Protein effects on the O 2 binding to the active site of the methane monooxygenase: ONIOM studies

Abstract

The protein effects on the initial step of O 2 binding to the diiron active site in the Methane Monooxygenase (MMO) were studied at the ONIOM(QM:MM) level with and without electronic embedding. The significant part of the hydroxylase component of MMO, every aminoacid residue at least one atom of which is within 11 Å radius from either of the iron-centers of the active site, was included into the calculations. The computed "real" system contained almost 1200 atoms and we treated it at, ONIOM low level, Amber molecular mechanics force field. Position of every atom of each amino acid residue within 7-Å radius from either of the iron atoms as well as all hydrogen atoms was optimized. The "model" system, treated at the B3LYP/lan12dz level (ONIOM high level) encompassed 44 atoms including: (i) two iron atoms, (ii) functional groups forming first coordination sphere, such as two water molecules, two imodazoles, two bridging (between the Fe atoms) and two terminal carboxylates, as well as (iii) the dioxygen molecule. The comparison of the obtained results in vacua and in protein, both with and without electronic embedding, clearly indicates that the protein profoundly affects initial binding of dioxygen molecule to the diiron center of the MMOH red. It was shown that at the early stages methane monooxygenase protein environment plays a crucial role as it effectively facilitates the activation of the dioxygen molecule. Furthermore, the obtained results demonstrated the usefulness of the ONIOM approach in studying such large systems including a dozen of hundreds atoms. © 2004 Wiley Periodicals, Inc.