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Protein environment facilitates O-2 binding in non-heme iron enzyme: An insight from ONIOM calculations on isopenicillin N synthase (IPNS)
Fukui Institute for Fundamental Chemistry, Kyoto University.ORCID iD: 0000-0002-1312-1202
Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan, Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322 .
2007 (English)In: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 111, no 31, 9380-9389 p.Article in journal (Refereed) Published
Abstract [en]

Binding of dioxygen to a non-heme enzyme has been modeled using the ONIOM combined quantum mechanical/molecular mechanical (QM/MM) method. For the present system, isopenicillin N synthase (IPNS), binding of dioxygen is stabilized by 8-10 kcal/mol for a QM:MM (B3LYP:Amber) protein model compared to a quantum mechanical model of the active site only. In the protein system, the free energy change of O-2 binding is close to zero. Two major factors consistently stabilize O-2 binding. The first effect, evaluated at the QM level, originates from a change in coordination geometry of the iron center. The active-site model artificially favors the deoxy state (O-2 not bound) because it allows too-large rearrangements of the five-coordinate iron site. This error is corrected when the protein is included. The corresponding effect on binding energies is 3-6 kcal/mol, depending on the coordination mode of O-2 (side-on or end-on). The second major factor that stabilizes O-2 binding is van der Waals interactions between dioxygen and the surrounding enzyme. These interactions, 3-4 kcal/mol at the MM level, are neglected in models that include only the active site. Polarization of the active site by surrounding amino acids does not have a significant effect on the binding energy in the present system.

Place, publisher, year, edition, pages
2007. Vol. 111, no 31, 9380-9389 p.
National Category
Physical Chemistry
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URN: urn:nbn:se:uu:diva-145466DOI: 10.1021/jp071878gISI: 000248480100028PubMedID: 17637052OAI: oai:DiVA.org:uu-145466DiVA: diva2:396520
Available from: 2011-02-10 Created: 2011-02-09 Last updated: 2017-12-11Bibliographically approved

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