The Role of Cavities in Protein Dynamics: Crystal Structure of a Photolytic Intermediate of a Mutant Myoglobin.Brunori, M., Vallone, B., Cutruzzola, F., Travaglini-Allocatelli, C., Berendzen, J., Chu, K., Sweet, R.M., Schlichting, I.
(2000) Proc.Natl.Acad.Sci.USA 97: 2058
- PubMed: 10681426
- DOI: 10.1073/pnas.040459697
- Primary Citation of Related Structures:
- PubMed Abstract:
- Crystal Structure of Myoglobin from a Synthetic Gene
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- Structural Dynamics of Liganddiffusion in the Protein Matrix: A Study on a New Myoglobin Mutant Y (B10) Q(E7) R(E10)
Brunori, M.,Cutruzzola, F.,Savino, C.,Travaglini-Allocatelli, C.,Vallone, B.,Gibson, Q.H.
(1999) Biophys.J. 76: 1259
We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the ...
We determined the structure of the photolytic intermediate of a sperm whale myoglobin (Mb) mutant called Mb-YQR [Leu-(B10)-->Tyr; His(E7)-->Gln; Thr(E10)-->Arg] to 1.4-A resolution by ultra-low temperature (20 K) x-ray diffraction. Starting with the CO complex, illumination leads to photolysis of the Fe-CO bond, and migration of the photolyzed carbon monoxide (CO*) to a niche in the protein 8.1 A from the heme iron; this cavity corresponds to that hosting an atom of Xe when the crystal is equilibrated with xenon gas at 7 atmospheres [Tilton, R. F., Jr., Kuntz, I. D. & Petsko, G. A. (1984) Biochemistry 23, 2849-2857]. The site occupied by CO* corresponds to that predicted by molecular dynamics simulations previously carried out to account for the NO geminate rebinding of Mb-YQR observed in laser photolysis experiments at room temperature. This secondary docking site differs from the primary docking site identified by previous crystallographic studies on the photolyzed intermediate of wild-type sperm whale Mb performed at cryogenic temperatures [Teng et al. (1994) Nat. Struct. Biol. 1, 701-705] and room temperature [Srajer et al. (1996) Science 274, 1726-1729]. Our experiment shows that the pathway of a small molecule in its trajectory through a protein may be modified by site-directed mutagenesis, and that migration within the protein matrix to the active site involves a limited number of pre-existing cavities identified in the interior space of the protein.
Department of Biochemical Sciences, Consiglio Nazionale delle Ricerche Centre of Molecular Biology, University "La Sapienza," 00185 Rome, Italy. firstname.lastname@example.org