Computer simulations of carbon monoxide photodissociation in myoglobin: Structural interpretation of the B states

Biophysical Journal

Volumn 74, Issue 2 I, 1998, Pages 789-802

  Meller, Jaroslaw ^a,b   Elber, Ron ^a  

^a HEBREW UNIVERSITY OF JERUSALEM   (Israel)

^b NICOLAUS COPERNICUS UNIVERSITY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON MONOXIDE; MYOGLOBIN;

ARTICLE; COMPUTER SIMULATION; ELECTRIC FIELD; INFRARED SPECTROSCOPY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PROTEIN STRUCTURE; WHALE;

EID: 0031880931     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(98)74004-4     Document Type: Article

References (35)

1. Alben, J. O., S. F. Beece, F. Bowne, W. Doster, L. Eisenstein, H. Frauenfelder, D. Good, J. D. McDonald, M. C. Marden, L. Reinischoh, A. H. Reynolds, E. Shyamsunder, and K. T. Yue. 1982. Infrared spectroscopy of photodissociated carboxy myoglobin at low temperature. Proc. Natl. Acad. Sci. USA. 79:3744-3748.
2. Antonini, E., and M. Brunori. 1971. Hemoglobin and Myoglobin and Their Interaction with Ligands. North Holland, Amsterdam.
3. Brooks, B. R., R. D. Bruccoleri, B. O. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem. 4:187-217.
4. Carver, T. E., R. E. Brantley, E. W. Singleton, R. M. Arduini, M. L. Quillin, G. N. Phillips, and J. S. Olson. 1992. A novel site directed mutant of myoglobin with an unusually high oxygen affinity and low oxidation rate. J. Biol. Chem. 267:14443-14450.
5. Darden, T. A., D. M. York, and L. G. Pedersen. 1993. Particle mesh Ewald: an N*log(N) method for Ewald sums in large systems. J. Chem. Phys. 98:10089-10092.
6. Elber, R., and M. Karplus. 1990. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112:9161-9175.
7. Elber, R., A. Roitberg, C. Simmerling, R. Goldstein, H. Li, G. Verkhivker, C. Keasar, J. Zhang, and A. Ulitsky. 1994. MOIL: a program for simulation of macromolecules. Comp. Phys. Comm. 91:159-189.
8. Essmann, U., L. Perera, M. L. Berkowitz, T. Darden, and L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103: 8577-8593.
9. Ewald, P. 1921. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 64:253-287.
10. Gibson, Q. H., R. Regan, R. Elber, J. S. Olson, and T. E. Carver. 1992. Distal pocket residues affect picosecond ligand recombination in myoglobin. J. Biol. Chem. 267:22022-22034.
11. Hartmann, H., S. Zinser, P. Komninos, R. T. Schneider, G. U. Nienhaus, and F. Parak. 1996. X-ray structure determination of a metastable state of carbon monoxy myoglobin after photodissociation. Proc. Natl. Acad. Sci. USA. 93:7013-7016.
12. Jorgensen, W. L., J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
13. Jorgensen, W. L., and D. L. Severance. 1990. Aromatic-aromatic interactions: free energy profiles for the benzene dimer in water, chloroform, and liquid benzene. J. Am. Chem. Soc. 112:4768-4774.
14. Jorgensen, W. L., and J. Tirado-Rives. 1988. The OPLS potential functions for proteins. Energy minimization for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110:1657-1666.
15. Kuczera, K. 1997. Dynamics and thermodynamics of globins. In Recent Developments in Theoretical Studies of Proteins. R. Elber, editor. World Scientific, Singapore. 1-64.
16. Kuczera, K., J. Kuriyan, and M. Karplus. 1989. Temperature dependence of the structure and dynamics of myoglobin. J. Mol. Biol. 213:351-373.
17. Li, H., R. Elber, and J. E. Straub. 1993. Molecular dynamics simulation of NO recombination to myoglobin mutants. J. Biol. Chem. 268: 17908-17916.
18. Lim, M., T. A. Jackson, and P. A. Anfinrud. 1995a. Mid-infrared vibrational spectrum of CO after photodissociation from heme: evidence for a ligand docking site in the heme pocket of hemoglobin and myoglobin. J. Chem. Phys. 102:4355-4366.
19. Lim, M., T. A. Jackson, and P. A. Anfinrud. 1995b. Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe-C-O. Science. 269:962-965.
20. Lim, M., T. A. Jackson, and P. A. Anfinrud. 1997. Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin. Nature Struct. Biol. 4:209-214.
21. Loncharich, R. J., and B. R. Brooks. 1989. The effect of truncating long-range forces on protein dynamics. Proteins. 6:32-35.
22. Ma, J., S. Huo, and J. E. Straub. 1997. Molecular dynamics simulation study of the B states of solvated carbonmonoxy myoglobin. J. Am. Chem. Soc. 119:2541-2551.
23. Perutz, M. F. 1979. Regulation of oxygen affinity of hemoglobin: influence of the structure of the globin on the heme iron. Annu. Rev. Biochem. 48:327-386.
24. Phillips, G. N., R. M. Arduini, B. A. Springer, and S. G. Sligar. 1990. Crystal structure of myoglobin from a synthetic gene. Proteins. 7:358-365.
25. Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical algorithms of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 32: 327-341.
26. Schaad, O., H. X. Zhou, A. Szabo, W. A. Eaton, and E. R. Henry. 1993. Simulation of the kinetics of ligand binding to a protein by molecular dynamics: geminate rebinding of nitric oxide to myoglobin. Proc. Natl. Acad. Sci. USA. 90:9547-9551.
27. Schlichting, I., J. Berendzen, G. N. Phillips, Jr., and R. M. Sweet. 1994. Crystal structure of photolyzed carbon monoxy myoglobin. Nature. 371:808-812.
28. Springer, B. A., S. G. Sligar, J. S. Olson, and G. N. Phillips. Jr. 1994. Mechanism of ligand recognition in myoglobin. J. Chem. Rev. 94: 699-714.
29. Srajer, V., T. Teng, T. Ursby, C. Pradervand, Z. Ren, S. Adaci, W. Schildkamp, D. Bourgeois, M. Wulff, and K. Moffat. 1996. Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography. Science. 274:1726-1729.
30. Steinbach, P. J., and B. R. Brooks. 1994. Protein hydration elucidated by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 90: 9135-9139.
31. Straub, J. E., and M. Karplus. 1991. Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: ligand dynamics in the first 10 ps. Chem. Phys. 158:221-231.
32. Teng, T., V. Srajer, and K. Moffat. 1994. Photolysis-induced structural changes in single crystals of carbon monoxy myoglobin at 40 K. Nature Struct. Biol. 1:701-705.
33. van Gunsteren, W. F., and H. J. C. Berendsen. 1977. Algorithms for molecular dynamics and constraint dynamics. Mol. Phys. 34:1311-1327.
34. Vitkup, D., G. A. Petsko, and M. Karplus. 1997. A comparison between molecular dynamics and x-ray results for dissociated CO in myoglobin. Nature Struct. Biol. 4:202-208.
35. Weiner, S. J., P. A. Kollman, D. A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, Jr., and P. Weiner. 1984. A new force field for molecular mechanics simulation of nucleic acids and proteins. J. Am. Chem. Soc. 110:1657-1666.