In-silico analysis of regulatory proteins involved in tricarboxylic acid cycle ofArabidopsis thalianaand structural analysis by Alphafold and other software

Abstract

AbstractPremiseIsocitrate dehydrogenase (IDH) and Oxoglutarate dehydrogenase (OGDH) are two enzymes referred to as rate-limiting enzymes of Tricarboxylic acid (TCA) cycle. Both the enzymes regulate 2-Oxogluterate production, which is branch that link carbohydrate and amino acid metabolism. The 3D structure of these two enzymes fromArabidopsis thalianahave not been solved yet.MethodsThrough template-based homology modeling by different software like Robetta and Alphafold, the three-dimensional structure of enzymes ofArabidopsis thalianahas been predicted. The expression analysis of enzymes was also performed using GENEVESTIGATOR and Expression Angler BAR.ResultsThe protein 3D structure prediction revealed that isocitrate dehydrogenase displayed an alternative mixed structure; and oxoglutarate dehydrogenase displayed an alpha-beta sheet structure. Structure validation by PROCHECK and ProSA databases has shown that Robetta has provided more real structure than Alphafold. By using a STRING database based on neighbourhood and co-expression parameters, the interactions of the enzymes within the TCA cycle and other metabolic pathways such as glutamate and L-leucine biosynthesis, pyruvate metabolism, and glycine decarboxylation were thoroughly observed.ConclusionsThe study of eight developmental stages revealed that isocitrate dehydrogenase was highly expressed during the senescence time as compared to oxoglutarate. In-silico 3D modeling of proteins IDH and OGDH studied here was successful via Robetta.