Structural assignment of spectra by characterization of conformational substates in bound MbCO

Biophysical Journal

Volumn 96, Issue 11, 2009, Pages 4363-4375

  Devereux, Michael ^a   Meuwly, Markus ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; CARBON MONOXIDE; CARBOXYMYOGLOBIN; IRON; MYOGLOBIN; PROTON;

ARTICLE; CONFORMATION; CONTROLLED STUDY; DIPOLE; ELECTRICITY; MOLECULAR DYNAMICS; PROTEIN STRUCTURE; PROTON TRANSPORT; QUANTUM MECHANICS; SIMULATION; SPECTROSCOPY; AMINO ACID SEQUENCE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; INFRARED SPECTROSCOPY; PROTEIN CONFORMATION; STATIC ELECTRICITY;

AMINO ACID SEQUENCE; CARBON MONOXIDE; COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; MYOGLOBIN; PROTEIN CONFORMATION; PROTONS; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; STATIC ELECTRICITY;

EID: 68949132998     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.01.064     Document Type: Article

References (49)

1. Frauenfelder, H., and B. McMahon. 2002. Hydration, slaving and protein function. Biophys. Chem. 98:35-48.
2. Yang, F., and G. N. Phillips, Jr. 1996. Crystal structures of CO-, deoxyand Met-myoglobins at various pH values. Biophys. J. 256:762-774.
3. Ansari, A., J. Berendzen, D. Braunstein, B. R. Cowen, H. Frauenfelder, et al. 1987. Rebinding and relaxation in the myoglobin pocket. Biophys. Chem. 26:337-355.
4. Johnson, J. B., D. C. Lamb, H. Frauenfelder, J. D. Mueller, B. McMahon, et al. 1996. Ligand binding to heme proteins. VI. Interconversion of taxonomic substates in carbonmonoxymyoglobin. Biophys. J. 71:1563-1573.
5. Phillips, G., M. Teodoro, T. Li, B. Smith, and J. Olson. 1999. Bound CO is a molecular probe of electrostatic potential in the distal pocket of myoglobin. J. Phys. Chem. B. 103:8817-8829.
6. Morikis, D., P. M. Champion, B. A. Springer, and S. G. Sligar. 1989. Resonance Raman investigations of site-directed mutants of myoglobin: effects of distal histidine replacement. Biochemistry. 28:4791-4800.
7. Osapay, K., Y. Theriault, P. E. Wright, and D. A. Case. 1994. Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift constraints. J. Mol. Biol. 244:183-197.
8. Merchant, K. A., W. G. Noid, D. E. Thompson, R. Akiyama, R. F. Loring, et al. 2003. Structural assignments and dynamics of the A substates of MbCO: spectrally resolved vibrational echo experiments and molecular dynamics simulations. J. Phys. Chem. B. 107:4-7.
9. Elber, R., and M. Karplus. 1987. Multiple conformational states of proteins - a molecular-dynamics analysis of myoglobin. Science. 235:318-321.
10. Kottalam, J., and D. A. Case. 1988. Dynamics of ligand escape from the heme pocket of myoglobin. J. Am. Chem. Soc. 110:7690-7697.
11. 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. 158:221-248.
12. Sagnella, D. E., and J. E. Straub. 1999. A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin. Biophys. J. 77:70-84.
13. Meuwly, M., O. M. Becker, R. Stote, and M. Karplus. 2002. NO rebinding to myoglobin: a reactive molecular dynamics study. Biophys. Chem. 98:183-207.
14. Nutt, D. R., and M. Meuwly. 2003. Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin. Biophys. J. 85:3612-3623.
15. Nutt, D. R., and M. Meuwly. 2004. CO migration in native and mutant myoglobin: atomistic simulations for the understanding of protein function. Proc. Natl. Acad. Sci. USA. 101:5998-6002.
16. Lim, M., T. A. Jackson, and P. A. Anfinrud. 1995. 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.
17. Nienhaus, K., J. S. Olson, S. Franzen, and G. U. Nienhaus. 2005. The origin of stark splitting in the initial photoproduct state of MbCO. J. Am. Chem. Soc. 127:40-41.
18. Meuwly, M. 2006. On the influence of the local environment on the CO stretching frequencies in native myoglobin: assignment of the B-states in MbCO. ChemPhysChem. 10:2061-2063.
19. Plattner, N., and M. Meuwly. 2008. The role of higher CO-multipole moments in understanding the dynamics of photodissociated carbon-monoxide in myoglobin. Biophys. J. 94:2505-2515.
20. Franzen, S. 2001. An electrostatic model for the frequency shifts in the carbonmonoxy stretching band of myoglobin: correlation of hydrogen bonding and the Stark tuning rate. J. Am. Chem. Soc. 124:13271-13280.
21. Rovira, C., B. Schulze, M. Eichinger, J. D. Evanseck, and M. Parrinello. 2001. Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study. Biophys. J. 81:435-445.
22. Müller, J. D., B. J. McMahon, E. Y. T. Chien, S. G. Sligar, and G. U. Nienhaus. 1999. Connection between the taxonomic substates and protonation of histidines 64 and 97 in carbonmonoxy myoglobin. Biophys. J. 77:1036-1051.
23. Braunstein, D. P., K. Chu, K. D. Egeberg, H. Frauenfelder, J. R. Mourant, et al. 1993. Ligand binding to heme proteins. III. FTIR studies of His-E7 and Val-E11 mutants of carbonmonoxymyoglobin. Biophys. J. 65:2447-2454.
24. Ivanov, D., J. T. Sage, M. Keim, J. R. Powell, S. A. Asher, et al. 1994. Determination of CO orientation in myoglobin by single-crystal infrared linear dichroism. J. Am. Chem. Soc. 116:4139-4140.
25. Loccisano, A., O. Acevedo, J. DeChancie, B. Schulze, and J. Evanseck. 2004. Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 ms A0 to A1-3 transition from ten 400 picosecond simulations. J. Mol. Graph. Model. 22:369-376.
26. Merchant, K. A., W. G. Noid, R. Akiyama, I. J. Finkelstein, A. Goun, et al. 2003. Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations. J. Am. Chem. Soc. 125:13804-13818.
27. Unno, M., J. F. Christian, J. S. Olson, J. T. Sage, and P. M. Champion. 1998. Evidence for hydrogen bonding effects in the iron ligand vibrations of carbonmonoxy myoglobin. J. Am. Chem. Soc. 120:2670-2671.
28. Ishikawa, H., K. Kwak, J. K. Chung, S. Kim, and M. D. Fayer. 2008. Direct observation of fast protein conformational switching. Proc. Natl. Acad. Sci. USA. 105:8619-8624.
29. Vojtechovsky, J., K. Chu, J. Berendzen, R. M. Sweet, and I. Schlichting, 1999. Crystal structures of myoglobin-ligand complexes at nearatomic resolution. Biophys. J. 77:2153-2174.
30. 3 state of carbonmonoxy myoglobin: molecular dynamics simulations, multivariate analysis, and quantum mechanical computations. J. Am. Chem. Soc. 121:6444-6454.
31. Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, et al. 1983. CHARMM: a program for macromolecular energy, minimization and dynamics calculations. J. Comput. Chem. 4:187-217.
32. MacKerell, Jr., A. D., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseck, et al. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
33. Kuriyan, J., S. Wilz, M. Karplus, and G. A. Petsko. 1986. X-ray structure and refinement of carbon-monoxy (Fe II)-myoglobin at 1.5 Angstrom resolution. J. Mol. Biol. 192:133-154.
34. Brooks, C. L., and M. Karplus. 1983. Deformable stochastic boundaries in molecular-dynamics. J. Chem. Phys. 79:6312-6325.
35. Jorgensen, W. L., J. D. 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.
36. Bader, R. F. W. 1990. Atoms in Molecules - A Quantum Theory. Oxford University Press, Oxford, UK.
37. Popelier, P. L. A. 2000. Atoms in Molecules. An Introduction. Pearson Education, London, UK.
38. Popelier, P. L. A. 1998. MORPHY98. UMIST, Manchester, England.
39. Aicken, F. M., and P. L. A. Popelier. 2000. Atomic properties of selected biomolecules. Part 1. The interpretation of atomic integration errors. Can. J. Chem. 78:415-426.
40. McQuarrie, D. A. 1976. Statistical Mechanics. Harper's Chemistry Series, New York.
41. Allen, M. P., and D. J. Tildesley. 1987. Computer Simulation of Liquids. Clarendon Press, Oxford, UK.
42. Frisch, M.J., G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, et al. 2004. Gaussian 03, Rev. C.01. Gaussian, Wallingford, CT.
43. Le Roy, R.J. 1996. LEVEL 6.1. Chem. Phys. Res. Reports CP-555R.
44. Bossa, C., A. Amadei, I. Daidone, M. Anselmi, B. Vallone, et al. 2005. Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavities. Biophys. J. 89:465-474.
45. Popelier, P. L. A., M. Devereux, and M. Rafat. 2004. The quantum topological electrostatic potential as a probe for functional group transferability. Acta Crystallogr. 60:427-433.
46. Autenrieth, F., E. Tajkhorshid, E. Baudry, and Z. Luthey-Schulten. 2004. Classical force field parameters for the heme prosthetic group of cytochrome c. J. Comput. Chem. 25:1613-1622.
47. Owrutsky, J. C., M. Li, B. Locke, and R. M. Hochstrasser. 1995. Vibrational relaxation of the CO stretch vibration in hemoglobin-CO, myoglobin-CO, and protoheme-CO. J. Phys. Chem. 99:4842-4846.
48. Li, X.-Y., and T. G. Spiro. 1988. Is bound carbonyl linear or bent in heme proteins? Evidence from resonance Raman and infrared spectroscopic data. J. Am. Chem. Soc. 110:6024-6033.
49. Park, E. S., S. S. Andrews, R. B. Hu, and S. G. Boxer. 1999. Vibrational Stark spectroscopy in proteins: a probe and calibration of electrostatic fields. J. Phys. Chem. B. 103:9813-9817.