0000000000420644
AUTHOR
Rafael García-meseguer
A molecular dynamics study on the role of the protonation state in the biosynthesis of R-PAC by AHAS
Abstract The effect of the protonation state of the hydroxyl-ethylthiamin diphosphate intermediate, HEThDP, on the enzyme-substrate interactions and their consequences on the biosynthesis of R-phenylacetylcarbinol, R-PAC, by the acetohydroxy acid synthase, AHAS, is addressed by molecular dynamics simulations. It is found that the form of HEThDP, which favors the formation of R-PAC, is that having the 4-aminopyrimidine ring with the N1′ atom protonated and the N4′ atom as aminopyrimidinium ion. Under this form both active sites of AHAS have the ability to perform the catalysis, unlike that observed for the other possible protonation states of N1′ and N4′ atoms.
Linking Electrostatic Effects and Protein Motions in Enzymatic Catalysis. A Theoretical Analysis of Catechol O-Methyltransferase
The role of protein motions in enzymatic catalysis is the subject of a hot scientific debate. We here propose the use of an explicit solvent coordinate to analyze the impact of environmental motions during the reaction process. The example analyzed here is the reaction catalyzed by catechol O-methyltransferase, a methyl transfer reaction from S-adenosylmethionine (SAM) to the nucleophilic oxygen atom of catecholate. This reaction proceeds from a charged reactant to a neutral product, and then a large electrostatic coupling with the environment could be expected. By means of a two-dimensional free energy surface, we show that a large fraction of the environmental motions needed to attain the…
The influence of the solvent's mass on the location of the dividing surface for a model Hamiltonian
The Transition State dividing surface is a key concept, not only for the precise calculation of the rate constant of a reaction, but also for the proper prediction of product ratios. The correct location of this surface is defined by the requirement that reactive trajectories do not recross it. In the case of reactions in solution the solvent plays an important role in the location of the dividing surface. In this paper we show with the aid of a model Hamiltonian that the effective mass of the solvent can dramatically change the location of the dividing surface. Keywords: Dynamical systems, Dividing surface, Reactions in solution, 2019 MSC: 00-01, 99-00
Studying the role of protein dynamics in an SN2 enzyme reaction using free-energy surfaces and solvent coordinates
Conformational changes are known to be able to drive an enzyme through its catalytic cycle, allowing, for example, substrate binding or product release. However, the influence of protein motions on the chemical step is a controversial issue. One proposal is that the simple equilibrium fluctuations incorporated into transition-state theory are insufficient to account for the catalytic effect of enzymes and that protein motions should be treated dynamically. Here, we propose the use of free-energy surfaces, obtained as a function of both a chemical coordinate and an environmental coordinate, as an efficient way to elucidate the role of protein structure and motions during the reaction. We sho…
Mechanistic study of the biosynthesis of R-phenylcarbinol by acetohydroxyacid synthase enzyme using hybrid quantum mechanics/molecular mechanics simulations
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 Cβ 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 17.4 kcal mol−1 at 27 °C. From this point, the reaction continues with the abstraction of Hβ atom of the HEThDP in…