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Processes
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Modeling and Simulation of Enzymatic Catalysis Processes
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Modeling and Simulation of Enzymatic Catalysis Processes

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Catalysis Enhanced Processes".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 6472

Special Issue Editor

Dr. Sérgio Filipe Sousa

E-Mail Website
Guest Editor
UCIBIO/REQUIMTE, BioSIM-Departamento de Biomedicina, Faculdade de Medicina da, Universidade do Porto, 4200-319 Porto, Portugal
Interests: quantum chemistry and other computational chemistry methods applied to the study of chemical reactions; enzymatic catalysis; drug discovery
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes play a central role in life, catalyzing many chemical and biological processes occurring in nature. Understanding how enzymes catalyze their reactions is essential, both from fundamental and practical perspectives, with application in a variety of areas, from more basic research that aims to understand how different events occur in the cell, to the development of new treatments for important diseases, and even in industrial biocatalytic applications.  

Computational methods can be used to simulate and model different enzymatic reactions, circumventing some of the limitations of the experimental methodologies typically used, and providing an alternative strategy to complement the information obtained from these methods. Computational modelling of these processes can provide a comparative analysis of different mechanistic proposals, helping researchers to discard mechanistic proposals and propose new ones. This modelling can enable the determination of the transition state structures and a detailed understanding of the amino acid residues more involved in the enzymatic reactions, providing important clues that can later be used in rational drug discovery and rational enzyme engineering.  

This Special Issue focuses on the application of computational methods for modeling and simulating enzymatic reaction mechanisms, including methodological developments and computational studies addressing the activity of specific enzymes.

Dr. Sérgio Filipe Sousa
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • computational enzymology
  • QM/MM methods
  • ONIOM
  • cluster modelling
  • quantum mechanics
  • molecular dynamics

Published Papers (2 papers)

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Research

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12 pages, 2094 KiB  
Article
A QM/MM Evaluation of the Missing Step in the Reduction Mechanism of HMG-CoA by Human HMG-CoA Reductase
by Paula Mihaljević-Jurič and Sérgio F. Sousa
Processes 2021, 9(7), 1085; https://doi.org/10.3390/pr9071085 - 23 Jun 2021
Viewed by 1842
Abstract
Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. [...] Read more.
Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. A second reduction step of this reaction mechanism has been the subject of much speculation in the literature, with different conflicting theories persisting to the present day. In this study, the different mechanistic hypotheses were evaluated with atomic-level detail through a combination of molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The obtained Gibbs free activation and Gibbs free reaction energy (15 kcal mol−1 and −40 kcal mol−1) show that this hydride step takes place with the involvement of a cationic His405 and Lys639, and a neutral Glu98, while Asp715 remains in an anionic state. The results provide an atomic-level portrait of this step, clearly demonstrating the nature and protonation state of the amino acid residues involved, the energetics associated, and the structure and charge of the key participating atoms in the several intermediate states, finally elucidating this missing step. Full article
(This article belongs to the Special Issue Modeling and Simulation of Enzymatic Catalysis Processes)
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21 pages, 494 KiB  
Perspective
On Catalytic Kinetics of Enzymes
by Jianshu Dong
Processes 2021, 9(2), 271; https://doi.org/10.3390/pr9020271 - 30 Jan 2021
Cited by 4 | Viewed by 3747
Abstract
Classical enzyme kinetic theories are summarized and linked with modern discoveries here. The sequential catalytic events along time axis by enzyme are analyzed at the molecular level, and by using master equations, this writing tries to connect the microscopic molecular behavior of enzyme [...] Read more.
Classical enzyme kinetic theories are summarized and linked with modern discoveries here. The sequential catalytic events along time axis by enzyme are analyzed at the molecular level, and by using master equations, this writing tries to connect the microscopic molecular behavior of enzyme to kinetic data (like velocity and catalytic coefficient k) obtained in experiment: 1/k = t equals to the sum of the times taken by the constituent individual steps. The relationships between catalytic coefficient k, catalytic rate or velocity, the amount of time taken by each step and physical or biochemical conditions of the system are discussed, and the perspective and hypothetic equations proposed here regarding diffusion, conformational change, chemical conversion, product release steps and the whole catalytic cycle provide an interpretation of previous experimental observations and can be testified by future experiments. Full article
(This article belongs to the Special Issue Modeling and Simulation of Enzymatic Catalysis Processes)
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