Protein simulations: The absorption spectrum of barnase point mutants

Protein Science

Volumn 13, Issue 7, 2004, Pages 1823-1831

  Somers, Ken R F ^a   Krüger, Peter ^a   Bucikiewicz, Sylwia ^a   De Maeyer, Marc ^a   Engelborghs, Yves ^a   Ceulemans, Arnout ^a  

^a UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

Ab initio; Absorption; Barnase; CASPT2; Force field; Molecular dynamics

Indexed keywords

BARNASE; FLUORESCENT DYE; TRYPTOPHAN;

AB INITIO CALCULATION; ABSORPTION SPECTROSCOPY; ARTICLE; CALCULATION; ELECTRIC FIELD; MOLECULAR DYNAMICS; NONHUMAN; PHASE TRANSITION; POINT MUTATION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN METABOLISM; QUANTUM MECHANICS; REPRODUCIBILITY; SIMULATION;

BACILLUS; BACTERIAL PROTEINS; POINT MUTATION; PROTEIN STRUCTURE, TERTIARY; RIBONUCLEASES; SOFTWARE; SPECTROPHOTOMETRY; TRYPTOPHAN;

EID: 3042677489     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.04652804     Document Type: Article

References (45)

1. Andersson, K., Malmqvist, P.-A., Roos, B.O., Sadlej, A.J., and Wolinski, K. 1990. Second-order perturbation-theory with a CASSCF reference function. J. Phys. Chem. 94: 5483-5488.
2. Andersson, K., Blomberg, M.R.A., Fülscher, M.P., Karlström, G., Lindh, R., Malmqvist, P.-Å., Neogrády, P., Olsen, J., Roos, B.O., Sadlej, A.J., et al. 1997. Molcas version 4. Lund University, Sweden.
3. Andersson, K., Barysz, M., Bernhardsson, A., Blomberg, M.R.A., Cooper, D.L., Fülscher, M.P., de Graaf, C., Hess, B.A., Karlström, G., Lindh, R., et al. 2002. Molcas version 5.4. Lund University, Sweden.
4. Arcus, V.L., Vuilleumier, S., Freund, S.M.V., Bycroft, M., and Fersht, A.R. 1995. A comparison of the pH, urea and temperature-denatured states of barnase by heteronuclear nmr: Implications for the initiation of protein folding. J. Mol. Biol. 254: 305-321.
5. Bayly, C.I., Cieplak, P., Cornell, W.D., and Kollman, P.A. 1993. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J. Phys. Chem. 97: 10269-10280.
6. Becke, A.D. 1993. Density-functional thermochemistry. 3. The role of exact exchange. J. Chem. Phys. 98: 5648-5652.
7. Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., and Hermans, J. 1981. Interaction models for water in relation to protein hydration. In Intermolecular forces (ed. B. Pullman) pp. 331-342. Reidel, Dordrecht, The Netherlands.
8. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer Jr., E.E., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112: 535-542.
9. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., and Karplus, M. 1983. CHARMM: A program for macromolecular energy. minimization, and dynamics calculations. J. Comp. Chem. 4: 187-217.
10. 1H nuclear magnetic resonance spectrum of barnase. Biochemistry 29: 7425-7432.
11. Bycroft, M., Ludvingen, S., Fersht, A.R., and Poulsen, F.M. 1991. Determination of the three-dimensional solution structure of bamase using nmr spectroscopy. Biochemistry 30: 8697-8701.
12. a states of indole. J. Chem. Phys. 95: 4320-4240.
13. b transitions of tryptophan: Applications of theory and experimental observations to fluorescence of proteins. Methods Enzymol. 278: 113-150.
14. Callis, P.R. and Burgess. B.K. 1997. Tryptophan fluorescence shifts in proteins from hybrid simulations: An electrostatic approach. J. Phys. Chem. 101: 9429-9432.
15. Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E.I., Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., et al. 1997. Amber 5. University of California, San Francisco, CA.
16. Cieplak, P., Cornell, W.D., Bayly, C., and Kollman, P.A. 1995. Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteins. J. Comp. Chem. 16: 1357-1377.
17. De Beuckeleer. K. 1998. "Physicochemical study of bamase and its tryptophane mutants." Ph.D. thesis. Katholieke Universiteit Leuven, Leuven, Belgium.
18. De Beuckeleer, K., Volckaert, G., and Engelborghs, Y. 1999. Time resolved fluorescence and phosphorescence properties of the individual tryptophan residues of barnase: Evidence for protein-protein interactions. Proteins 36: 42-53.
19. De Smet, J., De Maeyer, M., Hazes, B., and Lasters, I. 1992. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 356: 539-542.
20. Demchenko. A.P. 1986. Ultraviolet spectroscopy of proteins. Springer, Berlin.
21. b coupling in the excited state of 3-methylindole and its polar clusters. J. Phys. Chem. 98: 12834-12843.
22. 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., et al. 1998. Gaussian 98 (revision a.9). Gaussian, Inc., Pittsburgh. PA.
23. Hellings, M., De Maeyer, M., Verheyden, S., Hao, Q., Van Damme, E.J.M., Peumans, W.J., and Engelborghs, Y. 2003. The dead-end elimination method, trytophan rotamers and fluorescence lifetimes. Biophys. J. 85: 1894-1902.
24. Hohenberg, P. and Kohn, W. 1964. Inhomogenous electron gas. Phys. Rev. 136: B864.
25. Hollas, J.M. 1963. Vapour-phase ultra-violet absorption spectra of indene, indole, coumarone and thionaphthene. Spectrochim. Acta 19: 753-767.
26. Horovitz, A. and Fersht. A.R. 1992. Co-operative interactions during protein folding. J. Mol. Biol. 224: 733-740.
27. Jorgensen, W.L., Chandrasekhar, J., Madura, J., Impey, R.W., and Klein, M.L. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79: 926-935.
28. Kohn, W. and Sham. L.J. 1965. Self-consistent equations including exchange and correlation effects. Phys. Rev. 140: A1133.
29. Konev. S.V. 1967. Fluorescence and phosphorescence of proteins and nucleic acids. Plenum Press, New York.
30. Lami, H. 1977. Presence of a low-lying "Rydberg" band in the vapour phase absorption spectra of indole and 1-methylindole. Chem. Phys. Lett. 48: 447-450.
31. Loewenthal, R., Sancho, J., and Fersht, A.R. 1991. Fluorescence spectrum of barnase: Contributions of three tryptophan residues and a histidine related pH dependence. Biochemistry 30: 6775-6779.
32. Roos, B.O. 1992. Lecture notes in chemistry 58. In European summerschool in quantum chemistry (ed. B.O. Roos). Springer-Verlag, Berlin.
33. Roos, B.O., Andersson, K., Fülscher, M.P., Malmqvist, P.-A., Serrano-Andrés, L., Pierloot, K., and Merchán, M. 1996. Multiconfigurational perturbation theory: Applications in electronic spectroscopy (eds. 1. Prigogine and S.A. Rice). Adv. Chem. Phys. 93: 219-331.
34. Serrano-Andrés, L. and Roos, B.O. 1996. Theoretical study of the absorption and emission spectra of indole in the gas phase and in a solvent. J. Am. Chem. Soc. 118: 185-195.
35. Short, K.W., Wagner, V., and Callis, P.R. 1999. Simulations of tryptophan fluorescence in proteins. 11. Comparison of CHARMM and CVFF force fields. Biophys. J. 76: A261.
36. Somers, K.R.F., Kryachko, E.S., and Ceulemans. A. 2004. Theoretical study of indole: Protonation, indolyl radical. tautomerism of indole, and its interaction with water. Chem. Phys. 301: 61-79.
37. Strickland, E.H., Horwitz, J., and Billups, C. 1970. Near-ultraviolet absorption bands of tryptophan. Studies using indole and 3-methylindole as models. Biochemistry 9: 4914-4921.
38. Szabo, A.G. and Rayner, D.M. 1980. Fluorescence decay of tryptophan conformers in aqueous solution. J. Am. Chem. Soc. 102: 554-563.
39. Toptygin, D. and Brand, L. 2000. Spectrally- and time-resolved fluorescence emission of indole during solvent relaxation: A quantative model. Chem. Phys. Lett. 322: 496-502.
40. b excitation bands. Photochem. Photobiol. 25: 441-444.
41. van Gunsteren, W.F., Billeter, S.R., Eising, A.A., Hünenberger, P.H., Krüger, P., Mark, A.E., Scott, W.R.P., and Tironi, I.G. 1996. Biomolecular simulation: The GROMOS96 manual and user guide. Vdf Hochschulverlag AG an der ETH Zürich, Zürich.
42. Vivian, J.T. and Callis, P.R. 2001. Mechanism of tryptophan fluorescence shifts in proteins. Biophys. J. 80: 2093-2109.
43. Willaert, K., Loewenthal, R., Sancho, J., Froeyen, M., Fersht, A., and Engelborghs, Y. 1992. Determination of the excited-state lifetimes of the tryptophan residues in barnase via multifrequency phase fluometry of tryptophan mutants. Biochemistry 31: 711-716.
44. York. D.M., Darden, T.A., and Pedersen, L.G. 1993. The effect of long-range electrostatic interactions in simulations of macromolecular crystals: A comparison of Ewald and truncated list methods. J. Chem. Phys. 99: 8345-8348.
45. Zegers, I., Deswarte, J., and Wyns, L. 1999. Trimeric domain-swapped barnase. Proc. Natl. Acad. Sci. 96: 818-822.