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Conformational Dynamics of Heme Pocket in Myoglobin and Hemoglobin

  • Kim, Seong-Heun (Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University) ;
  • Heo, Jeong-Hee (Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University) ;
  • Lim, Man-Ho (Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University)
  • Published : 2005.01.20

Abstract

The conformational dynamics of heme pocket, a small vacant site near the binding site of heme proteins -myoglobin (Mb) and hemoglobin (Hb), was investigated after photolysis of carbon monoxide from MbCO and HbCO in D$_2$O solution at 283 K by probing time-resolved vibrational spectra of photolyzed CO. Two absorption bands, arising from CO in the heme pocket, evolve nonexponentially in time. The band at higher energy side blue shifts and broadens with time and the one at lower energy side narrows significantly with a negligible shift. These spectral evolutions are induced by protein conformational changes following photolysis that modify structure and electric field of heme pocket, and ligand dynamics in it. The conformational changes affecting the spectrum of photolyzed CO in heme pocket likely modulates ligand-binding activity.

Keywords

References

  1. Springer, B. A.; Sligar, S. G.; Olson, J. S.; Phillips, G. N., Jr. Chem. Rev. 1994, 94, 699 https://doi.org/10.1021/cr00027a007
  2. Perutz, M. F.; Mathews, F. S. J. Mol. Biol. 1966, 21, 199 https://doi.org/10.1016/0022-2836(66)90088-X
  3. Takano, T. J. Mol. Biol. 1977, 110, 569 https://doi.org/10.1016/S0022-2836(77)80112-5
  4. Stryer, L. Biochemistry; W. H. Freeman and Co.: San Francisco, 1988; Vol. 3rd
  5. Swiss-Prot Protein Database; National Center of Biotechnology Information: Bethesda, 1994
  6. Lim, M.; Jackson, T. A.; Anfinrud, P. A. J. Chem. Phys. 1995, 102, 4355 https://doi.org/10.1063/1.469484
  7. Lim, M.; Jackson, T. A.; Anfinrud, P. A. Science 1995, 269, 962 https://doi.org/10.1126/science.7638619
  8. Lim, M.; Jackson, T. A.; Anfinrud, P. A. Nature Struct. Biol. 1997, 4, 209 https://doi.org/10.1038/nsb0397-209
  9. Luisi, B.; Liddington, B.; Fermi, G.; Shibayama, N. J. Mol. Biol. 1990, 214, 7 https://doi.org/10.1016/0022-2836(90)90139-D
  10. Phillips, S. E. V. J. Mol. Biol. 1980, 142, 531 https://doi.org/10.1016/0022-2836(80)90262-4
  11. Shaanan, B. J. Mol. Biol. 1983, 171, 31 https://doi.org/10.1016/S0022-2836(83)80313-1
  12. Agmon, N.; Hopfield, J. J. J. Chem. Phys. 1983, 79, 2042 https://doi.org/10.1063/1.445988
  13. Kuczera, K.; Lambry, J. C.; Martin, J. L.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5805
  14. Lim, M.; Jackson, T. A.; Anfinrud, P. A. Proc. Natl. Acad. Sci. U.S.A. 1993, 90, 5801
  15. Petrich, J. W.; Lambry, J. C.; Kuczera, K.; Karplus, M.; Poyart, C.; Martin, J. L. Biochemistry 1991, 30, 3975 https://doi.org/10.1021/bi00230a025
  16. Hagen, S. J.; Hofrichter, J.; Eaton, W. A. J. Phys. Chem. 1996, 100, 12008 https://doi.org/10.1021/jp960219t
  17. Steinbach, P. J.; Ansari, A.; Berendzen, J.; Braunstein, D.; Chu, K.; Cowen, B. R.; Ehrenstein, D.; Frauenfelder, H.; Johnson, J. B. et al. Biochemistry 1991, 30, 3988 https://doi.org/10.1021/bi00230a026
  18. Tian, W. D.; Sage, J. T.; Srajer, V.; Champion, P. M. Phys. Rev. Lett. 1992, 68, 408 https://doi.org/10.1103/PhysRevLett.68.408
  19. Deak, J.; Chiu, H.; Lewis, C. M.; Miller, R. J. D. J. Phys. Chem. B 1998, 102, 6621 https://doi.org/10.1021/jp980492q
  20. Genberg, L.; Richard, L.; McLendon, G.; Miller, R. J. D. Science 1991, 251, 1051 https://doi.org/10.1126/science.1998121
  21. Findsen, E. W.; Scott, T. W.; Chance, M. R.; Friedman, J. M.; Ondrias, M. R. J. Am. Chem. Soc. 1985, 107, 3355 https://doi.org/10.1021/ja00297a056
  22. Causgrove, T. P.; Dyer, R. B. Biochemistry 1993, 32, 11985 https://doi.org/10.1021/bi00096a007
  23. Causgrove, T. P.; Dyer, R. B. J. Phys. Chem. 1996, 100, 3273 https://doi.org/10.1021/jp952483c
  24. Kim, S.; Jin, G.; Lim, M. Bull. Korean Chem. Soc. 2003, 24, 1470 https://doi.org/10.5012/bkcs.2003.24.10.1470
  25. Brunori, M.; Vallone, B.; Cutruzzola, F.; Travaglini-Allocatelli, C.; Berendzen, J.; Chu, K.; Sweet, R. M.; Schlichting, I. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 2058
  26. Chu, K.; Vojtchovsky, J.; McMahon, B. H.; Sweet, R. M.; Berendzen, J.; Schlichting, I. Nature 2000, 403, 921 https://doi.org/10.1038/35002641
  27. Schott, F.; Lim, M.; Jackson, T. A.; Smirnov, A.; Soman, J.; Olson, J. S.; George, N.; Phillips, J.; Wulff, M.; Anfinrud, P. A. Science 2003, 300, 1944 https://doi.org/10.1126/science.1078797
  28. Lim, M.; Jackson, T. A.; Anfinrud, P. A. J. Am. Chem. Soc. 2004, 126, 7946 https://doi.org/10.1021/ja035475f
  29. Anfinrud, P. A.; Lim, M.; Jackson, T. A. Proc. SPIE-Int. Soc. Opt. Eng. (Longer Wavelength Lasers and Applications) 1994, 2138, 107
  30. Kim, S.; Jin, G.; Lim, M. J. Phys. Chem. B 2005, ASAP
  31. Lim, M.; Wolford, M. F.; Hamm, P.; Hochstrasser, R. M. Chem. Phys. Lett. 1998, 290, 355 https://doi.org/10.1016/S0009-2614(98)00533-8
  32. Hamm, P.; Lim, L.; Hochstrasser, R. M. J. Phys. Chem. B 1998, 102, 6123 https://doi.org/10.1021/jp9813286
  33. Hamm, P.; Kaindl, R. A.; Stenger, J. Opt. Lett. 2000, 25, 1798 https://doi.org/10.1364/OL.25.001798
  34. Lim, M. Bull. Korean Chem. Soc. 2002, 23, 865 https://doi.org/10.5012/bkcs.2002.23.6.865
  35. Alben, J. O.; Beece, D.; Bowne, S. F.; Doster, W.; Eisenstein, L.; Frauenfelder, H.; Good, D.; McDonald, J. D.; Marden, M. C.; Mo, P. P.; Reinisch, L.; Reynolds, A. H.; Shyamsunder, E.; Yue, K. T. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 3744
  36. Anfinrud, P. A.; Han, C.; Hochstrasser, R. M. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 8387
  37. Petrich, J. W.; Poyart, C.; Martin, J. L. Biochemistry 1988, 27, 4049 https://doi.org/10.1021/bi00411a022
  38. Henry, E. R.; Sommer, J. H.; Hofrichter, J.; Eaton, W. A. J. Mol. Biol. 1983, 166, 443 https://doi.org/10.1016/S0022-2836(83)80094-1
  39. Lian, T.; Locke, B.; Kholodenko, Y.; Hochstrasser, R. M. J. Phys. Chem. 1994, 98, 11648 https://doi.org/10.1021/j100096a005
  40. Venyaminov, S. Y.; Prendergast, F. G. Anal. Biochem. 1997, 248, 234 https://doi.org/10.1006/abio.1997.2136
  41. Li, P.; Champion, P. M. Biophys. J. 1994, 66, 430 https://doi.org/10.1016/S0006-3495(94)80793-3
  42. Lim, M.; Jackson, T. A.; Anfinrud, P. A. J. Phys. Chem. 1996, 100, 12043 https://doi.org/10.1021/jp9536458
  43. Lingle, R., Jr.; Xu, X.; Zhu, H.; Yu, S. C.; Hopkins, J. B. J. Phys. Chem. 1991, 95, 9320 https://doi.org/10.1021/j100176a053
  44. Lingle, R., Jr.; Xu, X.; Zhu, H.; Yu, S. C.; Hopkins, J. B.; Straub, K. D. J. Am. Chem. Soc. 1991, 113, 3992 https://doi.org/10.1021/ja00010a052
  45. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: a Theoretical Perspective of Dynamics, Structure and Thermodynamics; John Wiley & Sons: New York, 1988
  46. Jackson, T. A.; Lim, M.; Anfinrud, P. A. Chem. Phys. 1994, 180, 131 https://doi.org/10.1016/0301-0104(93)E0414-Q
  47. Ansari, A.; Jones, C. M.; Henry, E. R.; Hofrichter, J.; Eaton, W. A. Biochemistry 1994, 33, 5128 https://doi.org/10.1021/bi00183a017
  48. Murray, L. P.; Hofrichter, J.; Henry, E. R.; Eaton, W. A. Biophy. Chem. 1988, 29, 63 https://doi.org/10.1016/0301-4622(88)87025-X
  49. Meuwly, M.; Becker, O. M.; Stote, R.; Karplus, M. Biophys. Chem. 2002, 98, 183 https://doi.org/10.1016/S0301-4622(02)00093-5
  50. McMahon, M. T.; deDios, A. C.; Godbout, N.; Salzmann, R.; Laws, D. D.; Le, H.; Havlin, R. H.; Oldfield, E. J. Am. Chem. Soc. 1998, 120, 4784 https://doi.org/10.1021/ja973272j
  51. Rudolph, S. A.; Boyle, S. O.; Dresden, C. F.; Gill, S. J. Biochemistry 1972, 11, 1098 https://doi.org/10.1021/bi00756a024
  52. Srajer, V.; Champion, P. M. Biochemistry 1991, 30, 7390 https://doi.org/10.1021/bi00244a005

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