Dominant features of protein reaction dynamics: Conformational relaxation and ligand migration

Biochimica et Biophysica Acta - General Subjects

Volumn 1724, Issue 3, 2005, Pages 411-424

  Tetreau, Catherine ^a   Lavalette, Daniel ^a  

^a INSTITUT CURIE   (France)

Author keywords

Hemoproteins; Kinetics of rebinding; Laser photolysis; Ligand migration; Protein dynamics; Protein relaxation

Indexed keywords

CARBON MONOXIDE; CYTOCHROME P450; HEMOPROTEIN; LIGAND; MYOGLOBIN; XENON;

ALGORITHM; BINDING AFFINITY; CHEMICAL STRUCTURE; CONFORMATION; ENTHALPY; GAS; HYDROPHOBICITY; KINETICS; LOW TEMPERATURE; MOLECULAR DYNAMICS; PHOTOLYSIS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SHORT SURVEY; SPECTROSCOPY; STATISTICAL ANALYSIS; THERMODYNAMICS;

EID: 23144435806     PISSN: 03044165     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagen.2005.04.024     Document Type: Review

References (55)

1. D. Beece, L. Eisenstein, H. Frauenfelder, D. Good, M.C. Marden, L. Reinisch, A.H. Reynolds, L.B. Sorensen, and K.T. Yue Solvent viscosity and protein dynamics Biochemistry 19 1980 5147 5157
2. S. Yedgar, C. Tetreau, B. Gavish, and D. Lavalette Viscosity dependence of O2 escape from respiratory proteins as a function of cosolvent molecular weight Biophys. J. 68 1995 665 670
3. P. Douzou Cryobiochemistry 1977 Academic Press Inc., Ltd. London
4. R.H. Austin, K.W. Beeson, L. Eisenstein, H. Frauenfelder, and I.C. Gunsalus Dynamics of ligand binding to myoglobin Biochemistry 14 1975 5355 5373
5. D. Lavalette, and C. Tetreau Viscosity-dependent energy barriers and equilibrium conformational fluctuations in oxygen recombination with Hemerythrin Eur. J. Biochem. 177 1988 97 108
6. D. Ehrenstein, and G.U. Nienhaus Conformational substates in azurin Proc. Natl. Acad. Sci. U. S. A. 89 1992 9681 9685
7. P.J. Steinbach Two-dimensional distributions of activation enthalpy and entropy from kinetics by the maximum entropy method Biophys. J. 70 1996 1521 1528
8. P.J. Steinbach, A. Ansari, J. Berendzen, D. Braunstein, K. Chu, B.R. Cowen, D. Ehrenstein, H. Frauenfelder, J.B. Johnson, D.C. Lamb, S. Luck, J.R. Mourant, G.U. Nienhaus, P. Ormos, R. Philipp, A. Xie, and R.D. Young Ligand binding to heme proteins: connection between dynamics and function Biochemistry 30 1991 3988 4001
9. C. Tetreau, M. Tourbez, and D. Lavalette Conformational relaxation in hemoproteins: the cytochrome P450cam case Biochemistry 39 2000 14219 14231
10. A.K. Livesey, M. Delaye, P. Licinio, and J.-C. Brochon Maximum entropy analysis of dynamic parameters via the Laplace transform Faraday Discuss. Chem. Soc. 83 1987 1 12
11. A.K. Livesey, and J.-C. Brochon Analyzing the distribution of decay constants in pulse-fluorimetry using the maximum entropy method Biophys. J. 52 1987 693 706
12. D. Lavalette, C. Tetreau, J.-C. Brochon, and A. Livesey Conformational fluctuations and protein reactivity Eur. J. Biochem. 196 1991 591 598
13. P.J. Steinbach, K. Chu, H. Frauenfelder, J.B. Johnson, D.C. Lamb, G.U. Nienhaus, T.B. Sauke, and R.D. Young Determination of rate distributions from kinetic experiments Biophys. J. 61 1992 235 245
14. D.G. Lambright, S. Balasubramanian, and S.G. Boxer Dynamics of protein relaxation in site-specific mutants of human myoglobin Biochemistry 32 1993 10116 10124
15. J.B. Johnson, D.C. Lamb, H. Frauenfelder, J.D. Müller, B. McMahon, and G.U. Nienhaus Ligand binding to heme proteins: VI. Interconversion of taxonomic substates in carbonmonoxymyoglobin Biophys. J. 71 1996 1563 1573
16. C. Tetreau, Y. Blouquit, E. Novikov, E. Quiniou, and D. Lavalette Competition with xenon elicits ligand migration and escape pathways in myoglobin Biophys. J. 86 2004 435 447
17. C. Tetreau, C. Di Primo, R. Lange, H. Tourbez, and D. Lavalette Dynamics of carbon monoxide binding with cytochromes P-450 Biochemistry 36 1997 10262 10275
18. C. Tetreau, L. Mouawad, S. Murail, P. Duchambon, Y. Blouquit, and D. Lavalette Disentangling ligand migration and heme pocket relaxation in cytochrome P450cam Biophys. J. 86 2004 1250 1263
19. E.E. Scott, and Q.H. Gibson Ligand migration in sperm whale myoglobin Biochemistry 36 1997 11909 11917
20. E.E. Scott, Q.H. Gibson, and J.S. Olson Mapping the pathways for O2 entry into and exit from myoglobin J. Biol. Chem. 276 2001 5177 5188
21. I. Schlichting, J. Berendzen, G.N. Phillips Jr., and R.M. Sweet Crystal structure of photolysed carbonmonoxy-myoglobin Nature 371 1994 808 812
22. H. Hartmann, S. Zinser, P. Komninos, R.T. Schneider, G.U. Nienhaus, and F. Parak X-ray structure determination of a metastable state of carbonmonoxy myoglobin after photodissociation Proc. Natl. Acad. Sci. U. S. A. 93 1996 7013 7016
23. K. Chu, J. Vojtechovsky, B.H. McMahon, R.M. Sweet, J. Berendzen, and I. Schlichting Structure of a ligand-binding intermediate in wild-type carbonmonoxymyoglobin Nature 403 2000 921 923
24. V. Srajer, T.-Y. Teng, T. Ursby, C. Praverdand, Z. Ren, S.-I. Adachi, W. Schildkamp, D. Bourgeois, M. Wulff, and K. Moffat Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography Science 274 1996 1726 1729
25. V. Srajer, Z. Ren, T.-Y. Teng, M. Schmidt, T. Ursby, D. Bourgeois, C. Pradervand, W. Schildkamp, M. Wulff, and K. Moffat Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond movie from time-resolved Laue X-ray diffraction Biochemistry 40 2001 13802 13815
26. D. Bourgeois, B. Vallone, F. Schotte, A. Arcovito, A.E. Miele, G. Sciara, M. Wulff, P. Anfinrud, and M. Brunori Complex lanscape of protein structural dynamics unveiled by nanosecond Laue Crystallography Proc. Natl. Acad. Sci. U. S. A. 100 2003 8704 8709
27. F. Schotte, M. Lim, T.A. Jackson, A.V. Smirnov, J. Soman, J.S. Olson, G.N. Phillips Jr., M. Wulff, and P.A. Anfinrud Watching a protein as it functions with 150-ps time-resolved X-ray crystallography Science 300 2003 1944 1947
28. J.O. Alben, D. Beece, S.F. Bowne, W. Doster, L. Eiseinstein, H. Frauenfelder, D. Good, J.D. McDonald, M.C. Marden, P.P. Moh, L. Reinisch, A. Reynolds, E. Shyamsunder, and K.T. Yue Infrared spectroscopy of photodissociated carboxymyoglobin at low temperatures Proc. Natl. Acad. Sci. U. S. A. 79 1982 3744 3748
29. J. Vojtechovsky, K. Chu, J. Berendzen, R.M. Sweet, and I. Schlichting Crystal structures of myoglobin-ligand complexes at near-atomic resolution Biophys. J. 77 1999 2153 2174
30. F. Yang, and J.G.N. Phillips Crystal structures of CO-, deoxy- and met-myoglobins at various pH values J. Mol. Biol. 256 1996 762 774
31. A. Ansari, J. Berendzen, D. Braunstein, B.R. Cowen, H. Frauenfelder, M.K. Hong, I.E.T. Iben, J.B. Johnson, P. Ormos, T.B. Sauke, R. Scholl, A. Schulte, P.J. Steinbach, J. Vittitow, and R.D. Young Rebinding and relaxation in the myoglobin pocket Biophys. Chem. 26 1987 337 355
32. W.T. Potter, M.P. Tucker, R.A. Houtchens, and W.S. Caughey Oxygen infrared spectra of oxyhemoglobins and oxymyoglobins. Evidence of two major liganded O2 structures Biochemistry 26 1987 4699 4707
33. C. Tetreau, E. Novikov, M. Tourbez, and D. Lavalette Kinetic evidence for three photolyzable taxonomic conformational substates in oxymyoglobin Biophys. J. 82 2002 2148 2155
34. M.K. Hong, D. Braunstein, B.R. Cowen, H. Frauenfelder, I.E. Iben, J.R. Mourant, P. Ormos, R. Scholl, A. Schulte, P.J. Steinbach, A.-H. Xie, and R.D. Young Conformational substates and motions in myoglobin. External influences on structure and dynamics Biophys. J. 58 1990 429 436
35. C. Jung, and F. Marlow Dynamic behavior of the active site structure in bacterial cytochrome P-450 Stud. Biophys. 120 1987 241 251
36. C. Jung, O. Ristau, H. Schulze, and S.G. Sligar The CO stretching mode infrared spectrum of substrate-free cytochrome P-450cam-CO. The effect of solvent conditions, temperature and pressure Eur. Biochem. J. 235 1996 660 669
37. C. Tetreau, M. Tourbez, A. Gorren, B. Mayer, and D. Lavalette Dynamics of carbon monoxide binding with neuronal nitric oxide synthase Biochemistry 38 1999 7210 7218
38. T.L. Poulos, B.C. Finzel, and A.J. Howard High-resolution crystal structure of cytochrome P450cam J. Mol. Biol. 195 1987 687 700
39. R. Raag, and T.L. Poulos Crystal structure of the carbon-monoxide- substrate-cytochrome P-450cam ternary complex Biochemistry 28 1989 7586 7592
40. A. Ostermann, R. Waschipky, F.G. Parak, and G.U. Nienhaus Ligand binding and conformational motions in myoglobin Nature 404 2000 205 208
41. R.F. Tilton, I.D. Kuntz, and G.A. Petsko Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 Å Biochemistry 23 1984 2849 2857
42. M. Brunori, F. Cutruzzola, C. Savino, C. Travaglini-Allocatelli, B. Vallone, and Q.H. Gibson Structural dynamics of ligand diffusion in the protein matrix: a study on a new myoglobin mutant Y(B10) Q(E7) R(E10) Biophys. J. 76 1999 1259 1269
43. F. Draghi, A.E. Miele, C. Travaglini-Allocatelli, B. Vallone, M. brunori, Q.H. Gibson, and J.S. Olson Controlling ligand binding in myoglobin by mutagenesis J. Biol. Chem. 277 2002 7509 7519
44. H. Ishikawa, T. Uchida, S. Takahashi, K. Ishimori, and I. Morishima Ligand migration in human myoglobin: steric effects of isoleucine 107(G8) on O2 and CO binding Biophys. J. 80 2001 1507 1517
45. M.L. Quillin, T. Li, J.S. Olson, G.N. Phillips Jr., Y. Dou, M. Ikeda-Saïto, R.M. Regan, M. Carlson, Q.H. Gibson, H. Li, and R. Elber Structural and functional effects of apolar mutations of the distal valine in myoglobin J. Mol. Biol. 245 1995 416 436
46. M.L. Carlson, R. Regan, R. Elber, H. Li, G.N. Phillips, J.S. Olson, and Q.H. Gibson Nitric oxide recombination to double mutants of myoglobin: role of ligand diffusion in a fluctuating heme pocket Biochemistry 33 1994 10597 10606
47. R. Elber, and M. Karplus 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 1990 9161 9175
48. Q.H. Gibson, R. Regan, R. Elber, J.S. Olson, and T.E. Carver Distal pocket residues affect picosecond ligand recombination in myoglobin J. Biol. Chem. 267 1992 22022 22034
49. H. Li, R. Elber, and J.E. Straub Molecular dynamics simulation of NO recombination to myoglobin mutants J. Biol. Chem. 268 1993 17908 17916
50. M.L. Carlson, R.M. Regan, and Q.H. Gibson Distal cavity fluctuations in myoglobin: protein motion and ligand diffusion Biochemistry 35 1996 1125 1136
51. K. Nienhaus, P. Deng, J.M. Kriegl, and G.U. Nienhaus Structural dynamics of myoglobin: spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W Biochemistry 42 2003 9633 9646
52. K. Nienhaus, P. Deng, J.M. Kriegl, and G.U. Nienhaus Structural dynamics of myoglobin: effect of internal cavities on ligand migration and binding Biochemistry 42 2003 9647 9658
53. D.D. Dlott, H. Frauenfelder, P. Langer, H. Roder, and E.E. DiIorio Nanosecond flash photolysis study of carbon monoxide binding to the b chain of hemoglobin Zürich [b63(E7)His→Arg] Proc. Natl. Acad. Sci. U. S. A. 80 1983 6239 6243
54. T. Kleinert, W. Doster, H. Leyser, W. Petry, V. Schwarz, and M. Settles Solvent composition and viscosity effects on the kinetics of CO binding to horse myoglobin Biochemistry 37 1998 717 733
55. G. Hummer, F. Schotte, and P.A. Anfinrud Unveiling functional protein motions with picosecond X-ray crystallography and molecular dynamics simulations Proc. Natl. Acad. Sci. U. S. A. 101 2004 15330 15334