Investigating the effects of carboxyl terminal elimination from ۶۰۴ retinal isoform of IMPDH۱: an experimental and molecular dynamics simulation approach

Mutations in inosine monophosphate dehydrogenase ۱ (IMPDH۱), are known to be a root cause of RetinitisPigmentosa (RP), a common hereditary blindness. Regulation of the activity of IMPDH۱ is dependent on theoccupation of nucleotide binding sites with GDP/GTP, performing an inhibitory effect. The retinal isoformsof IMPDH۱, identified with distinct catalytic activity, contain additional terminal peptides which theirpossible roles in regulation of enzymatic activity relies undiscovered. The current study investigated theprobable interactions of N-ter peptide extension of ۶۰۴-isoform in absence of the C-ter peptide. MDsimulations on dimer structures of wild-type and engineered proteins were performed using GROMACS۲۰۱۹.۱ simulation Package and CHARMM۳۶ force field. The energy of the system was minimized and thesystem was equilibrated using Velocity-rescaling and Parrinello-Rahman algorithms for NVT and NPTequilibrations, respectively. The final production step of the system continued up to ۲۰ ns. Further, RMSDand RMSF analyses were performed. The proteolytic digestion indicated a rapid digestion of the recombinantprotein in contrast to the wild type ۶۰۴-isoform, recommending a higher accessibility of α-Chymotrypsin todigestion sites due to the removal of C-ter peptide. Our computational data, also, revealed the formation of anovel helix of N-ter peptide in GTP۲ binding site. This helix formation could affect the regulation of enzyme'scatalytic activity, either by masking the nucleotide binding site or acting as an GTP-independent internalinhibitory element.Andashti, B. et al. (۲۰۲۰). The functional impact of the C/N-terminal extensions of the mouse retinalIMPDH۱ isoforms: a kinetic evaluation. Molecular and cellular biochemistry, ۴۶۵(۱-۲), ۱۵۵–۱۶۴.Buey, R. M. et al. (۲۰۱۵). Guanine nucleotide binding to the Bateman domain mediates the allostericinhibition of eukaryotic IMP dehydrogenases. Nature communications, ۶, ۸۹۲۳

Keywords:

Retinitis Pigmentosa , IMPDH۱ , Moleular Dynamics Simulation , retinal isoforms