Comparison of Empirical Force Fields for Bacteriochlorophyll: an Influence on Hydration and Long-Time Dynamics of Bacterial Photoreaction Centers
DOI:
https://doi.org/10.15407/ujpe61.10.0886Keywords:
bacterial photoreaction centers, Rhodobacter Sphaeroides, molecular dynamics, force field, cofactor hydrationAbstract
The choice of an adequate empirical force field for photosynthetic cofactors is the major prerequisite of realistic molecular dynamics simulations of bacterial and plant photoreaction centers. In this work, we compare two available sets of parameters for bacteriochlorophyll in extended 200 ns simulations of photoreaction centers from Rhodobacter Sphaeroides in the membrane environment. It is shown that the most popular and widely used set of parameters produces artifacts in cofactor positions and orientations. It is also shown that the hydration of cofactors may vary, by dramatically depending on the used force field. Some recommendations for the further force field development are made.
References
R.K. Clayton, Primary processes in bacterial photosynthesis, Ann. Rev. Biophys. Bioengin. 2, No. 1, 131 (1973) [DOI: 10.1146/annurev.bb.02.060173.001023].
W.W. Parson and R.J. Cogdell, The primary photochemical reaction of bacterial photosynthesis, Biochem. Biophys. Acta 416, No. 1, 105 (1975).
Y.M. Barabash, N.M. Berezetskaya, L.N. Christophorov, A.O.Goushcha, and V.N. Kharkyanen, Effects of structural memory in protein reactions, J. Chem. Phys. 116, No. 10, 4339 (2002) [DOI: 10.1063/1.1447906].
A.O. Goushcha, A.J. Manzo, G.W. Scott, L.N. Christophorov, P.P. Knox, Y.M. Barabash, M.T. Kapoustina, N.M. Berezetska, and V.N. Kharkyanen, Self-regulation phenomena applied to bacterial reaction centers: 2. Nonequilibrium adiabatic potential: Dark and light conformations revisited, Biophys. J. 84, No. 2, 1146 (2003) [DOI: 10.1016/S0006-3495(03)74930-3].
A.O. Goushcha, V.N. Kharkyanen, G.W. Scott, and A.R. Holzwarth, Self-regulation phenomena in bacterial reaction centers. I. General theory, Biophys. J. 79, No. 3, 1237 (2000) [DOI: 10.1016/S0006-3495(00)76378-8].
U. Ermler, G. Fritzsch, S.K. Buchanan, and H. Michel, Structure of the photosynthetic reaction centre from Rhodobacter sphaeroides at 2.65 A resolution: cofactors and protein-cofactor interactions, Structure 2, No. 10, 925 (1994) [DOI: 10.1016/S0969-2126(94)00094-8].
G. Katona, A. Snijder, P. Gourdon, U. Andreasson, O. Hansson, L.-E. Andreasson, and R. Neutze, Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center, Nat. Struct. Mol. Biol. 12, N 7, 630 (2005) [DOI: 10.1038/nsmb948].
M. Malferrari, F. Francia, and G. Venturoli, Coupling between electron transfer and protein–solvent dynamics: FTIR and laser-flash spectroscopy studies in photosynthetic reaction center films at different hydration levels, J. Phys. Chem. B 115, No. 49, 14732 (2011) [DOI: 10.1021/jp2057767].
S.K. Chamorovsky, P.M. Krasil’nikov, and P.P. Knox, Effect of isotope substitution and controlled dehydration on the photoinduced electron transport reactions of quinone acceptors and multiheme cytochrome c in bacterial photosynthetic reaction center. Biokhim. 67, No. 11, 1298 (2002) [DOI: 10.1023/A:102131792535].
J.A. Potter, P.K. Fyfe, D. Frolov, M.C. Wakeham, R. van Grondelle, B. Robert, and M.R. Jones, Strong effects of an individual water molecule on the rate of light-driven charge separation in the Rhodobacter sphaeroides reaction center, J. Biol. Chem. 280, No. 29, 27155 (2005) [DOI: 10.1074/jbc.M501961200].
M. Ceccarelli, P. Procacci, and M. Marchi, An ab initio force field for the cofactors of bacterial photosynthesis, J. Computat. Chem. 24, No. 2, 129 (2003) [DOI: 10.1002/jcc.10198].
W.D. Cornell, P. Cieplak, C.I. Bayly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J.W. Caldwell, and P.A. Kollman, A second generation force field for the simulation of proteins, nucleic acids, and organic molecules, J. Am. Chem. Soc. 117, No. 19, 5179 (1995) [DOI: 10.1021/ja00124a002].
L. Zhang, D.-A. Silva, Y. Yan, X. Huang, Force field development for cofactors in the photosystem II, J. Computat. Chem. 33, No. 25, 1969 (2012) [DOI: 10.1002/jcc.23016].
M. Ceccarelli and M. Marchi, Simulation and modeling of the Rhodobacter sphaeroides bacterial reaction center: Structure and interactions, J. Phys. Chem. B 107, No. 6, 1423 (2003) [DOI: 10.1021/jp0270001].
S. Vasil’ev and D. Bruce, A protein dynamics study of photosystem II: The effects of protein conformation on reaction center function, Biophys. J. 90, No. 9, 3062 (2006) [DOI: 10.1529/biophysj.105.076075].
K. Karki and D. Roccatano, Molecular dynamics simulation study of chlorophyll a in different organic solvents, J. Chem. Theory Comput. 7, No. 4, 1131 (2011) [DOI: 10.1021/ct100462].
W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives, Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118, No. 45, 11225 (1996) [DOI: 10.1021/ja9621760].
B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theory Comput. 4, No. 3, 435 (2008) [DOI: 10.1021/ct700301q].
S.O. Yesylevskyy, ProtSqueeze: Simple and effective automated tool for setting up membrane protein simulations, J. Chem. Inf. Model. 47, 1986 (2007) [DOI: 10.1021/ci600553y].
U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen, A smooth particle mesh Ewald method, J. Chem. Phys. 103, No. 19, 8577 (1995) [DOI: 10.1063/1.470117].
B. Hess, P-LINCS: A parallel linear constraint solver for molecular simulation, J. Chem. Theory Comput. 4, No. 1, 116 (2008) [DOI: 10.1021/ct700200b].
S. Miyamoto and P.A. Kollman, Settle: An analytical version of the SHAKE and RATTLE algorithm for rigid water models, J. Comput. Chem. 13, No. 8, 952 (1992) [DOI: 10.1002/jcc.540130805].
Y. Duan, C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations, J. Comput. Chem. 24, No. 16, 1999 (2003) [DOI: 10.1002/jcc.10349].
S. Marsili, G.F. Signorini, R. Chelli, M. Marchi, and P. Procacci, ORAC: A molecular dynamics simulation program to explore free energy surfaces in biomolecular systems at the atomistic level, J. Comput. Chem. 31, No. 5, 1106 (2010) [DOI: 10.1002/jcc.21388].
S.O. Yesylevskyy, Pteros: Fast and easy to use open-source C++ library for molecular analysis, J. Comput. Chem. 33, No. 19, 1632 (2012) [DOI: 10.1002/jcc.2298].
Downloads
Published
How to Cite
Issue
Section
License
Copyright Agreement
License to Publish the Paper
Kyiv, Ukraine
The corresponding author and the co-authors (hereon referred to as the Author(s)) of the paper being submitted to the Ukrainian Journal of Physics (hereon referred to as the Paper) from one side and the Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine, represented by its Director (hereon referred to as the Publisher) from the other side have come to the following Agreement:
1. Subject of the Agreement.
The Author(s) grant(s) the Publisher the free non-exclusive right to use the Paper (of scientific, technical, or any other content) according to the terms and conditions defined by this Agreement.
2. The ways of using the Paper.
2.1. The Author(s) grant(s) the Publisher the right to use the Paper as follows.
2.1.1. To publish the Paper in the Ukrainian Journal of Physics (hereon referred to as the Journal) in original language and translated into English (the copy of the Paper approved by the Author(s) and the Publisher and accepted for publication is a constitutive part of this License Agreement).
2.1.2. To edit, adapt, and correct the Paper by approval of the Author(s).
2.1.3. To translate the Paper in the case when the Paper is written in a language different from that adopted in the Journal.
2.2. If the Author(s) has(ve) an intent to use the Paper in any other way, e.g., to publish the translated version of the Paper (except for the case defined by Section 2.1.3 of this Agreement), to post the full Paper or any its part on the web, to publish the Paper in any other editions, to include the Paper or any its part in other collections, anthologies, encyclopaedias, etc., the Author(s) should get a written permission from the Publisher.
3. License territory.
The Author(s) grant(s) the Publisher the right to use the Paper as regulated by sections 2.1.1–2.1.3 of this Agreement on the territory of Ukraine and to distribute the Paper as indispensable part of the Journal on the territory of Ukraine and other countries by means of subscription, sales, and free transfer to a third party.
4. Duration.
4.1. This Agreement is valid starting from the date of signature and acts for the entire period of the existence of the Journal.
5. Loyalty.
5.1. The Author(s) warrant(s) the Publisher that:
– he/she is the true author (co-author) of the Paper;
– copyright on the Paper was not transferred to any other party;
– the Paper has never been published before and will not be published in any other media before it is published by the Publisher (see also section 2.2);
– the Author(s) do(es) not violate any intellectual property right of other parties. If the Paper includes some materials of other parties, except for citations whose length is regulated by the scientific, informational, or critical character of the Paper, the use of such materials is in compliance with the regulations of the international law and the law of Ukraine.
6. Requisites and signatures of the Parties.
Publisher: Bogolyubov Institute for Theoretical Physics, National Academy of Sciences of Ukraine.
Address: Ukraine, Kyiv, Metrolohichna Str. 14-b.
Author: Electronic signature on behalf and with endorsement of all co-authors.
.png){kind=small}
