Molecular dynamics simulations of bczbp, a deacetylase from bacillus cereus: Active site loops determine substrate accessibility and specificity

Journal of Chemical Theory and Computation

Volumn 5, Issue 12, 2009, Pages 3299-3311

  Fadouloglou, Vasiliki E ^a,b   Stavrakoudis, Athanassios ^c   Bouriotis, Vassilis ^b,d   Kokkinidis, Michael ^b,d   Glykos, Nicholas M ^a  

^a DEMOCRITUS UNIVERSITY OF THRACE   (Greece)

^b UNIVERSITY OF CRETE   (Greece)

^c UNIVERSITY OF IOANNINA   (Greece)

^d INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 73949118375     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct9002338     Document Type: Article

References (20)

1. Read, T. D.; Peterson, S. N.; Tourasse, N.; Baillie, L. W.; Paulsen, I. T.; Nelson, K. E.; Tettelin, H.; Fouts, D. E.; Eisen, J. A.; Gill, S. R.; Holtzapple, E. K.; Okstad, O. A.; Helgason, E.; Rilstone, J.; Wu, M.; Kolonay, J. F.; Beanan, M. J.; Dodson, R. J.; Brinkac, L. M.; Gwinn, M.; DeBoy, R. T.; Madpu, R.; Daugherty, S. C.; Durkin, A. S.; Haft, D. H.; Nelson, W. C.; Peterson, J. D.; Pop, M.; Khouri, H. M.; Radune, D.; Benton, J. L.; Mahamoud, Y.; Jiang, L.; Hance, I. R.; Weidman, J. F.; Berry, K. J.; Plaut, R. D.; Wolf, A. M.; Watkins, K. L.; Nierman, W. C.; Hazen, A.; Cline, R.; Redmond, C.; Thwaite, J. E.; White, O.; Salzberg, S. L.; Thomason, B.; Friedlander, A. M.; Koehler, T. M.; Hanna, P. C.; Kolsto, A. B.; Fraser, C. M. The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 2003, 423, 81-86.
2. Ivanova, N.; Sorokin, A.; Anderson, I.; Galleron, N.; Candelon, B.; Kapatral, V.; Bhattacharyya, A.; Reznik, G.; Mikhailova, N.; Lapidus, A.; Chu, L.; Mazur, M.; Goltsman, E.; Larsen, N.; D'Souza, M.; Walunas, T.; Grechkin, Y.; Pusch, G.; Haselkorn, R.; Fonstein, M.; Ehrlich, S. D.; Overbeek, R.; Kyrpides, N. Genome sequence of Bacillus cereus and comparative analysis with Bacillus anthracis. Nature. 2003, 423, 87-91.
3. Psylinakis, E.; Boneca, I. G.; Mavromatis, K.; Deli, A.; Hayhurst, E.; Foster, S. J.; Varum, K. M.; Bouriotis, V. Peptidoglycan N-acetylglucosamine deacetylases from Bacillus cereus, highly conserved proteins in Bacillus anthracis. J. Biol. Chem. 2005, 280, 30856-30863.
4. Fadouloglou, V. E.; Kotsifaki, D.; Gazi, A. D.; Fellas, G.; Meramveliotaki, C.; Deli, A.; Psylinakis, E.; Bouriotis, V.; Kokkinidis, M. Purication, crystallization and preliminary characterization of a putative LmbE-like deacetylase from Bacillus cereus. Acta Crystallogr. 2006, F62, 261-264.
5. Fadouloglou, V. E.; Deli, A.; Glykos, N. M.; Psylinakis, E.; Bouriotis, V.; Kokkinidis, M. Crystal structure of the BcZBP, a zinc-binding protein from Bacillus cereus: Functional insights from structural data. FEBS J. 2007, 274, 3044-3054.
6. Kale, L.; Skeel, R.; Bhandarkar, M.; Brunner, R.; Gursoy, A.; Krawetz, N.; Phillips, J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 1999, 151, 283-312.
7. Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual Molecular Dynamics. J. Mol. Graphics 1996, 14, 33-38.
8. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; 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.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; WiorkiewiczKuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics Studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
9. Stote, R. H.; Karplus, M. Zinc binding in proteins and solution: A simple but accurate nonbonded representation. Proteins 1995, 23, 12-31.
10. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald. An Nlog (N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
11. Brünger, A. T. Management of Trajectories. In X-PLOR; version 3.1, Yale University Press: New Haven, CT, 1992; pp 143-158.
12. Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-317.
13. Ichiye, T.; Karplus, M. Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins 1991, 11, 205-217.
14. Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Essential dynamics of proteins. Proteins 1993, 17, 412-425.
15. Mu, Y.; Nguyen, P. H.; Stock, G. Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins 2005, 58, 45-52.
16. Altis, A.; Nguyen, P. H.; Hegger, R.; Stock, G. Dihedral angle principal component analysis of molecular dynamics simulations. J. Chem. Phys. 2007, 126, 244111.
17. Glykos, N. M. Carma: A molecular dynamics analysis program. J. Comput. Chem. 2006, 27, 1765-1768.
18. Dal Peraro, M.; Spiegel, K.; Lamoureux, G.; Vivo, M. D.; DeGrado, W. F.; Klein, M. L. Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations. J. Struct. Biol. 2007, 157, 444-453.
19. Notredame, C.; Higgins, D. G.; Heringa, J. T-coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 2000, 302, 205-217.
20. Clamp, M.; Cuff, J.; Searle, S. M.; Barton, G. J. The Jalview Java alignment editor. Bioinformatics 2004, 20, 426-427.