title: Protein environment facilitates O2 binding in non-heme iron enzyme. An insight from ONIOM calculations on isopenicillin N synthase (IPNS).
abstract: 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 O2 binding is close to zero. Two major factors consistently stabilize O2 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 (O2 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 O2 (side-on or end-on). The second major factor that stabilizes O2 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.
authors.affiliation: Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.
authors.forename: Marcus
authors.initials: M
authors.lastname: Lundberg
authors.forename: Keiji
authors.initials: K
authors.lastname: Morokuma
mesh_terms: D001233:Aspergillus nidulans / Q000201:enzymology; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006418:Heme / Q000737:chemistry; D007501:Iron / Q000737:chemistry*; D008958:Models, Molecular; D015394:Molecular Structure; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism*; D010100:Oxygen / Q000737:chemistry* / Q000378:metabolism*; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins; D006418:Heme; D007501:Iron; D010088:Oxidoreductases; C038370:isopenicillin N synthetase; D010100:Oxygen