Large-scale QM/MM calculations of electronic excitations in yellow protein: Toward petascale level of protein calculations

Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Volumn , Issue , 2007, Pages 614-619

  Freindorf, Marek ^a   Jones, Matthew D ^a   Shao, Yihan ^b   Kong, Jing ^b   Furlani, Thomas R ^a  

^a UNIVERSITY AT BUFFALO   (United States)

^b Q Chem Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; DATA STRUCTURES; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; QUANTUM CHEMISTRY;

AMBER FORCE FIELDS; ELECTRONIC EXCITATIONS; EXPERIMENTAL DATUMS; GAS PHASE; GEOMETRY OPTIMIZATIONS; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR MECHANICALS; PHOTOACTIVE YELLOW PROTEINS; QM/MM CALCULATIONS; QUANTUM MECHANICALS; WATER SOLUTIONS; YELLOW PROTEINS;

DYNAMICS;

EID: 47649120168     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2007.4375624     Document Type: Conference Paper

References (13)

1. T.E. Mayer, "Isolation and characterization of soluble cytochromes, ferredoxins and other chromophoric proteins from the halophilic phototrophic bacterium Ectothiorhodospira halophila", Biochim. Biophys. Acta, 806, 1985, pp. 175-183.
2. W.W. Sprenger, , W.D. Hoff, J.P. Armitage,, and K.J.J. Hellingwerf, "The Eubacterium Ectothiorhodospira halophila Is Negatively Phototactic, with a Wavelength Dependence That Fits the Absorption Spectrum of the Photoactive Yellow Protein", J. Bacteriol., 175, 1993, pp. 3096-3104.
3. M. Baca, G.E.0. Borgstahl, M. Boissinot, P.M. Burke, DeW.R. Williams, K.A. Slater and E.D. Getzof, "Complete Chemical Structure of Photoactive Yellow Protein: Novel Thioester-Linked 4-Hydroxycinnamyl Chromophore and Photocycle Chemistry", Biochemistry, 33, 1994, pp. 14369-14377.
4. G. E. O. Borgstahl, DeW.R. Williams, and E.D. Getzoff, "1.4 A Structure of Photoactive Yellow Protein, a Cytosolic Photoreceptor: Unusual Fold, Active Site, and Chromophore", Biochemistry, 34, 1995, pp. 6278-6287.
5. I. B. Nielsen, S. Boye-Peronne, M.O.A. El Ghazaly, M.B. Kristensen, S. Brondsted Nielsen, and L.H. Andersen, "Absorption Spectra of Photoactive Yellow Protein Chromophores in Vacuum", Biophys. Journal, 89, 2005, pp. 2597-2604.
6. Z. He, C.H. Martin, R. Birge, and K.F. Freed, "Theoretical Studies on Excited States of a Phenolate Anion in the Environment of Photoactive Yellow Protein", J. Phys. Chem. A, 104, 2000, pp. 2939-2952.
7. A. Sergi, M. Gruning, M. Ferrario, and F. Buda, "Density Functional Study of the Photoactive Yellow Protein's Chromophore", J. Phys. Chem. B, 105, 2001, pp. 4386-4391.
8. V. Molina, and M. Merchan, "On the absorbance changes in the photocycle of the photoactive yellow protein: A quantum-chemical analysis", Proc. Natl. Acad. Soc., 98, 2001, pp. 4299-4304.
9. G. Groenhof, M.F. Lensink, H.J.C. Berendsen, J.G. Snijders, and A.E. Mark, "Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore", Proteins, 48, 2002, pp. 202-211.
10. D.A. Case, D.A. Pearlman, J.W. Caldwell, T.E. Cheatham III, W.S. Ross, C.L. Simmerling, T.A. Darden, K.M. Merz, R.V. Stanton, A.L. Cheng, J.J. Vincent, M. Crowley, V. Tsui, R.J. Radmer, Y. Duan, J. Pitera, M. Massova, G.L. Seibel, U.C. Singh, P.K. Weiner, P.A. Kollman, AMBER 8, University of California, San Francisco 2004.
11. CHARMM: The Energy Function and Its Parameterization with an Overview of the Program, in The Encyclopedia of Computational Chemistry, 1, P.v.R. Schleyer et al., editors (John Wiley & Sons: Chichester, by A.D. MacKerell, Jr., B. Brooks, C.L. Brooks, III, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998, pp. 271-277,
12. Y. Shao, L. Fusti-Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S.T. Brown, A.T.B. Gilbert, L.V. Slipchenko, S.V. Levchenko, D.P. ONeill, R.A. Distasio Jr., R.C. Lochan, T. Wang, G.J.O. Beran, N.A. Besley, J.M. Herbert, C.Y. Lin, T. Van Voorhis, S.H. Chien, A. Sodt, R.P. Steele, V.A. Rassolov, P.E. Maslen, P.P. Korambath, R.D. Adamson, B. Austin, J. Baker, E.F.C. Byrd, H. Dachsel, R.J. Doerksen, A. Dreuw, B.D. Dunietz, A.D. Dutoi, T.R. Furlani, S.R. Gwaltney, A. Heyden, S. Hirata, C.-P. Hsu, G. Kedziora, R.Z. Khalliulin, P. Klunzinger, A.M. Lee, M.S. Lee, W. Liang, I. Lotan, N. Nair, B. Peters, E.I. Proynov, P.A. Pieniazek, Y.M. Rhee, J. Ritchie, E. Rosta, C.D. Sherrill, A.C. Simmonett, J.E. Subotnik, H.L. Woodcock III, W. Zhang, A.T. Bell, A.K. Chakraborty, D.M. Chipman, F.J. Keil, A. Warshel, W.J. Hehre, H.F. Schaefer III, J. Kong, A.I. Krylov, P.M.W. Gill, M. Head-Gordon, "Advances in methods and algorithms in a modern quantum chemistry program package", Phys. Chem. Chem. Phys., 8, 2006, pp. 3172-3191.
13. M. Freindorf, Y. Shao, T.R. Furlani, J. Kong, "Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential", J. Comput. Chem. 26, 2005, pp. 1270-1278.