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Abstract <p>This paper presents the results of a study on the physicochemical characteristics of the binding between single-layer graphene nanosheets (GNs) and typical enzymes of the antioxidant system of the fish <i>Danio rerio</i>. The enzymes chosen as target proteins were superoxide dismutase 1 (SOD1), glutathione peroxidase 8 (Gpx8) and catalase (Cat). Virtual molecular structures of the target enzyme and GN were modeled and optimized. Two GN sizes were studied: 25 × 25 and 35 × 35 Å. Using UniProt DB and PrankWeb, annotated binding amino acid residues were compared with amino acid residues associated with GN obtained from the prediction results. For all proteins except Gpx8, the topology of amino acid residues potentially involved in binding to nanosheets was precisely localized. The number of amino acid residues involved in the formation of the molecular cavity ranged from 13 to 30. Molecular interactions between enzymes, proteins and GN were predicted using the rigid molecular docking method using AutoDock software. The study showed the formation of more stable GN-enzyme complexes for 25 × 25 Å GN with fairly low binding energies. The Gibbs free energy values for each combination of GN-enzyme complexes range from –10.1 to ‒15.9&#xa0;kcal/mol. The article discusses the potential biological effects of the studied carbon-based GNs on the antioxidant system of fish <i>D. rerio</i>. The presented approach seems promising for studying and predicting the cytotoxicity of pollutants based on graphene nanoparticles.</p>

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Intermolecular Interactions of Graphene Nanosheets with Enzymes of the Danio rerio Antioxidant System

  • 期刊论文

  • 发表日期：

    2025年12月1日

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  • P. D. Timkin,
  • D. D. Kotelnikov,
  • A. A. Penzin,
  • I. E. Pamirsky,
  • S. M. Ugai,
  • E. Yu. Koiava,
  • V. V. Chaika,
  • K. S. Golokhvast

摘要

Abstract

This paper presents the results of a study on the physicochemical characteristics of the binding between single-layer graphene nanosheets (GNs) and typical enzymes of the antioxidant system of the fish Danio rerio. The enzymes chosen as target proteins were superoxide dismutase 1 (SOD1), glutathione peroxidase 8 (Gpx8) and catalase (Cat). Virtual molecular structures of the target enzyme and GN were modeled and optimized. Two GN sizes were studied: 25 × 25 and 35 × 35 Å. Using UniProt DB and PrankWeb, annotated binding amino acid residues were compared with amino acid residues associated with GN obtained from the prediction results. For all proteins except Gpx8, the topology of amino acid residues potentially involved in binding to nanosheets was precisely localized. The number of amino acid residues involved in the formation of the molecular cavity ranged from 13 to 30. Molecular interactions between enzymes, proteins and GN were predicted using the rigid molecular docking method using AutoDock software. The study showed the formation of more stable GN-enzyme complexes for 25 × 25 Å GN with fairly low binding energies. The Gibbs free energy values for each combination of GN-enzyme complexes range from –10.1 to ‒15.9 kcal/mol. The article discusses the potential biological effects of the studied carbon-based GNs on the antioxidant system of fish D. rerio. The presented approach seems promising for studying and predicting the cytotoxicity of pollutants based on graphene nanoparticles.