An extended dead-end elimination algorithm to determine gap-free lists of low energy states

Journal of Computational Chemistry

Volumn 28, Issue 14, 2007, Pages 2325-2335

  Kloppmann, Edda ^a   Ullmann, G Matthias ^a   Becker, Torsten ^a  

^a UNIVERSITÄT BAYREUTH   (Germany)

Author keywords

Bacteriorhodopsin; Dead end elimination; Global energy minimum; Homology modelling; pH titration; Protein design; Protonation state; X DEE

Indexed keywords

ALGORITHMS; BACTERIA; ENERGY GAP; PROTEINS; PROTONATION; THEOREM PROVING;

BACTERIORHODOPSIN; DEAD-END ELIMINATION (DEE) THEOREM; GLOBAL ENERGY MINIMUM; HOMOLOGY MODELING; PH TITRATION; PROTEIN DESIGNS; PROTONATION STATES;

ELECTRON ENERGY LEVELS;

AMINO ACID; BACTERIORHODOPSIN; PROTON;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; PH; THERMODYNAMICS;

ALGORITHMS; AMINO ACIDS; BACTERIORHODOPSINS; HYDROGEN-ION CONCENTRATION; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTONS; THERMODYNAMICS;

EID: 34548580355     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20749     Document Type: Article

References (38)

1. Desmet, J.; de Maeyer, M.; Hazes, B.; Lasters, I. Nature 1992, 356, 539.
2. Goldstein, R. F. Biophys J 1994, 66, 1335.
3. Leach, A. R.; Lemon, A. P. Proteins 1998, 33, 227.
4. Pierce, N. A.; Spriet, J. A.; Desmet, J.; Mayo, S. L. J Comput Chem 2000, 21, 999.
5. Hellings, M.; de Maeyer, M.; Verheyden, S.; Hao, Q.; van Damme, E. J.; Peumans, W. J.; Engelborghs, Y. Biophys J 2003, 85, 1894.
6. Adcock, S. A. J Comput Chem 2004, 25, 16.
7. Stiebritz, M. T.; Muller, Y. A. Acta Crystallogr D Biol Crystallogr 2006, 62, 648.
8. Looger, L. L.; Hellinga, H. W. J Mol Biol 2001, 307, 429.
9. Shah, P. S.; Hom, G. K.; Mayo, S. L. J Comput Chem 2004, 25, 1797.
10. Georgiev, I.; Lilien, R. H.; Donald, B. R. Bioinformatics 2006, 22, e174.
11. Lukashin, A. V.; Rosa, J. J. Bioinformatics 1999, 11, 947.
12. Zhang, N.; Zeng, C.; Wingreen, N. S. Proteins 2004, 57, 565.
13. Ullmann, G. M.; Knapp, E.-W. Eur Biophys J 1999, 28, 533.
14. Chen, I.; Mathis, P.; Koepke, J.; Michel, H. Biochemistry 2000, 39, 3502.
15. Becker, T.; Ullmann, R. T.; Ullmann, G. M. J Phys Chem B 2007, 777, 2957.
16. Nicholls, D. G.; Ferguson, S. J. Bioenergetics 3; Academic Press: London, 2002.
17. Mulkidjanian, A. Y. FEBS Lett 1999, 463, 199.
18. Gunner, M. R.; Mao, J.; Song, Y.; Kim, J. Biochim Biophys Acta 2006, 1757, 942.
19. Onufriev, A.; Smondryev, A.; Bashford, D. J Mol Biol 2003, 332, 1183.
20. Kloppmann, E.; Becker, T.; Ullmann, G. M. Proteins 2005, 61, 953.
21. Bombarda, E.; Becker, T.; Ullmann, G. M. J Am Chem Soc 2006, 128, 12129.
22. Honig, B.; Nicholls, A. Science 1995, 268, 1144.
23. Schaefer, M.; Karplus, M. J Phys Chem 1996, 100, 1578.
24. Stoeckenius, W. Prot Sci 1999, 8, 447.
25. Haupts, U.; Tittor, J.; Oesterhelt, D. Annu Rev Biophys Biomol Struct 1999, 28, 367.
26. Heberle, J.; Fitter, J.; Sass, H. J.; Büldt, G. Biophys Chem 2000, 85, 229.
27. Lanyi, J. K.; Luecke, H. Curr Opin Struct Biol 2001, 11, 415.
28. Neutze, R.; Pebay-Peyroula, E.; Edman, K.; Royant, A.; Navarro, J.; Landau, E. M. Biochim Biophys Acta 2002, 1565, 144.
29. Heßling, B.; Souvignier, G.; Gerwert, K. Biophys J 1993, 65, 1929.
30. Zscherp, C.; Schlesinger, R.; Tittor, J.; Oesterhelt, D.; Heberle, J. Proc Natl Acad Sci USA 1999, 96, 5498.
31. Garczarek, F.; Brown, L. S.; Lanyi, J. K.; Gerwert, K. Proc Natl Acad Sci USA 2005, 102, 3633.
32. Bashford, D. In Scientific computing in object-oriented parallel environments; Ishikawa, Y.; Oldehoeft, R. R.; Reynders, J. V. W.; Tholburn, M. Eds.; Springer: Berlin, 1997, pp. 233.
33. Luecke, H.; Schobert, B.; Richter, H.-T.; Cartailler, J.-R; Lanyi, J. K. J Mol Biol 1999, 291, 899.
34. Facciotti, M. T.; Rouhani, S.; Burkard, E T.; Betancourt, F. M.; Downing, K. H.; Rose, R. B.; McDermott, G.; Glaeser, R. M. Biophys J 2001, 81, 3442.
35. Belrhali, H.; Nollert, R; Royant, A.; Menzel, C.; Rosenbusch, J. P.; Landau, E. M.; Pebay-Peyroula, E. Structure 1999, 7, 909.
36. Calimet, N.; Ullmann, G. M. J Mol Biol 2004, 339, 571.
37. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Prodhom, D. T. N. B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
38. Landau, D. R; Binder, K. A Guide to Monte Carlo Simulations in Statistical Physics; University Press: Cambridge, 2005.