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  • Title: Ab initio calculations on iron-porphyrin model systems for intermediates in the oxidative cycle of cytochrome P450s.
    Author: de Groot MJ, Havenith RW, Vinkers HM, Zwaans R, Vermeulen NP, van Lenthe JH.
    Journal: J Comput Aided Mol Des; 1998 Mar; 12(2):183-93. PubMed ID: 9690176.
    Abstract:
    Geometry optimizations for several spin states of the iron(III)-S-methyl- porphyrin complex, the iron (III)-oxo-S-methyl-porphyrin complex and the respective anions were performed in order to examine models for intermediates in the oxidative cycle of cytochrome P450. The aim of this study was to obtain insights into the ground states of the intermediates of this catalytic cycle and to use the ab initio calculated geometries and charge distributions to suggest better and more realistic parameters for forcefields which are generally used for modeling P450s. The results indicate that the ground states of both the iron(III)-S-methyl-porphyrin complex and the iron(III)-oxo-S-methyl-porphyrin complex are sextet spin states (high spin). The ground states of the anions of both complexes are probably quintet spin states. The fact that experimentally a shift from low spin to high spin is observed upon binding of the substrate suggests that the ab initio calculations for the iron(III)-S-methyl-porphyrin complex in vacuum give a correct representation of the (hydrophobic) substrate-bound state of the active site of P450. The ab initio geometries of the iron-porphyrin complexes are very similar to the experimentally observed geometries, except for the longer iron-sulfur bond in ab initio calculations, which is probably caused by the omission of polarization functions on the sulfur atom during the geometry optimization. The charge distribution in all ab initio calculated complexes can be described by a series of concentric rings of alternating charge, thus allowing a relatively large positive charge on the iron atom. The commonly used forcefields generally underestimate the charge differences between the iron atom and the different parts of the porphyrin moiety or ignore the charges completely. Although forcefield calculations can reproduce the experimental geometry of iron-porphyrin moieties, extension of the forcefields with charges obtained from ab initio calculations should give a better description of the heme moiety in protein modeling and docking experiments.
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