Structural Analysis of the Drosophila melanogaster GSTome

• Published in: Biomolecules (Basel, Switzerland) Vol. 14; no. 7; p. 759
• Main Authors: Petiot, Nicolas, Schwartz, Mathieu, Delarue, Patrice, Senet, Patrick, Neiers, Fabrice, Nicolaï, Adrien
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 26-06-2024; MDPI
• Subjects: AlphaFold; Amino acid sequence; Amino acids; Analysis; Artificial intelligence; Binding sites; Conserved sequence; Crystallography; Detoxification; Dimerization; dimerization interface; Drosophila; Drosophila melanogaster; Enzymes; Glutathione; Glutathione transferase; Hydrophobicity; Insects; Life Sciences; Ligands; multiple sequence alignment; NMR; Nuclear magnetic resonance; Nucleotide sequence; Organisms; Physiological aspects; Proteins; X-ray crystallography; glutathione transferase; binding sites; normal mode analysis; AlphaFold; multiple sequence alignment; dimerization interface; Drosophila melanogaster
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom14070759

Glutathione transferase (GST) is a superfamily of ubiquitous enzymes, multigenic in numerous organisms and which generally present homodimeric structures. GSTs are involved in numerous biological functions such as chemical detoxification as well as chemoperception in mammals and insects. GSTs catalyze the conjugation of their cofactor, reduced glutathione (GSH), to xenobiotic electrophilic centers. To achieve this catalytic function, GSTs are comprised of a ligand binding site and a GSH binding site per subunit, which is very specific and highly conserved; the hydrophobic substrate binding site enables the binding of diverse substrates. In this work, we focus our interest in a model organism, the fruit fly
(
), which comprises 42 GST sequences distributed in six classes and composing its GSTome. The goal of this study is to describe the complete structural GSTome of
to determine how changes in the amino acid sequence modify the structural characteristics of GST, particularly in the GSH binding sites and in the dimerization interface. First, we predicted the 3D atomic structures of each GST using the AlphaFold (AF) program and compared them with X-ray crystallography structures, when they exist. We also characterized and compared their global and local folds. Second, we used multiple sequence alignment coupled with AF-predicted structures to characterize the relationship between the conservation of amino acids in the sequence and their structural features. Finally, we applied normal mode analysis to estimate thermal B-factors of all GST structures of
. Particularly, we extracted flexibility profiles of GST and identify key residues and motifs that are systematically involved in the ligand binding/dimerization processes and thus playing a crucial role in the catalytic function. This methodology will be extended to guide the in silico design of synthetic GST with new/optimal catalytic properties for detoxification applications.