Modeling protonated water networks in bacteriorhodopsin

Physical Chemistry Chemical Physics

Volumn 6, Issue 8, 2004, Pages 1848-1859

  Rousseau, Roger ^a   Kleinschmidt, Volker ^a   Schmitt, Udo W ^a   Marx, Dominik ^a  

^a RUHR UNIVERSITY BOCHUM   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; BACTERIORHODOPSIN; HYDROGEN; LIPID; PROTEIN; PROTON; PROTON PUMP; WATER;

ATOM; CHEMICAL STRUCTURE; CONFERENCE PAPER; DENSITY FUNCTIONAL THEORY; ELECTRON; FORCE; GAS; HYDRATION; HYDROGEN BOND; LIPID BILAYER; MEMBRANE; MODEL; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; MOLECULE; PARAMETER; PROTON TRANSPORT; QUALITATIVE ANALYSIS; SIMULATION; SOLVATION; STRUCTURE ANALYSIS; TIME;

EID: 2342666659     PISSN: 14639076     EISSN: None     Source Type: Journal    
DOI: 10.1039/b313220j     Document Type: Conference Paper

References (49)

1. T. Hiral and S. Subramaniam, FEBS, 2003, 545, 2.
2. R. Neutze, E. Pebay-Peyroula, K. Edman, A. Royant, J. Navarro and E. Landau, Biochim. Biophys. Acta, 2002, 1562, 144.
3. J. K. Lanyi, Biochim. Biophys. Acta, 2000a, 1459, 339.
4. U. Haupts, J. Tittor and D. Oesterhelt, Annu. Rev. Biophys. Biomol. Struct., 1999, 28, 367.
5. H. Kandori, Biochim. Biophys. Acta, 2000, 1460, 177.
6. H. Luecke and J. Lanyi, Adv. Protein Chem., 2003, 63, 111.
7. W. Kühlbrand, Nature, 2000, 406, 569.
8. L. Onsager, Science, 1967, 156, 541.
9. J. F. Nagle and H. J. Morowitz, Proc. Natl. Acad. Sci. USA, 1978, 75, 298.
10. R. Car and M. Parrinello, Phys. Rev. Lett., 1985, 55, 2471.
11. D. Marx and J. Hutter, in Modern Methods and Algorithms of Quantum Chemistry, ed. J. Grotendorst, NIC, FZ Jülich, 2000, pp. 301-449, for downloads see http://www.theochem.ruhr-unibochum.de/go/cprev.html.
12. A. Laio, J. VandeVondele and U. Rothlisberger, J. Chem. Phys., 2002, 116, 6941.
13. X. Daura, A. E. Mark and W. F. van Gunsteren, J. Comput. Chem., 1998, 19, 535.
14. W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger and W. F. van Gunsteren, J. Phys. Chem. A, 1999, 103, 3596.
15. W. F. van Gunsteren, S. R. Billeter, A. A. Eising, P. H. Hüunenberger, P. Krüger, A. E. Mark, W. R. P. Scott and I. G. Tironi, Biomolecular Simulation, GROMOS96 Manual and User Guide BIOMOS b.v. ETH, Zürich, 1996.
16. P. Carloni, U. Rothlisberger and M. Parrinello, Acc. Chem. Res., 2002, 35, 455.
17. Note that native BR is found in the purple membrane as a trimeric complex. By focussing on one monomer, it is implicitly assumed that proton transfer occurring in one channel is essentially independent from the environment beyond this channel.
18. H. Luecke, B. Schobert, H.-T. Richter, J.-P. Cartailler and J. K. Lanyi, Science, 1999, 286, 255.
19. R. B. Gennis and T. G. Ebrey, Science, 1999, 286, 252.
20. J. Lanyi, J. Phys. Chem. B, 2000b, 104, 11441.
21. R. Rammelsberg, G. Huhn, M. Lübben and K. Gerwert, Biochemistry, 1998, 37, 5001.
22. V. Z. Spassov, H. Luecke, K. Gerwert and D. Bashford, J. Mol. Biol., 2001, 312, 203.
23. A. Royant, K. Edmann, T. Ursby, E. Pebay-Peyroula, E. M. Landau and R. Neutze, Nature, 2000, 406, 645.
24. H. Heller, M. Schaefer and K. Schulten, J. Phys. Chem., 1993, 97, 8343.
25. See the web site http://www.lrz-muenchen.de/~heller.
26. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, J. Comp. Chem., 1983, 4, 187.
27. A. D. MacKerell et al., J. Phys. Chem B, 1998, 102, 3586.
28. J. Baudry, S. Crouzy, B. Roux and J. C. Smith, J. Chem. Inf. Comput. Sci., 1997, 37, 1018.
29. A. D. Becke, Phys. Rev. A, 1988, 38, 3098.
30. C. Lee, W. Yang and R. G. Parr, Phys. Rev. B, 1988, 37, 785.
31. GAUSSIAN98, Revision A.11.1, M. J. Frisch et al., Gaussian, Inc., Pittsburgh, PA, 1998.
32. A. E. Reed, L. A. Curtiss and F. Weinhold, Chem. Rev., 1988, 88, 899.
33. U. Singh and P. Kollman, J. Comput. Chem., 1984, 5, 129.
34. R. F. W. Bader, Atoms in Molecules: A Quantum Theory, Clarendon Press, Oxford, 1990.
35. E. Lindahl, B. Hess and D. van der Spoel, J. Mol. Mod., 2001, 7, 306.
36. P. Hakansson, P. Westlund, E. Lindahl and O. Edholm, Phys. Chem. Chem. Phys., 2001, 3, 5311.
37. L. Kal, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan and K. Schulten, J. Comput. Phys., 1999, 151, 283.
38. NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign, see http://www.ks.uiuc.edu/Research/namd/.
39. H. Luecke, H.-T. Richter and J. K. Lanyi, Science, 1998, 280, 1934.
40. CPMD3.4, J. Hutter, P. Ballone, M. Bernasconi, P. Focher, E. Fois, S. Goedecker, D. Marx, M. Parrinello and M. Tuckerman, MPI für Festkörperforschung, Stuttgart and IBM Research Laboratory, Zürich, see http://www.cpmd.org/.
41. N. Troullier and J. L. Martins, Phys. Rev. B, 1991, 43, 1993.
42. C. Chaudhuri, Y.-S. Wang, J. C. Jiang, Y. T. Lee, H.-C. Chang and G. Niedner-Schatteburg, Mol. Phys., 2001, 99, 1161.
43. N. Marzari and D. Vanderbilt, Phys. Rev. B, 1997, 56, 12847.
44. P. L. Silvestrelli and M. Parrinello, Phys. Rev. Lett., 1999, 82, 3308.
45. D. van der Spoel, P. J. van Maaren and J. C. Berendsen, J. Chem. Phys., 1998, 108, 10220.
46. D. Marx, M. E. Tuckerman, J. Hutter and M. Parrinello, Nature (London), 1999, 397, 601.
47. U. W. Schmitt and G. A. Voth, J. Chem. Phys., 1999, 111, 9361.
48. M. L. Brewer, U. W. Schmitt and G. A. Voth, Biophys. J., 2001, 80, 1692.
49. A. D. Becke and K. E. Edgecombe, J. Chem. Phys., 1990, 92, 5397.