Assigning Vibrational Spectra of Ferryl-Oxo Intermediates of Cytochrome c Oxidase by Periodic Orbits and Molecular Dynamics.
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 tempo...
| Publicado en: | Journal of the American Chemical Society Vol. 130; no. 37; pp. 12385 - 12394 |
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| Autores principales: | , , |
| Formato: | Artículo |
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American Chemical Society
9/17/2008
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| Acceso en línea: | Ver este registro en EBSCOhost |
| fields | @attributes: recordID: 1 pdfLink: plink: https://search.ebscohost.com/login.aspx?direct=true&db=hlh&AN=34543303&site=ehost-live header: @attributes: shortDbName: hlh uiTerm: 34543303 longDbName: Humanities International Complete uiTag: AN controlInfo: bkinfo: jinfo: jid: 00027863 ACS jtl: Journal of the American Chemical Society issn: 00027863 maglogo: N pubinfo: dt: 9/17/2008 vid: 130 iid: 37 pid: 997 pub: American Chemical Society artinfo: ui: 34543303 10.1021/ja801840y ppf: 12385 ppct: 9 formats: tig: atl: Assigning Vibrational Spectra of Ferryl-Oxo Intermediates of Cytochrome c Oxidase by Periodic Orbits and Molecular Dynamics. aug: au: Daskalakis, Vangelis Farantos, Stavros C. Varotsis, Constantinos affil: Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1527, 7/110, Voutes-Heraklion, Crete, Greece Department of Chemistry, University of Crete, P.O. Box 2208, 71305, Voutes-Heraklion, Crete, Greece su: Biomolecules Polyatomic molecules Biocomplexity Cytochrome oxidase Vibrational spectra Molecular dynamics Chemical bonds Resonance Raman effect sug: subj: Biomolecules Polyatomic molecules Biocomplexity Cytochrome oxidase Vibrational spectra Molecular dynamics Chemical bonds Resonance Raman effect ab: 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 spacial 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 ([sup16]O minus [sup18]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 selected protonated/deprotonated conformations of amino acids, we translate the spectral lines to molecular motions. It is demonstrated that for the active site stable periodic orbits exist for a substantial energy range. Families of periodic orbits which are associated with the vibrations of F[supIV]=O bond mark the regions of phase space where nearby trajectories remain localized, as well as assign the spectral bands of the active site in the protein matrix. We demonstrate that proton movement adjacent to active site, which occurs during the P ↠ F transition, can lead to significant perturbations of the Fe[supIV]=O isotopic difference vibrational spectra in cytochrome C oxidase, without a change in oxidation state of the metal sites. This finding links spectroscopic characteristics to protonation events occurring during enzymatic turnover. pubtype: Academic Journal doctype: Article src: R language: English refInfo: copyright: @attributes: flag: Y dt: @attributes: year: 2008 holdings: @attributes: islocal: N |
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