Simulation of transient infrared spectra of a photoswitchable peptide

Journal of Chemical Physics

Volumn 135, Issue 22, 2011, Pages

  Kobus, Maja ^a   Lieder, Martin ^a   Nguyen, Phuong H ^b   Stock, Gerhard ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

^b INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDE I MODE; CONFORMATIONAL DYNAMICS; CONFORMATIONAL STATE; EXPLICIT EXPRESSIONS; EXPONENTIAL TIME; FREQUENCY SHIFT; IR SPECTRUM; ISOTOPE LABELING; MOLECULAR SYSTEMS; NONEQUILIBRIUM MOLECULAR DYNAMICS SIMULATION; NONSTATIONARY; PHOTO-INDUCED; PHOTO-SWITCHABLE; PHOTOPRODUCTS; SAMPLING STRATEGIES; THEORETICAL FORMULATION; TIME EVOLUTIONS; TIME-SCALES; TRANSIENT INFRARED SPECTRA; TWO-DIMENSIONAL IR SPECTRA; VIBRATIONAL FREQUENCY SHIFT;

AMIDES; EXPERIMENTS; FREQUENCY SHIFT KEYING; ISOTOPES; MOLECULAR DYNAMICS; PEPTIDES; SPECTROSCOPY;

DYNAMICS;

OLIGOPEPTIDE; WATER;

ARTICLE; CHEMISTRY; INFRARED SPECTROPHOTOMETRY; LIGHT; LIGHT RELATED PHENOMENA; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; REPRODUCIBILITY; TIME;

LIGHT; MOLECULAR DYNAMICS SIMULATION; OLIGOPEPTIDES; OPTICAL PROCESSES; PROTEIN CONFORMATION; REPRODUCIBILITY OF RESULTS; SPECTROPHOTOMETRY, INFRARED; TIME FACTORS; WATER;

EID: 83755205986     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.3664747     Document Type: Article

References (35)

1. M. Cho, Two-Dimensional Optical Spectroscopy (CRC, London, 2009).
2. P. Hamm and M. Zanni, Concepts and Methods of 2D Infrared Spectroscopy (Cambridge University Press, Cambridge, 2011).
3. H. Chung, Z. Ganim, K. Jones, and A. Tokmakoff, Proc. Natl. Acad. Sci. U.S.A. 36, 14237 (2007). 10.1073/pnas.0700959104 (Pubitemid 350003246)
4. K. Hauser, C. Krejtschi, R. Huang, L. Wu, and T. A. Keiderling, J. Am. Chem. Soc. 130, 2984 (2008). 10.1021/ja074215l (Pubitemid 351455969)
5. J. R. Kumita, O. S. Smart, and G. A. Woolley, Proc. Natl. Acad. Sci. U.S.A. 97, 3803 (2000). 10.1073/pnas.97.8.3803 (Pubitemid 30226042)
6. J. A. Ihalainen, B. Paoli, S. Muff, E. H. G. Backus, J. Bredenbeck, G. A. Woolley, A. Caflisch, and P. Hamm, Proc. Natl. Acad. Sci. U.S.A. 105, 9588 (2008). 10.1073/pnas.0712099105 (Pubitemid 352031331)
7. C. Renner and L. Moroder, ChemBioChem 7, 869 (2006). 10.1002/cbic. 200500531 (Pubitemid 43938606)
8. J. Bredenbeck, J. Helbing, A. Sieg, T. Schrader, W. Zinth, C. Renner, R. Behrendt, L. Moroder, J. Wachtveitl, and P. Hamm, Proc. Natl. Acad. Sci. U.S.A. 100, 6452 (2003). 10.1073/pnas.1036583100 (Pubitemid 36666602)
9. J. Bredenbeck, J. Helbing, R. Behrendt, C. Renner, L. Moroder, J. Wachtveitl, and P. Hamm, J. Phys. Chem. B 107, 8654 (2003). 10.1021/jp034552q
10. T. E. Schrader, W. J. Schreier, T. Cordes, F. O. Koller, G. Babitzki, R. Denschlag, C. Renner, M. Löweneck, S. Dong, L. Moroder, P. Tavan, and W. Zinth, Proc. Natl. Acad. Sci. U.S.A. 104, 15729 (2007). 10.1073/pnas.0707322104 (Pubitemid 350035368)
11. C. Renner, J. Cramer, R. Behrendt, and L. Moroder, Biopolymers 63, 382 (2002). 10.1002/bip.10127
12. P. H. Nguyen, H. Staudt, J. Wachtveitl, and G. Stock, J. Phys. Chem. B 115, 13084 (2011). 10.1021/jp207945p
13. P. H. Nguyen, P. Hamm, and G. Stock, in Proteins: Energy, Heat and Signal Flow, edited by, D. Leitner, and, J. Straub, (Taylor and Francis/CRC, London, 2009), pp. 151-169.
14. P. H. Nguyen, R. D. Gorbunov, and G. Stock, Biophys. J. 91, 1224 (2006). 10.1529/biophysj.106.084996 (Pubitemid 44174243)
15. S. Mukamel, Principles of Nonlinear Optical Spectroscopy (Oxford University Press, Oxford, 1995).
16. W. Pollard, S.-Y. Lee, and R. A. Mathies, J. Chem. Phys. 92, 4012 (1990). 10.1063/1.457815
17. B. Strodel and G. Stock, J. Chem. Phys. 124, 114105 (2006). 10.1063/1.2166629
18. R. Kubo, Adv. Chem. Phys. 15, 101 (1969). 10.1002/SERIES2007
19. Y. Tanimura, J. Phys. Soc. Jpn. 75, 082001 (2006). 10.1143/JPSJ.75.082001
20. S. Roy, M. S. Pshenichnikov, and T. L. C. Jansen, J. Phys. Chem. B 115, 5431 (2011). 10.1021/jp109742p
21. T. la Cour Jansen, A. G. Dijkstra, T. M. Watson, J. D. Hirst, and J. Knoester, J. Chem. Phys. 125, 044312 (2006). 10.1063/1.2218516 (Pubitemid 44179405)
22. W. Zhuang, D. Abramavicius, T. Hayashi, and S. Mukamel, J. Phys. Chem. B 110, 3362 (2006). 10.1021/jp055813u
23. H. J. Bakker and J. L. Skinner, Chem. Rev. 110, 1498 (2010). 10.1021/cr9001879
24. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark, and H. J. C. Berendsen, J. Comput. Chem. 26, 1701 (2005). 10.1002/jcc.20291 (Pubitemid 43076182)
25. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hünenberger, P. Krüger, A. E. Mark, W. R. P. Scott, and I. G. Tironi, Biomolecular Simulation: The Gromos96 Manual and User Guide (Vdf Hochschulverlag AG an der ETH Zürich, Zürich, 1996).
26. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, and J. Hermans, in Intermolecular Forces, edited by, B. Pullman, (Reidel, Dordrecht, 1981), pp. 331-342.
27. P. H. Nguyen, Y. Mu, and G. Stock, Proteins 60, 485 (2005). 10.1002/prot.20485 (Pubitemid 41061640)
28. J. R. Schmidt, S. A. Corcelli, and J. L. Skinner, J. Chem. Phys. 121, 8887 (2004). 10.1063/1.1791632
29. P. Bour and T. A. Keiderling, J. Phys. Chem. B 109, 23687 (2005). 10.1021/jp054107q (Pubitemid 43081544)
30. T. la Cour Jansen and J. Knoester, J. Chem. Phys. 124, 044502 (2006). 10.1063/1.2148409 (Pubitemid 43166334)
31. L. Wang, C. T. Middleton, M. T. Zanni, and J. L. Skinner, J. Phys. Chem. B 115, 3713 (2011). 10.1021/jp200745r
32. R. D. Gorbunov and G. Stock, Chem. Phys. Lett. 437, 272 (2007). 10.1016/j.cplett.2007.02.033 (Pubitemid 46428247)
33. R. D. Gorbunov, D. S. Kosov, and G. Stock, J. Chem. Phys. 122, 224904 (2005). 10.1063/1.1898215 (Pubitemid 40844916)
34. A. Tokmakoff, J. Phys. Chem. A 104, 4247 (2000). 10.1021/jp993207r
35. M. Maroncelli and G. R. Fleming, J. Chem. Phys. 89, 5044 (1988). 10.1063/1.455649