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Protein Free Energy Corrections in ONIOM QM:MM Modeling: A Case Study for Isopenicillin N Synthase (IPNS)
Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.
Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan.ORCID iD: 0000-0002-1312-1202
Kyoto Univ, Fukui Inst Fundamental Chem, Sakyo Ku, Kyoto 6068103, Japan; Emory Univ, Cherry L Emerson Ctr Sci Computat, Atlanta, GA 30322 USA; Emory Univ, Dept Chem, Atlanta, GA 30322 USA.
2011 (English)In: Journal of Chemical Theory and Computation, ISSN 1549-9618, E-ISSN 1549-9626, Vol. 7, no 2, 390-401 p.Article in journal (Refereed) Published
Abstract [en]

The protein environment can have significant effects on the enzyme catalysis even though the reaction occurs locally at the reaction center. In this paper, we describe an efficient scheme that includes a classical molecular dynamics (MD) free-energy perturbation (FEP) correction to the reaction energy diagram, as a complement to the protein effect obtained from static ONIOM (QM:MM) calculations. The method is applied to eight different reaction steps, from the O2-bound reactant to formation of a high-valent ferryl-oxo intermediate, in the nonheme iron enzyme isopenicillin N synthase (IPNS), for which the QM:MM energy diagram has previously been computed [ Lundberg, M. et al. J. Chem. Theory Comput. 2009, 5, 220 ‚àí 234 ]. This large span of the reaction coordinate is covered by dividing each reaction step into microsteps using a virtual reaction coordinate, thus only requiring ONIOM information about the stationary points themselves. Protein effects are important for C‚àíH bond activation and heterolytic O‚àíO bond cleavage because both these two steps involve charge transfer, and compared to a static QM:MM energies, the dynamics of the protein environment changes the barrier for O‚àíO bond cleavage by several kcal/mol. The origin of the dynamical contribution is analyzed in two terms, the geometrical effect caused by the change in average protein geometry (compared to the optimized geometry) in the room temperature MD simulation with the solvent, and the statistical (entropic) effect resulting from fluctuations in the interactions between the active site and the protein environment. These two effects give significant contributions in different steps of the reaction.

Place, publisher, year, edition, pages
American Chemical Society , 2011. Vol. 7, no 2, 390-401 p.
National Category
Chemical Sciences
URN: urn:nbn:se:uu:diva-145460DOI: 10.1021/ct1005592ISI: 000287049200014PubMedID: 26596161OAI: oai:DiVA.org:uu-145460DiVA: diva2:396524
Available from: 2011-02-10 Created: 2011-02-09 Last updated: 2016-10-28

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