Simulation of the substrate cavity dynamics of quercetinase

Journal of Molecular Biology

Volumn 344, Issue 3, 2004, Pages 725-738

  Van Den Bosch, M ^a   Swart, M ^b   Van Gunsteren, W F ^c   Canters, Gerard W ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

^c ETH ZURICH   (Switzerland)

Author keywords

copper protein; flavonol; loop mobility; molecular dynamics; substrate cavity

Indexed keywords

COPPER DERIVATIVE; ENZYME; FLAVONOL DERIVATIVE; KAEMPFEROL; OXYGENASE; QUERCETIN 2,3 DIOXYGENASE; QUERCETINASE; UNCLASSIFIED DRUG; WATER;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; ENTHALPY; ENZYME MECHANISM; ENZYME SUBSTRATE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN INTERACTION; SIMULATION;

HOMO;

EID: 7944226403     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.09.056     Document Type: Article

References (19)

1. F. Fusetti, K.H. Schroter, R.A. Steiner, P.I. van Noort, T. Pijning, and H.J. Rozeboom Crystal structure of the copper-containing quercetin 2,3- dioxygenase from Aspergillus japonicus Structure 10 2002 259 268
2. R.A. Steiner, K.H. Kalk, and B.W. Dijkstra Anaerobic enzyme-substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase Proc. Natl Acad. Sci. USA 99 2002 16625 16630
3. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern-recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
4. P.H. Hünenberger, A.E. Mark, and W.F. van Gunsteren Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations J. Mol. Biol. 252 1995 492 503
5. van der Spoel, D., Hess, B., Feenstra, K. A., Lindahl, E., Berendsen, H. J. C. (1999). GROMACS User Manual, Version 2.0, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
6. W.F. van Gunsteren, S.R. Billeter, A.A. Eising, P.H. Hünenberger, P. Krüger, and A.E. Mark Biomolecular Simulation: GROMOS96 Manual and User Guide 1996 Vdf Hochschulverlag AG an der ETH Zuerich Switzerland
7. B.C. Oostenbrink, J.W. Pitera, M.M.H. van Lipzig, J.H.N. Meerman, and W.F. van Gunsteren Simulations of the estrogen receptor ligand-binding domain: Affinity of natural ligands and xenoestrogens J. Med. Chem. 43 2000 4594 4605
8. W. Koch, and M.C. Holthausen A Chemist's Guide to Density Functional Theory 2001 Wiley-VCH Weinhem
9. E.J. Baerends, J. Autschbach, A. Berces, C. Bo, P.M. Boerrigter, and L. Cavallo ADF 2002.01; SCM, Theoretical Chemistry 2000 Vrije Universiteit Amsterdam
10. G. te Velde, F.M. Bickelhaupt, E.J. Baerends, C. Fonseca Guerra, S.J.A. van Gisbergen, J.G. Snijders, and T. Ziegler Chemistry with ADF J. Comput. Chem. 22 2001 931 967
11. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, and H. Weissig The Protein Data Bank Nucl. Acids Res. 28 2000 235 242
12. A.D. Becke Density-functional exchange-energy approximation with correct asymptotic behavior Phys. Rev. A 38 1988 3098 3100
13. Perdew, J.P. (1986). Density-functional approximation for the correlation energy of the inhomogeneous electron gas. Phys. Rev. B, 33 8822-8824. [Erratum: Ibid. (1986). 34, 7406].
14. M. Swart, P.T. van Duijnen, and J.G. Snijders A Charge analysis derived from an atomic multipole expansion J. Comput. Chem. 22 2001 79 88
15. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, and J. Hermans Interaction models for water in relation to protein hydration B. Pullman Intermolecular Forces 1981 Reidel Dordrecht, The Netherlands 331 342
16. N. Guex, and M.C. Peitsch SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling Electrophoresis 18 1997 2714 2723 (http://www.expasy.org/spdbv/)
17. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 18 1997 1463 1472
18. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J.R. Haak Molecular dynamics with coupling to an external bath J. Chem. Phys. 81 1984 3684 3690
19. T. Oka, F.J. Simpson, and H.G. Krishnamurty Degradation of rutin by Aspergillus flavus. Studies of specificity, inhibition and possible reaction mechanism of quercetinase Can. J. Microbiol. 18 1972 493 508