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Quantum Chemical Modelling of Enzymatic Reactions

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A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Computational Catalysis".

Deadline for manuscript submissions: closed (31 December 2019) | Viewed by 24235

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Special Issue Editors

Prof. Dr. Tiziana Marino

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Guest Editor

Department of Chemistry and Chemical Technologies, Bridge Pietro Bucci, Building 14C, I-87036 Rende(CS), Italy
Interests: biological macromolecular systems; DFT; metal ions of biological interest
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Nino Russo

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Guest Editor

Department of Chemistry and Chemical Technologies, Università della Calabria, Via P. Bucci, Ponte Bucci cubo 14c, 87036 Rende, CS, Italy
Interests: theoretical and computational methods; reaction mechanism; oxidative stress; excited states
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Enzymes are sophisticated natural machines that are able to selectively and efficiently catalyze a huge number of reactions indispensable for vital processes in both the vegetal and animal kingdoms. For a long time, the enzymes’ functions were essentially concentrated on their ability to stabilize low energy transition states that allow explaining the catalytic power of natural enzymes. Very recently, other important effects, such as preorganization, energetic destabilization of reaction intermediates, dynamics and the role of product complexes in the catalytic turnover, have emerged as key factors to explain some of the behaviors of complex enzyme chemistry.

In the last few years, the proposal of new artificial enzymes has also received great attention since the opening of a new scientific frontier that, not only enlarges the knowledge base on the enzyme structure and functions, but also opens new interesting applications in many technological fields.

DFT studies of mechanisms for enzymes and metalloenzymes over the past 15 years have increased a great deal, becoming of equal importance compared to traditional spectroscopic studies. Lately, the QM/MM approach also achieved a significant role in the field of theoretical methodologies devoted to the untangling of different aspects of enzymatic catalysis.

This Special Issue aims to cover recent progress and advances in elucidating the catalytic role of important members of enzymatic families, implicated in important biological processes, as well as of artificial enzymes that will be involved in technological and industrial applications.

Prof. Dr. Tiziana Marino
Prof. Dr. Nino Russo
Guest Editors

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Keywords

Catalytic mechanism
potential energy surface
rate determining step
molecular dynamics
quantum mechanics model
QM/MM model

Published Papers (4 papers)

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Research

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16 pages, 2237 KiB

Open AccessArticle

Fine-Tuning of Sequence Specificity by Near Attack Conformations in Enzyme-Catalyzed Peptide Hydrolysis

by S. Kashif Sadiq

Catalysts 2020, 10(6), 684; https://doi.org/10.3390/catal10060684 - 18 Jun 2020

Cited by 3 | Viewed by 2813

Abstract

The catalytic role of near attack conformations (NACs), molecular states that lie on the pathway between the ground state (GS) and transition state (TS) of a chemical reaction, is not understood completely. Using a computational approach that combines Bürgi–Dunitz theory with all-atom molecular dynamics simulations, the role of NACs in catalyzing the first stages of HIV-1 protease peptide hydrolysis was previously investigated using a substrate that represents the recognized SP1-NC cleavage site of the HIV-1 Gag polyprotein. NACs were found to confer no catalytic effect over the uncatalyzed reaction there (

Δ Δ G_{N}^{‡} \sim

0 kcal/mol). Here, using the same approach, the role of NACs across multiple substrates that each represent a further recognized cleavage site is investigated. Overall rate enhancement varies by

| Δ Δ G^{‡} | \sim

12–15 kcal/mol across this set, and although NACs contribute a small and approximately constant barrier to the uncatalyzed reaction (<

Δ

_{N}^{‡ u}

> = 4.3 ± 0.3 kcal/mol), they are found to contribute little significant catalytic effect (

| Δ Δ G_{N}^{‡} | \sim

0–2 kcal/mol). Furthermore, no correlation is exhibited between NAC contributions and the overall energy barrier (

R^{2}

= 0.01). However, these small differences in catalyzed NAC contributions enable rates to match those required for the kinetic order of processing. Therefore, NACs may offer an alternative and subtle mode compared to non-NAC contributions for fine-tuning reaction rates during complex evolutionary sequence selection processes—in this case across cleavable polyproteins whose constituents exhibit multiple functions during the virus life-cycle. Full article

(This article belongs to the Special Issue Quantum Chemical Modelling of Enzymatic Reactions)

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12 pages, 4666 KiB

Open AccessArticle

Identification of a Reaction Intermediate and Mechanism of Action of Intermediary Enzymes in Plumbagin Biosynthetic Pathway Using Molecular Dynamics Simulation

by Muralidharan K S, Roopa Lalitha, Shanmugam Girija, Pravin Kumar R, Akshai P S, Meghana N Swamy, Nayana M and Malaiyandi Jayanthi

Catalysts 2020, 10(3), 280; https://doi.org/10.3390/catal10030280 - 01 Mar 2020

Cited by 2 | Viewed by 3593

Abstract

The biosynthesis of plumbagin is known to occur via the acetate polymalonate pathway; however there are several intermediary steps that remain unidentified that leads to its synthesis. The study identifies enzyme naphthoate synthase to catalyze the cyclization of O-malonyl benzoyl CoA to form an intermediate that is acted upon by thioesterase before the reaction proceeds to form plumbagin. Two possible structures were predicted for this intermediate using quantum mechanics studies. A total of 60 ns molecular dynamics simulations revealed the most probable intermediate structure of the predicted two. Full article

(This article belongs to the Special Issue Quantum Chemical Modelling of Enzymatic Reactions)

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Review

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28 pages, 9249 KiB

Open AccessFeature PaperReview

The Effects of the Metal Ion Substitution into the Active Site of Metalloenzymes: A Theoretical Insight on Some Selected Cases

by Mario Prejanò, Marta Erminia Alberto, Nino Russo, Marirosa Toscano and Tiziana Marino

Catalysts 2020, 10(9), 1038; https://doi.org/10.3390/catal10091038 - 10 Sep 2020

Cited by 34 | Viewed by 7981

Abstract

A large number of enzymes need a metal ion to express their catalytic activity. Among the different roles that metal ions can play in the catalytic event, the most common are their ability to orient the substrate correctly for the reaction, to exchange electrons in redox reactions, to stabilize negative charges. In many reactions catalyzed by metal ions, they behave like the proton, essentially as Lewis acids but are often more effective than the proton because they can be present at high concentrations at neutral pH. In an attempt to adapt to drastic environmental conditions, enzymes can take advantage of the presence of many metal species in addition to those defined as native and still be active. In fact, today we know enzymes that contain essential bulk, trace, and ultra-trace elements. In this work, we report theoretical results obtained for three different enzymes each of which contains different metal ions, trying to highlight any differences in their working mechanism as a function of the replacement of the metal center at the active site. Full article

(This article belongs to the Special Issue Quantum Chemical Modelling of Enzymatic Reactions)

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25 pages, 4701 KiB

Open AccessFeature PaperReview

A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases

by Amy Timmins and Sam P. De Visser

Catalysts 2018, 8(8), 314; https://doi.org/10.3390/catal8080314 - 31 Jul 2018

Cited by 51 | Viewed by 9055

Abstract

Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl⁻/Br⁻), they react to form hypohalides (OCl⁻/OBr⁻) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl⁻/Br⁻) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place. Full article

(This article belongs to the Special Issue Quantum Chemical Modelling of Enzymatic Reactions)

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