Photosynthetica 2005, 43(3):417-420 | DOI: 10.1007/s11099-005-0066-2

Force field development on pigments of photosystem 2 reaction centre

P. Palencar1, F. Vacha1,3,*, M. Kuty1,2
1 Institute of Physical Biology, University of South Bohemia, Nove Hrady, Czech Republic
2 Institute of Landscape Ecology, Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
3 Institute of Plant Molecular Biology, Academy of Sciences of the Czech Republic, Ceske Budejovice, Czech Republic

We developed new parameters for molecular dynamics (MD) simulations, namely partial atomic charges, equilibrium bond-lengths, angles, dihedrals, atom types, and force constants of chlorophyll a (Chl) and plastoquinone (PQ), and both reduced and neutral form of primary acceptor (PHO) molecule. These parameters are essential for MD simulations that can interpret various structure functional relationships during primary processes of charge separation and stabilization in photosystem 2 reaction centres.

Additional key words: chlorophyll; photosystem 2; plastoquinone

Received: February 14, 2005; Accepted: April 11, 2005; Published: September 1, 2005  Show citation

ACS AIP APA ASA Harvard Chicago Chicago Notes IEEE ISO690 MLA NLM Turabian Vancouver
Palencar, P., Vacha, F., & Kuty, M. (2005). Force field development on pigments of photosystem 2 reaction centre. Photosynthetica, 43(3), 417-420. doi: 10.1007/s11099-005-0066-2
Share...
Download citation
  • BibTeX (.bib)
  • Bookends (.ris)
  • EasyBib (.ris)
  • EndNote (.enw)
  • EndNote 8 (.xml)
  • ISI WoS (.isi)
  • Medlars (.medlars)
  • Mendeley (.ris)
  • MODS (.xml)
  • Papers (.ris)
  • RefWorks (.txt)
  • RefManager (.ris)
  • RIS (.ris)
  • MS Word (.xml)
  • Zotero (.ris)
    • Open full article

    References

    1. Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. - Clarendon Press, Oxford 1987.
    2. Autenrieth, F., Tajkhorshid, E., Baudry, J., Luthey-Schulten, Z.: Classical force field parameters for the heme prosthetic group of cytochrome c. - J. Comput. Chem. 25:1613-1622, 2004. Go to original source...
    3. Bayly, C.I., Cieplak, P., Cornell, W. D., Kollman, P. A.: A well-behaved electrostatic potential based method using charge restraints for determining atom-centered charges: The RESP model. - J. phys. Chem. 97: 10269-10280, 1993. Go to original source...
    4. 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. 4:187-217, 1983. Go to original source...
    5. Ceccarelli, M., Procacci, P., Marchi, M.: An ab initio force field for the cofactors of bacterial photosynthesis. - J. Comput. Chem. 24:129-142, 2003. Go to original source...
    6. Cornell, W. D., Cieplak, P., Bayly, C.I., Gould, I.R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J.W., Kollman, P.A.: A 2nd gene ration force-field for the simulation of proteins, nucleic acids, and organic-molecules. - J. amer. chem. Soc. 117:5179-5197, 1995. Go to original source...
    7. Ferreira, K. N., Iverson, T.M., Maghlaoui, K., Barber, J., Iwata, S.: Architecture of the photosynthetic oxygen-evolving center. - Science 303:1831-1838, 2004. Go to original source...
    8. Foloppe, N., Ferrand, M., Breton, J., Smith, J.C.: Structural model of the photosynthetic reaction center of Rhodobacter capsulatus. - Proteins: Struct. Funct. Genet. 22:226-244, 1995. Go to original source...
    9. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Zakrzewski, V.G., Montgomery, J. A., Stratmann, R.E., Burant, J. C., Dapprich, S., Millam, J.M., Daniels, A. D., Kudin, K.N., Strain, M.C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G. A., Ayala, P.Y., Cui, Q., Morokuma, K., Malick, D.K., Rabuck, A.D., Raghavachari, K., Foresman, J.B., Cioslowski, J., Ortiz, J. V., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Gonzalez, C., Challacombe, M., Gill, P.M.W., Johnson, B.G., Chen, W., Wong, M.W., Andres, J.L., Head-Gordon, M., Replogle, E.S., Pople, J.A.: Gausian 98. - Gaussian, Pittsburgh 1998.
    10. Kuczera, K., Kuriyan, J., Karplus, M.: Temperature dependence of the structure and dynamics of myoglobin. A simulation ap-proach. - J. mol. Biol. 213:351-373, 1990. Go to original source...
    11. 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 102:3586-3616, 1998. Go to original source...
    12. MacKerell, A. D., Jr.: Empirical force fields for biological macromolecules: overview and issues. - J. Comput. Chem. 25:1584-1604, 2004. Go to original source...
    13. Mulliken, R.S.: Electron population analysis on LCAO-MO molecular wave functions. I. - J. chem. Phys. 23:1833-1840, 1955. Go to original source...
    14. Roothan, C.C.J.: New developments in molecular orbital theory. - Rev. mod. Phys. 23:69, 1951. Go to original source...
    15. Stewart, J. J.P.: Optimization of parameters for semiempirical methods. 1. Method. - J. Comput. Chem. 10:209-220, 1989. Go to original source...
    16. Tsai, H.H., Simpson, M.C.: HBFF-SVD force field treatment of Ni(II) porphine: Important long range cross terms. - J. phys. Chem. A 107:526-541, 2003. Go to original source...
    17. Vacha, F., Durchan, M., Siffel, P.: Excitonic interactions in the reaction centre of photosystem II studied by using circular dichroism. - Biochim. biophys. Acta. 1554:147-152, 2002. Go to original source...
    18. Vacha, F., Pseneik, J., Kuty, M., Durchan, M., Siffel, P.: Evidence for localization of accumulated chlorophyll cation on the D1-accessory chlorophyll in reaction centre of photosystem II. - Photosynth. Res. In press, 2005. Go to original source...

    Return to the content