Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations

Omar Alvarado; Rafael García-Meseguer; Jose Javier Ruiz-Pernía; Iñaki Tuñon; Eduardo J Delgado

doi:10.1016/j.abb.2021.108807

Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations

Arch Biochem Biophys. 2021 Apr 15:701:108807. doi: 10.1016/j.abb.2021.108807. Epub 2021 Feb 12.

Authors

Omar Alvarado¹, Rafael García-Meseguer², Jose Javier Ruiz-Pernía³, Iñaki Tuñon³, Eduardo J Delgado⁴

Affiliations

¹ Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile; Departamento de Química, Facultad de Ciencias, Universidad del Bío-Bío, Avenida Collao 1202, Concepción, Chile.
² School of Mathematics, University of Bristol, Bristol, United Kingdom; Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain.
³ Department of Physical Chemistry, Universitat de Valencia, 46100, Burjassot, Spain.
⁴ Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile. Electronic address: ejldr@icloud.com.

PMID: 33587902
DOI: 10.1016/j.abb.2021.108807

Abstract

The biosynthesis of R-phenylacetylcarbinol (R-PAC) by the acetohydroxy acid synthase, (AHAS) is addressed by molecular dynamics simulations (MD), hybrid quantum mechanics/molecular mechanics (QM/MM), and QM/MM free energy calculations. The results show the reaction starts with the nucleophilic attack of the C2α atom of the HEThDP intermediate on the C_β atom of the carbonyl group of benzaldehyde substrate via the formation of a transition state (TS1) with the HEThDP intermediate under 4'-aminopyrimidium (APH⁺) form. The calculated activation free energy for this step is 17.4kcal mol^-1 at 27 °C. From this point, the reaction continues with the abstraction of H_β atom of the HEThDP intermediate by the O_β atom of benzaldehyde to form the intermediate I. The reaction is completed with the cleavage of the bond C2α-C2 to form the product R-PAC and to regenerate the ylide intermediate under the APH⁺ form, allowing in this way to reinitiate to the catalytic cycle once more. The calculated activation barrier for this last step is 15.9kcal mol^-1 at 27 °C.

Keywords: AHAS; Mechanism; QM/MM simulations; R-PAC.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Acetolactate Synthase / chemistry*
Benzyl Alcohols / chemical synthesis*
Benzyl Alcohols / chemistry
Molecular Dynamics Simulation*
Quantum Theory

Substances

Benzyl Alcohols
Acetolactate Synthase