Molecule dynamics and combined QM/MM study on one-carbon unit transfer reaction catalyzed by GAR transformylase |
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| Authors: | Qing-An Qiao Yueqing Jin Zhengting Cai Rongjun Qu Chuanlu Yang Meishan Wang |
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| Institution: | (1) School of Chemistry and Materials Science, Yantai Normal University, 264025 Yantai, China;(2) Library of Yantai Normal University, 264025 Yantai, China;(3) Institute of Theoretical Chemistry, Shandong University, 250100 Jinan, China;(4) Department of Physics, Yantai Normal University, 264025 Yantai, China |
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| Abstract: | Both a molecule dynamic study and a combined quantum mechanics and molecule mechanics (QM/MM) study on Glycinamide ribonucleotide
transformylase (GAR Tfase) catalytic mechanism are presented. The results indicate a direct one-carbon unit transfer process
but not a stepwise mechanism in this reaction. The residues near the active center can fix the cofactor (N10-formyltetrahydrofolate)
and GAR in proper relative positions by a H-bond network. The transition state and the minimum energy pathway are located
on the potential energy surface. After all the residues (including H2O molecules) are removed from the system the activation energy has increased from 145.1 kJ/mol to 243.3 kJ/mol, and the formly
transfer reaction is very hard to achieve. The interactions between coenzyme, GAR and residues near the reactive center are
discussed as well. |
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| Keywords: | GAR Tfase QM/MM method formyl transfer |
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