Protein effects on the O₂ binding to the active site of the methane monooxygenase: ONIOM studies

Abstract

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 vacuo 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.

Ab initioquantum chemistry: Methodology and applications

“…Ab initio calculations provide a wealth of detail that is not available from experiment and a degree of confidence in the results that is not available from more empirical approaches. In systems such as methane monooxygenase, in which a substantial number of careful calculations have been performed by several groups (81,(91)(92)(93)(94)(95)(96) and close contact with experiment has been achieved for many aspects of the catalytic process, a comprehensive picture of the functioning of the enzyme is beginning to be assembled by means of the interaction of theory and experiment. Last, the coupling of ab initio quantum QM͞MM methods with simulation and protein structure prediction techniques permits investigation of events in which reactive chemistry is coupled to substantial conformational changes, such as the catalytic loop motion in triose phosphate isomerase (82).…”

Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors

“…Despite various limitations and crude approximations molecular mechanics (MM) and molecular dynamics (MD) methods have been used to study a wide variety of phenomena, including structure and dynamics of simple and complex structures, thermodynamics of ligands binding to proteins, conformational transitions in nucleic acids, and many others [11][12][13][14][15][16][17][18][19][20][21]. Recent developments in hybrid quantum mechanics (QM) and MM method created new opportunities in more accurate assessment of interaction energies [22][23][24][25]. In particular ONIOM method nicely resolved problems with QM and MM boundary and was successfully utilized in studies on mechanism of enzymatic reactions or calculations of interaction energies between proteins and their ligands [26][27][28][29][30][31].…”

Intermediates in Dioxygen Activation by Methane Monooxygenase: A QM/MM Study

“…Indeed, all previous QM models have consistently computed a substantially larger iron-iron distance than those found experimentally, and including second sphere ligands or electrostatic effects of the protein and solvent in a continuum model, did not entirely solve this problem. 19,41,44,50 To understand the origin of the short Fe-Fe distance found in the current study, we analyze our data and determine the forces acting on the various atoms of our QM/MM//RDFT model. The calculations of forces were carried out in vacuum and with point charges in place of MM atoms to distinguish electrostatic from strain effects of the protein.…”

“…It has also been observed for H red using ONIOM methods 50 but, whereas with our QM/MM methodology the agreement with the experimental Fe-Fe distance is very good (~ 0.02 Å), the results with ONIOM method were significantly less accurate (0.15-0.25 Å), probably due to quantitative errors in the QM/MM interface model employed in ref. [ 50 ].…”