Assigning vibrational spectra of ferryl-oxo intermediates of cytochrome C oxidase by periodic orbits and molecular dynamics

Journal of the American Chemical Society
Vangelis DaskalakisConstantinos Varotsis

Abstract

Complexity is inherent in biological molecules not only because of the large number of atoms but also because of their nonlinear interactions responsible for chaotic behaviours, localized motions, and bifurcation phenomena. Thus, versatile spectroscopic techniques have been invented to achieve temporal and spatial resolution to minimize the uncertainties in assigning the spectra of complex molecules. Can we associate spectral lines to specific chemical bonds or species in a large molecule? Can energy stay localized in a bond for a substantial period of time to leave its spectroscopic signature? These longstanding problems are investigated by studying the resonance Raman spectra of ferryl-oxo intermediates of cytochrome c oxidase. The difference spectra of isotopically substituted ferryl oxygen ((16)O minus (18)O) in the cytochrome c oxidase recorded in several laboratories show one or two prominent positive peaks which have not been completely elucidated yet. By applying the hierarchical methods of nonlinear mechanics, and particularly the study of periodic orbits in the active site of the enzyme, in conjunction with molecular dynamics calculations of larger systems which include the embraced active site by the protein and sele...Continue Reading

Citations

Jun 30, 1985·Biochimica Et Biophysica Acta·R BarbarasG Ailhaud
Oct 30, 2009·International Journal of Molecular Sciences·Vangelis Daskalakis, Constantinos Varotsis
Aug 4, 2011·Biochimica Et Biophysica Acta·Eftychia PinakoulakiConstantinos Varotsis
Oct 27, 2009·Biochimica Et Biophysica Acta·Margareta R A Blomberg, Per E M Siegbahn
Dec 8, 2009·The Journal of Physical Chemistry. B·Vangelis DaskalakisConstantinos Varotsis

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