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Current issue   Ukr. J. Phys. 2016, Vol. 61, N 10, p.886-892
http://dx.doi.org/10.15407/ujpe61.10.0886    Paper

Yesylevskyy S., Berezetskaya N., Olenchuk M.

Department of Physics of Biological Systems, Institute of Physics, Nat. Acad. of Sci. of Ukraine
(46, Prosp. Nauky, Kyiv 03680, Ukraine; e-mail: yesint4@gmail.com)

Comparison of Empirical Force Fields for Bacteriochlorophyll: an Influence on Hydration and Long-Time Dynamics of Bacterial Photoreaction Centers

Section: Soft Matter
Original Author's Text: English

Abstract: 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.

Key words: bacterial photoreaction centers, Rhodobacter Sphaeroides, molecular dynamics, force field, cofactor hydration.


  1. R.K. Clayton, Primary processes in bacterial photosynthesis, Ann. Rev. Biophys. Bioengin. 2, No. 1, 131 (1973).
  2. W.W. Parson and R.J. Cogdell, The primary photochemical reaction of bacterial photosynthesis, Biochem. Biophys. Acta 416, No. 1, 105 (1975).
  3. 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).
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  8. 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).
  9. 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).
  10. 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).
  11. 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).
  12. 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).
  13. 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).
  14. 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).
  15. 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).
  16. 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).
  17. 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).
  18. 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).
  19. S.O. Yesylevskyy, ProtSqueeze: Simple and effective automated tool for setting up membrane protein simulations, J. Chem. Inf. Model. 47, 1986 (2007).
  20. 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).
  21. B. Hess, P-LINCS: A parallel linear constraint solver for molecular simulation, J. Chem. Theory Comput. 4, No. 1, 116 (2008).
  22. 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).
  23. 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).
  24. 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).
  25. S.O. Yesylevskyy, Pteros: Fast and easy to use open-source C++ library for molecular analysis, J. Comput. Chem. 33, No. 19, 1632 (2012).