Force field development on pigments of photosystem 2 reaction centre

Photosynthetica

Volumn 43, Issue 3, 2005, Pages 417-420

  Palencar P ^a   Vacha F ^a,c   Kuty M ^a,b  

^a UNIVERSITY OF SOUTH BOHEMIA   (Czech Republic)

^b INSTITUTE OF LANDSCAPE ECOLOGY   (Czech Republic)

^c INSTITUTE OF PLANT MOLECULAR BIOLOGY   (Czech Republic)

Author keywords

Chlorophyll; Photosystem 2; Plastoquinone

Indexed keywords

EID: 26444596128     PISSN: 03003604     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11099-005-0066-2     Document Type: Article

References (18)

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.
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.
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.
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.
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 generation force-field for the simulation of proteins, nucleic acids, and organic-molecules. - J. amer. chem. Soc. 117: 5179-5197, 1995.
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.
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.
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 approach. - J. mol. Biol. 213: 351-373, 1990.
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.
12. MacKerell, A.D., Jr.: Empirical force fields for biological macromolecules: overview and issues. - J. Comput. Chem. 25: 1584-1604, 2004.
13. Mulliken, R.S.: Electron population analysis on LCAO-MO molecular wave functions. I. - J. chem. Phys. 23: 1833-1840, 1955.
14. Roothan, C.C.J.: New developments in molecular orbital theory. - Rev. mod. Phys. 23: 69, 1951.
15. Stewart, J.J.P.: Optimization of parameters for semiempirical methods. 1. Method. - J. Comput. Chem. 10: 209-220, 1989.
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.
17. Vácha, F., Durchan, M., Šiffel, P.: Excitonic interactions in the reaction centre of photosystem II studied by using circular dichroism. - Biochim. biophys. Acta. 1554: 147-152, 2002.
18. Vácha, F., Pšenčík, J., Kutý, M., Durchan, M., Šiffel, P.: Evidence for localization of accumulated chlorophyll cation on the D1-accessory chlorophyll in reaction centre of photosystem II. - Photosynth. Res. In press, 2005.