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First principles calculation of the reaction rates for ligand binding to myoglobin: the cases of NO and CO

Lábas, Anikó and Menyhárd, K Dóra and Harvey, Jeremy N and Oláh, Julianna (2018) First principles calculation of the reaction rates for ligand binding to myoglobin: the cases of NO and CO. CHEMISTRY-A EUROPEAN JOURNAL, 24 (20). pp. 5350-5358. ISSN 0947-6539

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Abstract

Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2, CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spin-forbidden reaction between high-spin iron(II) and the ligand yielding a low spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. As it involves several steps occurring on different time-scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiment and revealed that the bottle-neck of NO and CO binding is different: for NO diffusion was found to be rate-limiting, while for CO the spin-forbidden step is the slowest.

Item Type: Article
Subjects: Q Science / természettudomány > QD Chemistry / kémia > QD02 Physical chemistry / fizikai kémia
Q Science / természettudomány > QD Chemistry / kémia > QD03 Inorganic chemistry / szervetlen kémia
Depositing User: Dr. Julianna Oláh
Date Deposited: 12 Sep 2018 11:58
Last Modified: 12 Sep 2018 12:27
URI: http://real.mtak.hu/id/eprint/83546

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