys. 1959, 30, 11.
30. Karplus, M. J. Am. Chem. Soc. 1963, 85, 2870.
31. Bystrov, V. F. Prog. Nucl. Magn. Reson. Spectrosc. 1976, 10, 41.
32. Pachler, K. G. R. Spectrochim. Acta 1963, 19, 2085.
33. Chandler, D. J. Chem. Phys. 1978, 68, 2959.
34. McCammon, J. A.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1979, 76, 3585.
35. Northrup, S. H.; Pear, M. R.; Lee, C.-Y.; McCammon, J. A.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 4035.
36. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation Package and Manual (GROMOS); Biomos: University of Groningen, Groningen, 1987.
37. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
38. Kessler, H.; Müller, A.; Pook, K.-H. Liebigs Ann. Chem. 1989, 903.
39. Kessler, H.; Müller, A.; Pook, K.-H. Liebigs Ann. Chem. 1989, 913.
40. Griesinger, C.; Sørensen, O. W.; Ernst, R. R. J. Magn. Reson. 1987, 75, 474.
41. Beutler, T. C.; van Gunsteren, W. F. Chem. Phys. Lett. 1995, 237, 308.
42. Fischman, A. J.; Live, D. H.; Wyssbrod, H. R.; Agosta, W. C.; Cowburn, D. J. Am. Chem. Soc. 1979, 102, 2533.
43. Wasylishen, R.; Schaefer, T. Can. J. Chem. 1972, 50, 2710.