The Quantum Chemical Cluster Approach in Biocatalysis.
Acc Chem Res. 2023.
PMID: 36976880
Free PMC article.
Review.
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The Quantum Chemical Cluster Approach in Biocatalysis.
Acc Chem Res. 2023 Apr 18;56(8):938-947. doi: 10.1021/acs.accounts.2c00795. Epub 2023 Mar 28.
Acc Chem Res. 2023.
PMID: 36976880
Free PMC article.
Review.
The quantum chemical cluster approach has been used for modeling enzyme active sites and reaction mechanisms for more than two decades. ...Finally, we discuss how the cluster approach can be used to guide the rational design of enzyme var …
The quantum chemical cluster approach has been used for modeling enzyme active sites and reaction mechanisms for …
Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach.
J Chem Inf Model. 2015 Jul 27;55(7):1349-60. doi: 10.1021/acs.jcim.5b00140. Epub 2015 Jul 1.
J Chem Inf Model. 2015.
PMID: 26091526
Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical …
Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophil …
Mechanisms of metal-dependent non-redox decarboxylases from quantum chemical calculations.
Comput Struct Biotechnol J. 2021 May 26;19:3176-3186. doi: 10.1016/j.csbj.2021.05.044. eCollection 2021.
Comput Struct Biotechnol J. 2021.
PMID: 34141138
Free PMC article.
Review.
Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-review, we summarize our recent work on several metal-dependent decarboxylases, where we used the so-called cluster approach to …
Quantum chemical calculations are today an extremely valuable tool for studying enzymatic reaction mechanisms. In this mini-re …
Modeling Catalysis in Allosteric Enzymes: Capturing Conformational Consequences.
Top Catal. 2022 Feb;65(1-4):165-186. doi: 10.1007/s11244-021-01521-1. Epub 2021 Nov 9.
Top Catal. 2022.
PMID: 36304771
Free PMC article.
Greater understanding of enzymatic mechanisms aids the discovery of new targets for biologics, the development of biocatalytic transformations, and de novo enzyme design. Methods using quantum mechanical (QM) potentials, such as Density Functional Theory (DFT), have enable …
Greater understanding of enzymatic mechanisms aids the discovery of new targets for biologics, the development of biocatalytic transformatio …
Computational Study of the Fries Rearrangement Catalyzed by Acyltransferase from Pseudomonas protegens.
ChemistryOpen. 2024 Jan 15:e202300256. doi: 10.1002/open.202300256. Online ahead of print.
ChemistryOpen. 2024.
PMID: 38224208
Free article.
In the present study, we report a mechanistic investigation of this activity of PpATase using quantum chemical calculations. A detailed mechanism is proposed, and the energy profile for the reaction is presented. ...The deprotonation of the C6-H of the substrate is …
In the present study, we report a mechanistic investigation of this activity of PpATase using quantum chemical calculations. A …
Computational enzymatic catalysis--clarifying enzymatic mechanisms with the help of computers.
Phys Chem Chem Phys. 2012 Sep 28;14(36):12431-41. doi: 10.1039/c2cp41180f. Epub 2012 Aug 6.
Phys Chem Chem Phys. 2012.
PMID: 22870506
Review.
Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in life. However, despite their critical role in nature, attaining a clear understanding of the way an enzyme acts, i.e. its catalytic mechanism, …
Enzymes play a biologically essential role in performing and controlling an important share of the chemical processes occurring in li …
Inhibition of the Fe(4)S(4)-cluster-containing protein IspH (LytB): electron paramagnetic resonance, metallacycles, and mechanisms.
J Am Chem Soc. 2010 May 19;132(19):6719-27. doi: 10.1021/ja909664j.
J Am Chem Soc. 2010.
PMID: 20426416
Free PMC article.
On the basis of previous work on organometallic complexes, together with computational docking and quantum chemical calculations, we propose a model for alkyne inhibition involving pi (or pi/sigma) "metallacycle" complex formation with the unique fourth Fe in the Fe …
On the basis of previous work on organometallic complexes, together with computational docking and quantum chemical calculatio …
Quantum chemistry as a tool in asymmetric biocatalysis: limonene epoxide hydrolase test case.
Angew Chem Int Ed Engl. 2013 Apr 22;52(17):4563-7. doi: 10.1002/anie.201300594. Epub 2013 Mar 19.
Angew Chem Int Ed Engl. 2013.
PMID: 23512539
Free PMC article.
Cluster model: Large active-site models (see figure) are used to investigate the selectivity of limonene epoxide hydrolase, both the wild type and mutants optimized through directed evolution. Good agreement is found between theory and the experimental data, thus demonstra …
Cluster model: Large active-site models (see figure) are used to investigate the selectivity of limonene epoxide hydrolase, both the …
Insights into the catalytic mechanism of coral allene oxide synthase: a dispersion corrected density functional theory study.
J Phys Chem B. 2013 Jun 6;117(22):6701-10. doi: 10.1021/jp403405b. Epub 2013 May 29.
J Phys Chem B. 2013.
PMID: 23676102
In this present work the mechanism by which cAOS catalyzes the formation of allene oxide from its hydroperoxy substrate was computationally investigated by using a DFT-chemical cluster approach. In particular, the effects of dispersion interactions and DFT fu …
In this present work the mechanism by which cAOS catalyzes the formation of allene oxide from its hydroperoxy substrate was computationally …
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