Molecular dynamics simulations of the chromophore binding site of Deinococcus radiodurans bacteriophytochrome using new force field parameters for the phytochromobilin chromophore

Journal of Physical Chemistry B

Volumn 113, Issue 4, 2009, Pages 945-958

  Kaminski, Steve ^a   Daminelli, Grazia ^a   Mroginski, Maria Andrea ^a  

^a TECHNISCHE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BINDING SITES; CONFORMATIONS; DYNAMICS; MOLECULAR DYNAMICS; MOLECULES; SIGNAL TRANSDUCTION; WATER ANALYSIS;

AB-INITIO; ATOMIC CHARGES; C-C BONDS; CONFORMATIONAL FLEXIBILITIES; CONFORMATIONAL STATE; DEINOCOCCUS RADIODURANS; DYNAMICAL FEATURES; EMPIRICAL FORCES; EXPERIMENTAL OBSERVATIONS; FORCE FIELD PARAMETERS; FORCE FIELDS; H BONDINGS; H-BONDS; METHINE BRIDGES; MOLECULAR DYNAMICS SIMULATIONS; PHOTO-INDUCED; PHYTOCHROMOBILIN; PRODUCTION RUNS; PROPIONIC; PROSTHETIC GROUPS; RESONANCE RAMAN SPECTROSCOPIES; SIDE CHAINS; STATISTICAL ANALYSIS; TETRAPYRROLE; TORSIONAL ANGLES; WATER MOLECULES;

CHROMOPHORES;

EID: 61949448315     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp8047532     Document Type: Article

References (31)

1. Rockwell, N. C.; Su, Y. S.; Lagarias, J. C. Phytochrome structure and signaling mechanisms. Annu. Rev. Plant Biol. 2006, 57, 837-858.
2. Quail, P. H. Phytochrome photosensory signalling networks. Nature Rev. Mol. Cell Biol. 2002, 3 (2), 85-93.
3. Briggs, W. R.; Spudich, J. L. Handbook of Photosensory Receptors; Wiley Verlag: Weinheim, Germany, 2005.
4. Wagner, J. R.; Brunzelle, J. S.; Forest, K. T.; Vierstra, R. D. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 2005, 438 (7066), 325-331.
5. Wagner, J. R.; Zhang, J. R.; Brunzelle, J. S.; Vierstra, R. D.; Forest, K. T. High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. J. Biol. Chem. 2007, 282 (16), 12298-12309.
6. von Stetten, D.; Günter, M.; Scheerer, P.; Murgida, D. H.; Mroginski, M. A.; Krauβ, N.; Lamparter, T.; Zhang, J.; Anstrom, D. M.: Vierstra, R. D.; Forest, K. T.; Hildebrandt, P. Chromophore heterogeneity and the photoconversion in phytochrome crystals and solution studied by resonance Raman spectroscopy. Angew. Chem. Int. Ed. 2008, 47, 1-4.
7. Wagner, J. R.; Zhang, J.; von Stetten, D.; Günter, M.; Murgida, D. H.; Mroginski, M. A.; Walker, J. M.; Forest, K. T.; Hiidebrandt, P.; Vierstra, R. D. Mutational analysis of Deinococcus Radiodurans Bacteriophytochrome reveals key amino acids necessary for structural integrity and the proton exchange cycle during phoroconversion. J. Biol. Chem. 2008, 283, 12212-12226.
8. Schmidt, P.; Gensch, T.; Remberg, A.; Gartner, W.; Braslavsky, S. E.; Schaffner, K. The complexity of the P-r to P-fr phototransformation kinetics is an intrinsic property of native phytochrome. Photochem. Photobiol. 1998, 68 (5), 754-761.
9. van Thor, J. J.; Mackeen, M.; Kuprov, I.; Dwek, R. A.; Wormald, M. R. Chromophore structure in the photocycle of the cyanobacterial phytochrome Cphl. Biophys. J. 2006, 91 (5), 1811-1822.
10. 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.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102 (18), 3586-3616.
11. Foloppe, N.; MacKerell, A. D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 2000, 21 (2), 86-104.
12. Reuter, N.; Lin, R.; Thiel, W. Green fluorescent proteins: Empirical force field for the neutral and deprotonated forms of the chromophore. Molecular dynamics simulation's of the wild type and S65T mutant. J. Phys. Chem. B 2002, 106 (24), 6310-6321.
13. Olkhova, E.; Hutter, M. C.; Lill, M. A.; Helms, V.; Michel, H. Dynamic water networks in cytochrome c oxidase from Paracoccus denítrificans investigated by molecular dynamics simulations. Biophys. J. 2004, 86 (4), 1873-1889.
14. Gaussian 03, revision C.02; Gaussian, Inc.: Wallingford, CT, 2004.
15. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. Charmm - A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4 (2), 187-217.
16. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD. J Comput. Chem. 2005, 26 (16), 1781-1802.
17. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79 (2), 926-935.
18. Becke, A. D. A New Mixing of Hartree-Fock and Local Density-Functional Theories. J. Chem. Phys. 1993, 98 (2), 1372-1377.
19. Breneman, C. M.; Wiberg, K. B. Determining Atom-Centered Monopoles from Molecular Electrostatic Potentials - the Need for High Sampling Density in Formamide Conformational-Analysis. J. Comput. Chem. 1990, 11 (3), 361-373.
20. Autenrieth, F.; Tajkhorshid, E.; Baudry, J.; Luthey-Schulten, Z. Classical force field parameters for the heme prosthetic group of cytochrome c. J. Comput. Chem. 2004, 25 (13), 1613-1622.
21. Brunger, A. T.; Karplus, M. Polar Hydrogen Positions in Proteins - Empirical Energy Placement and Neutron-Diffraction Comparison. Proteins-Struct. Funct. Genet. 1988, 4 (2), 148-156.
22. Feller, S. E.; Zhang, Y. H.; Pastor, R. W.; Brooks, B. R. Constant-Pressure Molecular-Dynamics Simulation - the Langevin Piston Method. J. Chem. Phys. 1995, 103 (11), 4613-4621.
23. Martyna. G. J.; Tobias, D. J.; Klein, M. L. Constant-Pressure Molecular-Dynamics Algorithms. J. Chem. Phys. 1994, 101 (5), 4177-4189.
24. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald - An N. Log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98 (12), 10089-10092.
25. van Gunsteren, W. F.; Berendsen, H. J. C. Algorithms for Macromolecular Dynamics and Constraint Dynamics, 34th ed.; 1977; pp (311-1327.
26. Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual molecular dynamics. J. Mol. Graph. 1996, 14 (1), 33.
27. Willis, B. T. M.; Prior, A. W. Thermal Vibrations in Crystallography; Cambridge University Press: New York, 1975.
28. Brooks, C. L.; Karplus, M.; Pettitt, B. M. A. Theoretical Perspective Of Dynamics, Structure, and Thermodynamics. Adv. Chem. Phys. 1988, 71, 1-200.
29. Essen, L. O,; Hughes, J.; Mailliet, J.; The structure of a complete phytochrome sensory module in the Pr ground state Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 14709-14714.
30. Yang, X.; Stojkovic, E. A.; Kuk, J.; Moffatt, K. Crystal structure of the chromophore binding domain of an unusual bacteriophytochrome, RpBphP3, reveals residues that modulate photoconversion. Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (30), 12571-12576.
31. Deloof, H.; Nilsson, L.; Rigler, R. Molecular-Dynamics Simulation of Galanin in Aqueous and Nonaqueous Solution. J. Am. Chem. Soc. 1992, 114 (11), 4028-4035.