Computational Modeling of the Interaction of Molecular Oxygen with the Flavin-dependent Enzyme RutA

Авторы: Polyakov I.V., Domratcheva T.M., Kulakova A.M., Nemukhin A.V., Grigorenko B.L.
Журнал: Supercomputing Frontiers and Innovations
Том: 9
Номер: 2
Год издания: 2022
Первая страница: 46
Последняя страница: 55
DOI: 10.14529/jsfi220204
Аннотация: Supercomputer molecular modeling methods are applied to characterize structure and dynamics of the flavin-dependent enzyme RutA in the complex with molecular oxygen. Followingconstruction of a model protein system, molecular dynamics (MD) simulations were carried out using either classical force field interaction potentials or the quantum mechanics/molecular mechanics (QM/MM) potentials. Several oxygen-binding pockets in the protein cavities were located inthese simulations. The QM/MM-based MD calculations rely on the interface between the quantumchemistry package TeraChem and the MD package NAMD. The results show a stable localizationof the oxygen molecule in the enzyme active site. Static QM/MM calculations carried out withtwo different packages, NWChem and TURBOMOLE, allowed us to establish the structure of theRutA-O2 complex. Biochemical perspectives of the hallmark reaction of incorporating oxygen intoorganic compounds emerged from these simulations are formulated.
Добавил в систему: Немухин Александр Владимирович

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