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Volumn 130, Issue 45, 2008, Pages 15002-15021

Toward a chemical mechanism of proton pumping by the B-type cytochrome c oxidases: Application of density functional theory to cytochrome ba3 of Thermus thermophilus

Author keywords

[No Author keywords available]

Indexed keywords

CARBON NANOTUBES; COPPER; ELECTRIC POWER PLANTS; IRON COMPOUNDS; LIPID BILAYERS; PORPHYRINS; PROBABILITY DENSITY FUNCTION; PROTONS; REDUCTION; STRUCTURAL OPTIMIZATION;

EID: 57349108758     PISSN: 00027863     EISSN: None     Source Type: Journal    
DOI: 10.1021/ja803112w     Document Type: Article
Times cited : (64)

References (162)
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    • Experimentally, the Fe-Cu distance in ba3-oxidase increases from ∼4.4 Å in the "as-isolated" structure to ∼5.2 Å in the chemically reduced, carbonylated form of the enzyme (B. Liu, Y. Chen, J. A. Fee, and C. D. Stout, unpublished observations). In the "4.4 Å structures", the bridging peroxo intermediates (4 and 5) exhibited the unusual behavior, during SCF geometry optimization (see Methods), of producing a very short O-O distance, more typical of dioxygen (∼1.2 Å) than of hydrogen peroxide (∼1.4 Å), whereas in the "5.2 A structure", geometry optimized structure 4 shows Fe-O at 1.97, Cu-O at 2.12, and O-O at 1.35 Å. One might expect the metal-metal distance to change somewhat during catalysis and that fixing the Fe-Cu distance might also introduce unaccounted strain. However, there is at present no realistic way to permit such motions in the theoretical model.
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    • Dr. B. Liu has re-refined the original data of Dr. L. Hunsicker-Wang, finding that the data support an I-His384 NE-to-Fe distance of 1.9 Å, as opposed to the value of 2.4 Å in the original publication (B. Liu, J. A. Fee, and C. D. Stout, unpublished observations).
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    • pump), which is ∼0.46 for the theoretical process and ∼0.36 if the experimental, overall reaction free energy of-38.7 kcal/mol is considered.
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