4.6 Article

Structural insights into the binding mode of D-sorbitol with sorbitol dehydrogenase using QM-polarized ligand docking and molecular dynamics simulations

Journal

BIOCHEMICAL ENGINEERING JOURNAL
Volume 114, Issue -, Pages 247-259

Publisher

ELSEVIER SCIENCE BV
DOI: 10.1016/j.bej.2016.07.008

Keywords

Sorbitol dehydrogenase; D-sorbitol; L-sorbose; QM/MM docking; MD simulations

Funding

  1. WTU Joint Research Grants of Konkuk University

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Gluconobacter oxydans is an organism involved in the incomplete oxidation mechanism of many sugars and alcohols. G. oxydans is involved in the biotransformation of D-sorbitol to L-sorbose via a membrane bound D-sorbitol dehydrogenase (SDH). The focus of this study was to investigate the binding of D-sorbitol to SDH and determine the amino acids involved in the formation of L-sorbose. In order to determine the crucial interactions of D-sorbitol with SDH, in silico polarized ligand docking was employed. QM/MM-based interaction studies suggested that His302, Met366, and Asp368 actively participate in D-sorbitol binding. MD simulation-based mutational studies confirmed that these amino acids are key residues in the binding of D-sorbitol. In particular, mutation of His302 resulted in the denaturation of protein structure and loss of stability. Overall, our results suggest that the role of His302 is to hold the D-sorbitol, and future replacement of polar amino acids in a surrounding pattern will be helpful to increase the production of sugars by G. oxydans. (C) 2016 Elsevier B.V. All rights reserved.

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