Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

Selvaraj, Chandrabose; Rudhra, Ondipilliraja; Alothaim, Abdulaziz S.; Alkhanani, Mustfa

doi:10.1016/bs.apcsb.2022.02.002

Cited by 10 publications

(10 citation statements)

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“…Recent studies have highlighted the significant role of conformational dynamics within the active site pocket in facilitating effective receptor-ligand interactions. 40,41 To gain insights into the functional characteristics of the mutants, it is essential to examine the molecular-level effects of the mutations. The conformational change in the substrate-binding pocket S4 of protease pb92, which comprises residues Leu94, Val102, Ile105, and Leu124 forming the lining of the pocket between regions 99-102 and 124-126, plays a crucial role 42,43 in determining the docking results, as depicted in Fig.…”

Section: Coupled Effect Of Mutation On Stability and Docking Resultsmentioning

confidence: 99%

Molecular dynamics studies of disulfide bonds for enhancing the stability of serine protease PB92

Zhao,

Zhang

2024

New J. Chem.

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Section: Coupled Effect Of Mutation On Stability and Docking Resultsmentioning

confidence: 99%

Molecular dynamics studies of disulfide bonds for enhancing the stability of serine protease PB92

Zhao,

Zhang

2024

New J. Chem.

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“…The enzyme active site is part of an enzyme to which substrates bind and where a reaction is catalyzed (Selvaraj et al., 2022). Determination of the active site was performed in order to determine the precise center coordinate of the docking grid box.…”

Section: Methodsmentioning

confidence: 99%

Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

Purnawita,

Rahayu,

Lioe

et al. 2024

Journal of Food Science

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Reuterin is a natural antifungal agent derived from certain strains of Limosilactobacillus reuteri. Our previous study revealed that 6 mM reuterin inhibited completely the conidial germination of aflatoxigenic Aspergillus flavus. This study investigated the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination, which was pre‐assumed that it correlated to the inhibition of some essential enzyme activity involved in conidial germination, specifically 1,3‐β‐glucan synthase, chitin synthase, and catalases (catalase, bifunctional catalase–peroxidase, and spore‐specific catalase). The complex of 1,3‐β‐glucan synthase and chitin synthase with reuterin had a lower binding affinity than that with the substrate. Conversely, the complex of catalases with reuterin had a higher binding affinity than that with the substrate. It was suggested that 1,3‐β‐glucan synthase and chitin synthase tended to bind the substrate rather than bind reuterin. In contrast, catalases tended to bind reuterin rather than bind the substrate. Therefore, reuterin could be a potential inhibitor of catalases but may not be an inhibitor of 1,3‐β‐glucan synthase and chitin synthase. In this in silico study, we predicted that the potential molecular mechanism of reuterin in inhibiting A. flavus conidial germination was due to the inhibition of catalases activities by competitively binding to the enzymes active sites, thus resulting in the accumulation of reactive oxygen species in cells, leading to cells damage.Practical ApplicationThis in silico study revealed that reuterin is a potential inhibitor of catalases in A. flavus, thereby interfering with the antioxidant system during conidial germination. This finding shows that reuterin can be used as an antifungal agent in food or agricultural products, inhibiting conidial germination completely.

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“…Thus, elucidating the role of each residue in the active site is the key to understanding the mechanism of the enzyme. 436,437 Typically, the roles of active site residues are deduced from the enzyme's structural data, with spectroscopic methods providing additional insights. 438,439 A more direct strategy involves modifying these residues to incorporate those with desired properties and observing how these changes affect enzyme activity.…”

Section: Enzymatic Mechanism Analysismentioning

confidence: 99%

Cellular and Biophysical Applications of Genetic Code Expansion

Yi,

Lee,

Seo

et al. 2024

Chem. Rev.

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Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein−protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.

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Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism

Cited by 10 publications

References 73 publications

Molecular dynamics studies of disulfide bonds for enhancing the stability of serine protease PB92

Molecular dynamics studies of disulfide bonds for enhancing the stability of serine protease PB92

Potential molecular mechanism of reuterin on the inhibition of Aspergillus flavus conidial germination: An in silico study

Cellular and Biophysical Applications of Genetic Code Expansion

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