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Open AccessArticle

Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations

Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, National Engineering Laboratory of AIDS Vaccine, College of Life Science, Jilin University, Changchun 130023, China
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Int. J. Mol. Sci. 2019, 20(5), 1188; https://doi.org/10.3390/ijms20051188
Received: 22 January 2019 / Revised: 2 March 2019 / Accepted: 5 March 2019 / Published: 8 March 2019
(This article belongs to the Special Issue Molecular Dynamics Simulations)
The aminotransferase from Bacillus circulans (BtrR), which is involved in the biosynthesis of butirosin, catalyzes the pyridoxal phosphate (PLP)-dependent transamination reaction to convert valienone to β-valienamine (a new β-glycosidase inhibitor for the treatment of lysosomal storage diseases) with an optical purity enantiomeric excess value. To explore the stereoselective mechanism of valienamine generated by BtrR, multiple molecular dynamics (MD) simulations were performed for the BtrR/PLP/valienamine and BtrR/PLP/β-valienamine complexes. The theoretical results showed that β-valienamine could make BtrR more stable and dense than valienamine. β-valienamine could increase the hydrogen bond probability and decrease the binding free energy between coenzyme PLP and BtrR by regulating the protein structure of BtrR, which was conducive to the catalytic reaction. β-valienamine maintained the formation of cation-p interactions between basic and aromatic amino acids in BtrR, thus enhancing its stability and catalytic activity. In addition, CAVER 3.0 analysis revealed that β-valienamine could make the tunnel of BtrR wider and straight, which was propitious to the removal of products from BtrR. Steered MD simulation results showed that valienamine interacted with more residues in the tunnel during dissociation compared with β-valienamine, resulting in the need for a stronger force to be acquired from BtrR. Taken together, BtrR was more inclined to catalyze the substrates to form β-valienamine, either from the point of view of the catalytic reaction or product removal. View Full-Text
Keywords: aminotransferase from Bacillus circulans BtrR; molecular dynamics simulation; principal component analysis; steered molecular dynamics simulation; stereoselective mechanism aminotransferase from Bacillus circulans BtrR; molecular dynamics simulation; principal component analysis; steered molecular dynamics simulation; stereoselective mechanism
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Liu, Y.; Wan, Y.; Zhu, J.; Li, M.; Yu, Z.; Han, J.; Zhang, Z.; Han, W. Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations. Int. J. Mol. Sci. 2019, 20, 1188.

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