Recyclization rate of a photocleaved peptide from multiscale simulation

Journal of the American Chemical Society

Volumn 132, Issue 6, 2010, Pages 1778-1779

  Nieber, Harald ^a   Hellweg, Arnim ^a   Doltsinis, Nikos L ^a,b  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b KING'S COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AB INITIO MOLECULAR DYNAMICS; CLASSICAL MOLECULAR DYNAMICS; MULTI-SCALE SIMULATION; NON-ADIABATIC; QUENCHING MECHANISMS; S-BRIDGE; TRANSFER MECHANISMS;

MOLECULAR DYNAMICS;

PEPTIDE;

ARTICLE; CHEMICAL BOND; CYCLIZATION; DENSITY FUNCTIONAL THEORY; MOLECULAR DYNAMICS; PROTEIN FOLDING; PROTEIN STRUCTURE;

AMINO ACID SEQUENCE; CYCLIZATION; KINETICS; MOLECULAR DYNAMICS SIMULATION; OLIGOPEPTIDES; PHOTOCHEMICAL PROCESSES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTONS; QUANTUM THEORY;

EID: 77249175653     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja9100497     Document Type: Article

References (18)

1. Dobson, C. M. Nature 2003, 426, 884.
2. Lu, H. S. M.; Volk, M.; Kholodenko, Y.; Gooding, E. A.; Hochstrasser, R. M.; DeGrado, W. F. J. Am. Chem. Soc. 1997, 119, 7173.
3. Volk, M.; Kholodenko, Y.; Lu, H. S. M.; Gooding, E. A.; DeGrado, W. F.; Hochstrasser, R. M. J. Phys. Chem. B 1997, 101, 8607.
4. Shea, J. E.; Brooks, C. L. Annu. Rev. Phys. Chem. 2001, 52, 499.
5. Sadqi, M.; Fushman, D.; Munoz, V. Nature 2006, 442, 317.
6. Kolano, C.; Helbing, J.; Kozinski, M.; Sander, W.; Hamm, P. Nature 2006, 444, 469.
7. Kolano, C.; Helbing, J.; Bucher, G.; Sander, W.; Hamm, P. J. Phys. Chem. B 2007, 111, 11297.
8. Doltsinis, N. L.; Marx, D. Phys. Rev. Lett. 2002, 88, 166402.
9. Doltsinis, N. L.; Marx, D. J. Theor. Comput. Chem. 2002, 1, 319.
10. Böckmann, M.; Doltsinis, N. L.; Marx, D. J. Phys. Chem. A 2010, 114, 745.
11. Böckmann, M.; Doltsinis, N. L.; Marx, D. Phys. Rev. E 2008, 78, 036101.
12. See: www.cpmd.org (accessed Jan 19, 2010).
13. Marx, D.; Hutter, J. Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods; Cambridge University Press: Cambridge, U.K., 2009.
14. See: http://www.gromacs.org (accessed Jan 19, 2010).
15. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225.
16. Böckmann, M.; Peter, C.; Doltsinis, N. L.; Delle Site, L.; Kremer, K.; Marx, D. J. Chem. Theory Comput. 2007, 3, 1789.
17. An additional series of simulations run with a 4.0 Å threshold yielded no major changes.
18. The ground-state QM/MM runs were stopped when a S-S distance less than either 2.2 Å (closed peptide) or 5.0 Å (open peptide) was reached.