Non-covalent interactions in the glutathione peroxidase active center and their influence on the enzyme activity

Tupikina, Elena Yu.

doi:10.1039/d2ob00890d

Cited by 7 publications

(9 citation statements)

References 35 publications

(54 reference statements)

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“…Synergistic strengthening of the halogen bond through formation of an additional hydrogen bond has been shown on the example of an enzyme of the hydrolase class, T4 lysozyme, where original tyrosine residue was replaced by chlorotyrosine 35,36 . In our recent work it was demonstrated that formation of weak but numerous non‐covalent interactions in the active site of glutathione peroxidase enzyme drive the reaction of peroxide reduction 37 . Furthermore, there have been several demonstrations of successful practical use of mutual influence of numerous non‐covalent interactions.…”

Section: Introductionmentioning

confidence: 90%

“…35,36 In our recent work it was demonstrated that formation of weak but numerous non-covalent interactions in the active site of glutathione peroxidase enzyme drive the reaction of peroxide reduction. 37 Furthermore, there have been several demonstrations of successful practical use of mutual influence of numerous non-covalent interactions. For instance, formation of additional hydrogen bonds between substrate and chiral template was used as a tool to control the enantioselectivity of reactions.…”

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confidence: 99%

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Mutual influence of non‐covalent interactions formed by imidazole: A systematic quantum‐chemical study

Shitov,

Krutin,

Tupikina

2024

J Comput Chem

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Imidazole is a five‐membered heterocycle that is part of a number of biologically important molecules such as the amino acid histidine and the hormone histamine. Imidazole has a unique ability to participate in a variety of non‐covalent interactions involving the NH group, the pyridine‐like nitrogen atom or the π‐system. For many biologically active compounds containing the imidazole moiety, its participation in formation of hydrogen bond NH⋯O/N and following proton transfer is the key step of mechanism of their action. In this work a systematic study of the mutual influence of various paired combinations of non‐covalent interactions (e.g., hydrogen bonds and π‐interactions) involving the imidazole moiety was performed by means of quantum chemistry (PW6B95‐GD3/def2‐QZVPD) for a series of model systems constructed based on analysis of available x‐ray data. It is shown that for considered complexes formation of additional non‐covalent interactions can only enhance the proton‐donating ability of imidazole. At the same time, its proton‐accepting ability can be both enhanced and weakened, depending on what additional interactions are added to a given system. The mutual influence of non‐covalent interactions involving imidazole can be classified as weak geometric and strong energetic cooperativity—a small change in the length of non‐covalent interaction formed by imidazole can strongly influence its strength. The latter can be used to develop methods for controlling the rate and selectivity of chemical reactions involving the imidazole fragment in larger systems. It is shown that the strong mutual influence of non‐covalent interactions involving imidazole is due to the unique ability of the imidazole ring to effectively redistribute electron density in non‐covalently bound systems with its participation.

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Section: Introductionmentioning

confidence: 90%

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confidence: 99%

Mutual influence of non‐covalent interactions formed by imidazole: A systematic quantum‐chemical study

Shitov,

Krutin,

Tupikina

2024

J Comput Chem

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“…However, the contribution of the induction and dispersion components is also relatively large and unneglectable. The sum of these two components accounts for about 38 1 for all of the investigated complexes.…”

Section: Sapt Analysismentioning

confidence: 99%

Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations

Lu,

Chen,

Liu

et al. 2024

IJMS

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Among various non-covalent interactions, selenium-centered chalcogen bonds (SeChBs) have garnered considerable attention in recent years as a result of their important contributions to crystal engineering, organocatalysis, molecular recognition, materials science, and biological systems. Herein, we systematically investigated π–hole-type Se∙∙∙O/S ChBs in the binary complexes of SeO2 with a series of O-/S-containing Lewis bases by means of high-level ab initio computations. The results demonstrate that there exists an attractive interaction between the Se atom of SeO2 and the O/S atom of Lewis bases. The interaction energies computed at the MP2/aug-cc-pVTZ level range from −4.68 kcal/mol to −10.83 kcal/mol for the Se∙∙∙O chalcogen-bonded complexes and vary between −3.53 kcal/mol and −13.77 kcal/mol for the Se∙∙∙S chalcogen-bonded complexes. The Se∙∙∙O/S ChBs exhibit a relatively short binding distance in comparison to the sum of the van der Waals radii of two chalcogen atoms. The Se∙∙∙O/S ChBs in all of the studied complexes show significant strength and a closed-shell nature, with a partially covalent character in most cases. Furthermore, the strength of these Se∙∙∙O/S ChBs generally surpasses that of the C/O–H∙∙∙O hydrogen bonds within the same complex. It should be noted that additional C/O–H∙∙∙O interactions have a large effect on the geometric structures and strength of Se∙∙∙O/S ChBs. Two subunits are connected together mainly via the orbital interaction between the lone pair of O/S atoms in the Lewis bases and the BD*(OSe) anti-bonding orbital of SeO2, except for the SeO2∙∙∙HCSOH complex. The electrostatic component emerges as the largest attractive contributor for stabilizing the examined complexes, with significant contributions from induction and dispersion components as well.

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“…10,11 Prompted by these considerations, considerable effort has been made to ascertain the mechanisms of action and modes of supramolecular association with biologically-relevant substrates. 12–21 Over and above biological roles/applications, selenium compounds attract interest in terms of the sensing of anions and molecules, 22–24 and, increasingly, catalysis, 25–28 materials, 29–31 covalent organic frameworks (COFs) 32,33 and as fluorescence probes 34 – all again demanding investigations of the supramolecular chemistry of selenium. Complementing these specialist reviews are more general overviews of the broader roles and implications of chalcogen-bonding.…”

Section: Introductionmentioning

confidence: 99%

Supramolecular architectures featuring Se⋯N secondary-bonding interactions in crystals of selenium-rich molecules: a comparison with their congeners

Tiekink

2023

CrystEngComm

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Non-covalent interactions in the glutathione peroxidase active center and their influence on the enzyme activity

Abstract: In this computational work, the structure of the active centre of the enzyme glutathione peroxidase (in three forms –SeH, –SeOH and –Se(O)OH) and the non-covalent interactions in it were investigated...

Cited by 7 publications

References 35 publications

Mutual influence of non‐covalent interactions formed by imidazole: A systematic quantum‐chemical study

Mutual influence of non‐covalent interactions formed by imidazole: A systematic quantum‐chemical study

Unveiling the Nature and Strength of Selenium-Centered Chalcogen Bonds in Binary Complexes of SeO2 with Oxygen-/Sulfur-Containing Lewis Bases: Insights from Theoretical Calculations

Supramolecular architectures featuring Se⋯N secondary-bonding interactions in crystals of selenium-rich molecules: a comparison with their congeners

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