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Title
| - Ab Initio Molecular Dynamics of Heme in Cytochrome c
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Abstract
| - Ab initio molecular dynamics (AIMD) calculations, based on the Car−Parrinello method, have been carriedout for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstitutedporphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Densityfunctional theory optimizations of these models confirm the basic electronic features and are the startingpoint for building more complex derivatives. AIMD simulations were performed after reaching the thermalstability at T = 300 K. The evolution of the Fe−Lax bond strengths is examined together with the relativerotations of the imidazole and methionine about the axial vector, which appear rather independent from eachother. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site.It is observed that two adjacent propionate groups induce some important effects. The axial Fe−Sδ bond isonly weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligandseems to be reduced by the formation of a strong hydrogen bond that involves the Im Nδ1−Hδ1 bond andone carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionicacid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of theprotein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogenbonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulatethe dissociation of the methionine from the heme.
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