Conformational dynamics of trialanine in water: A molecular dynamics study

Journal of Physical Chemistry B

Volumn 106, Issue 20, 2002, Pages 5294-5301

  Mu, Yuguang ^a   Stock, Gerhard ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

VIBRATIONAL SPECTROSCOPY;

COMPUTER SIMULATION; CONFORMATIONS; ENTROPY; FREE ENERGY; HYDROGEN BONDS; MOLECULAR VIBRATIONS; SOLUTIONS; SPECTROSCOPIC ANALYSIS;

MOLECULAR DYNAMICS;

EID: 0037162186     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp013977e     Document Type: Article

References (44)

1. Allen, M.P.; Tildesley, D.J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
2. McCammon, J.A.; Harvey, S.C. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: New York, 1987.
3. Leach, A.R. Molecular Modeling; Pearson Education Limited: London, 1996.
4. Karplus, M.J.; Petsko, G.A. Nature (London) 1990, 347, 631.
5. Van Gunsteren, W.F.; Berendsen, H.J.C. Angew. Chem., Int. Ed. Engl. 1990, 29, 992.
6. Kollman, P.A. Chem. Rev. 1993, 93, 2395.
7. Brooks, C.L., III; Case, D.A. Chem. Rev. 1993, 93, 2487.
8. Ernst, R.R.; Bodenhausen, G.; Wokaun, A. Principles of Nuclear Magnetic Resonance in One and Two Dimensions; Clarendon Press: Oxford, 1987.
9. See, for example, papers in Special Issue on Multidimensional Spectroscopies; Mukamel, S., Hochstrasser, R.M., Eds.; Chem. Phys. 2001, 266.
10. Hamm, P.; Lim, M.; Hochstrasser, R.M. J. Phys. Chem. B 1998, 102, 6123.
11. Zanni, M.T.; Ge, N.-H.; Kim, Y.S.; Hochstrasser, R.M. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11 265.
12. Wontersen, S.; Hamm, P. J. Phys. Chem. B 2000, 104, 11316. Woutersen, S.; Hamm, P. J. Chem. Phys. 2001, 114, 2727.
13. Wontersen, S.; Hamm, P. J. Phys. Chem. B 2000, 104, 11316. Woutersen, S.; Hamm, P. J. Chem. Phys. 2001, 114, 2727.
14. Woutersen, S.; Mu, Y.; Stock, G.; Hamm, P. Proc. Natl. Acad. Sci. U.S.A.. 2001, 98, 11 254.
15. Pettitt, B.M.; Karplus, M.J. J. Phys. Chem. 1988, 92, 3994.
16. Tobias, D.J.; Brooks, C.L., III J. Phys. Chem. 1992, 96, 3864.
17. Cornell, W.D.; Gould, I.R.; Kollman, P. J. Mol. Struct. 1997, 392, 101.
18. Hah, W.-G.; Jalkanen, K.J.; Elstner, M.; Suhai, S. J. Phys. Chem. B 1998, 102, 2587.
19. Apostolakis, J.; Ferrara, P.; Calfish, A. J. Chem. Phys. 1999, 110, 2099.
20. Smith, P.E. J. Chem. Phys. 1999, 111, 5568.
21. Kalko, S.G.; Guiàrdia, E.; Padró, J.A. J. Phys. Chem. B 1999, 103, 3935.
22. Bolhuis, P.G.; Dellago, C.; Chandler, D. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5877.
23. Van Gunsteren, W.F.; Billeter, S.R.; Eising, A.A.; Huenenberger, P.H.; Krueger, P.; Mark, A.E.; Scott, W.R.P.; Tirono, I.G. BiomolecuIar Simulation: The GROMOS96 Manual and User Guide; Vdf Hochschul-verlage AG an der ETH Zürich: Zürich, 1996.
24. Berendsen, H.J.C.; Postma, J.P.M.; Van Gunsteren, W.F.; Hermans, J. In Intermolecular Forces; Pullman, B., Ed.; D. Reidel: Dordrecht, The Netherlands, 1981; p 331.
25. Ryckaert, J.P.; Cicotti, G.; Berendsen, H.J.C. J. Comput. Phys. 1977, 23, 327.
26. Berendsen, H.J.C.; Postma, J.P.M.; Van Gunsteren, W.F.; Dinola, A.; Haak, J.R. J. Chem. Phys. 1984, 81, 3684.
27. Chandler, D. Introduction to Modern Statistical Mechanics; Oxford University Press: Oxford, 1987.
28. i+1). The resulting loop error was smaller than 1 kJ/mol for both PMF calculations.
29. Kumar, S.; Bouzida, J.; Swendsen, R.; Kollman, P.; Rosenberg, J. J. Comput. Chem. 1992, 13, 169.
30. Schlitter, J. Chem. Phys. Lett. 1993, 215, 617.
31. Schaefer, H.; Mark, A.E.; Van Gunsteren, W.F. J. Chem. Phys. 2000, 113, 7809.
32. Andricioaei, I.; Karplus, M. J. Chem. Phys. 2001, 115, 6289.
33. McLachlan, A.D. J. Mol. Biol. 1979, 128, 49.
34. Straatsma, T.P.; McCammon, J.A. J. Chem. Phys. 1994, 101, 5032.
35. As discussed in ref 35, a time resolution of 2 ps appears appropriate because it is shorter than the rotational correlation time of SPC water (3.4 ps).
36. Bonvin, A.M.J.J.; Sunnerhagen, M.; Otting, G.; Van Gunsteren, W.F. J. Mol. Biol. 1998, 282, 859.
37. Carrington, A.; McLachlan, A.D. Introduction to Magnetic Resonance; Harper & Row: New York, 1967.
38. Torri, H.; Tasumi, M. J. Raman Spectrosc. 1998, 29, 81.
39. The coupling autocorrelation function pertaining to a specific conformer was calculated through an ensemble average over all segments of the trajectory occupying the conformer for longer than t = 20 ps.
40. Wei, D.; Guo, H.; Salahub, D.R. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2001, 64, 011907.
41. Liu, H.; Elstner, M.; Kaxiras, E.; Frauenstein, T.; Hermans, J.; Yang, W. Proteins 2001, 44, 484.
42. Schweitzer-Stenner, R.; Eker, F.; Huang, Q.; Griebenow, K. J. Am. Chem. Soc. 2001, 123, 9628.
43. Dorai, K.; Griesinger, C., to be submitted for publication.
44. Woutersen, S.; Mu, Y.; Stock, G.; Hamm, P., to be submitted for publication.