Cytochrome [c.sub.2] exit strategy: Dissociation studies and evolutionary implications
Article Abstract:
An all-atom large-scale steered molecular dynamics (SMD) simulation is combined with evolutionary studies and binding free energy analysis in order to propose and explore dissociation pathways of cytochrome (cyt [c.sub.2]) from the reaction center (RC) of Rhodobacter sphaeroides embedded in a membrane without the light-harvesting complex I. The results have shown that the redox-dependent variations might lead to changes in structural flexibility, behavior of the interfacial water molecules and in the binding free energy of the complex.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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Ab initio molecular dynamics of heme in cytochrome c
Article Abstract:
Ab initio molecular dynamics (AIMD) calculations, based on the Car Parrinello method are performed for three models of heme c, present in cytochrome c, and both the reduced (Fe(II)) and oxidized (Fe(III)) forms are analyzed. It is found that the simplest models IR and IO with no substituent on the hema are useful in tuning up the MD simulations and establishing a direct reference for the studies of more complex systems.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2007
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Improved density functional theory/electrostatic calculation of the His291 protonation state in cytochrome c oxidase: Self-consistent charges for solvation energy calculation
Article Abstract:
The solvation energies for the cytochrome c oxidase (CcO) binuclear center were reevaluated using an improved density functional theory (DFT)/electrostatic procedure. The calculations show that including an accurate reaction field at the ab inito stage of the calculations gives rise to an increase of the absolute values of the solvation energy and these calculations support the proposed His291 model of the CcO pump.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
User Contributions:
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