Recognition of gluconeogenic enzymes; Icl1, Fbp1, and Mdh2 by Gid4 ligase: A molecular docking study.
The pro/N-degron pathway is an evolved protein degradation pathway through the ubiquitin-proteasome system. It is a vital pathway to attain protein homeostasis inside the liver cells with varying glucose levels. N-terminal proline exists in more than 300 proteins in Saccharomyces cerevisiae, but only three of them are the gluconeogenic enzymes; isocitrate lyase (Icl1), fructose-1,6-bisphosphatase (Fbp1), and malate dehydrogenase (Mdh2). The present in silico study aims to structurally illustrate the binding of Icl1 enzyme to Gid4 ligase concerning its peers; Fbp1 and Mdh2. Based on the molecular docking scores and interactions, one can attribute the binding stability of Gid4 with degrons, to peptides of length six up to eight from the N-terminal. Moreover, the percent change in the docking score provides a rationale for the unique Gid4-Icl11-4 interaction. The present study provides insights on the binding attitude of Gid4 ligase to degrons of different lengths, so one will consider in designing peptidomimetics to target Gid4 ligase.
['Elfiky|Abdo A|AA|0000-0003-4600-6240', 'Ismail|Alaa M|AM|', 'Elshemey|Wael M|WM|']
D019295:Computational Biology D006597:Fructose-Bisphosphatase D007522:Isocitrate Lyase D008291:Malate Dehydrogenase D062105:Molecular Docking Simulation D012441:Saccharomyces cerevisiae
gluconeogenic enzymes molecular docking protein degradation Gid4 E3 ligase pro/N-end rule structural bioinformatics