Dynamics of ligand rebinding to unfolded MbCO by guanidine HCl

Biophysical Journal

Volumn 94, Issue 11, 2008, Pages

  Park, Jaeheung ^a   Kim, Jooyoung ^a   Lee, Taegon ^a   Lim, Manho ^a  

^a Pusan National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON DIOXIDE; CARBOXYMYOGLOBIN; GUANIDINE; LIGAND; MYOGLOBIN;

BINDING SITE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; KINETICS; LETTER; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING;

BINDING SITES; CARBON DIOXIDE; COMPUTER SIMULATION; GUANIDINE; KINETICS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MYOGLOBIN; PROTEIN BINDING; PROTEIN DENATURATION; PROTEIN FOLDING;

EID: 44849086442     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.108.130641     Document Type: Article

References (21)

1. Klein-Seetharaman, J., M. Oikawaz, S. B. Grimshaw, J. Winner, E. Duchardt, T. Ueda, T. Imoto, L. J. Smith, C. M. Dobson, and H. Schwalbe. 2002. Long-range interactions within a nornnative protein. Science. 295:1719-1722.
2. Dobson, C. M., A. Sali, and M. Karplus. 1998. Protein folding: a perspective from theory and experiment. Angew. Chem. Int. Ed. 37:869-893.
3. Shortle, D., and M. S. Ackerman. 2001. Persistence of native-like topology in a denatured protein in 8 M urea. Science. 293:487-489.
4. Springer, B. A., S. G. Sligar, J. S. Olson, and G. N. Phillips, Jr. 1994. Mechanisms of ligand recognition in myoglobin. Chem. Rev. 94:699-714.
5. Hargrove, M. S., and J. S. Olson. 1996. The stability of holomyoglobin is determined by heme affinity. Biochemistry. 35:11310-11318.
6. Moczygemba, C., J. Guidry, and P. Wittung-Stafshede. 2000. Heme orientation affects holo-myoglobin folding and unfolding kinetics. FEBS Lett. 470:203-206.
7. Choi, J., and M. Terazima. 2002. Denaturation of a protein monitored by diffusion coefficients. Myoglob. J. Phys. Chem. B. 106:6587-6593.
8. Kim, S., J. Heo, and M. Lim. 2005. Conformational dynamics of heme pocket in myoglobin and hemoglobin. Bull. Korean Chem. Soc. 26:151-156.
9. Henry, E. R., J. H. Sommer, J. Hofrichter, and W. A. Eaton. 1983. Geminate recombination of carbon monoxide to myoglobin. J. Mol. Biol. 166:443-451.
10. Cao, W., X. Ye, G. Y. Georgiev, S. Berezhna, T. Sjodin, A. A. Demidov, W. Wang, J. T. Sage, and P. M. Champion. 2004. Proximal and distal influences on ligand binding kinetics in microperoxidase and heme model compounds. Biochemistry. 43:7017-7027.
11. Aron, J., D. A. Baldwin, H. M. Marques, J. M. Pratt, and P. A. Adams. 1986. Hemes and hemoproteins. 1. Preparation and analysis of the heme-containing octapeptide (microperoxidase-8) and identification of the monomeric form in aqueous solution. J. Inorg. Biochem. 27: 227-243.
12. Lim, M., T. A. Jackson, and P. A. Anfinrud. 1997. Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin. Nat. Struct. Biol. 4:209-214.
13. Srajer, V., Z. Ren, T.-Y. Teng, M. Schmidt, T. Ursby, D. Bourgeois, C. Pradervand, W. Schildkamp, M. Wulff, and K. Moffat. 2001. Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue x-ray diffraction. Biochemistry. 40:13802-13815.
14. Schotte, F., J. Soman, J. S. Olson, M. Wulff, and P. A. Anfinrud. 2004. Picosecond time-resolved x-ray crystallography: probing protein function in real time. J. Struct. Biol. 147:235-246.
15. Schlichting, I., J. Berendzen, G. N. Phillips, Jr., and R. M. Sweet. 1994. Crystal structure of photolyzed carbonmonoxy-myoglobin. Nature. 371:808-812.
16. Teng, T. Y., V. Srajer, and K. Moffat. 1994. Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K. Nat. Struct. Biol. 1:701-705.
17. Jackson, T. A. 1996. Probing the dynamics of ligand motion in myoglobin and hemoglobin using time-resolved mid-IR spectroscopy. In Chemistry. Harvard University, Cambridge, MA.
18. 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.
19. -1, and it decays with a time constant of 270±50 ps, comparable to the vibrational relaxation time of CO in the primary heme pocket (21). The nascent vibrationally excited CO population was 5±1%, also similar to the value obtained in native Mb (8,18).
20. The time dependence of the integrated absorbance contains information on the GR rates, transitions among states, and the vibrational relaxation of the excited CO. The time-independent rate constants involving all rebinding from and interconversion among the three states cannot reproduce the C-state kinetics. A stretched exponential function was used to account for the diffusive nature of ligand motion and/or the distribution of rates reflecting transitions from many cavities. Since CO moving out from cavities toward D will results in immediate spectral loss, the transition rate to D from C is set time-independent. The transition rates found to be too slow to be of any consequence were set to 0. The inverse rate coefficients are given along the arrow. The values in the diffusive motion correspond to those at 0.3 ps and 1 ns.
21. Sagnella, D. E., J. E. Straub, T. A. Jackson, M. Lim, and P. A. Anfinrud. 1999. Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations. Proc. Natl. Acad. Sci. USA. 96:14324-14329.