Abstract
Many biological mechanisms involve the interaction of proteins or binding of other molecules to proteins. The precise prediction of functionally active binding sites on the protein surface could play an important role in predicting the nature of protein-protein or protein-ligand interactions. The present research was conducted on 8-oxoguanine DNA glycosylase geneOGG1 sequence from Arabian camel (camelus dromedaries) to predict the protein structure. In this study, 1790 long amiono acid (AA) sequences of OGG1 fromC. dromedarieswere used to predict its protein structure based on multiple alignments by Lometes & Illterative ITasser simulations. Because the full structure ofOGG1 protein cannot be predicted based on the homology modeling using conserved regions of other mammalian species, we predicted the 3D structure of two domains of the OGG1 protein. The two regions predicted were OGG1 protein domain 1 (D1) comprised of amino acids from 1-1000 and OGG1 protein domain 2 (D2) comprised of amino acids from 1000-1790. The 3D protein structures were validated using RAMPAGE Ramachandran plot and functional structures were predicted based on the homologous regions from other species including human, rat, mouse and panda. The functional group predications were established using the Eukaryote Linear Motif (ELM) resource. Among the important functions predicted for OGG1 proteins were LIG_BRCT_BRCA1_1 instances of Phosphopeptide motif which directly interacts with the BRCT (carboxy-terminal) domain of the breast cancer gene BRCA1, LIG_FHA_2 of Phosphothreonine motif binding a subset of FHA domains that have a preference for an acidic amino acid at the replication fork, and MOD_TYR_ITSM of the CD150 subfamily of receptors that bind to and are regulated by SH2 adaptor molecule. These sites may constitute target for drug design for many pharmaceutical and biotechnological purposes. The target site of binding region for OGG1 was predicted both in D1 and D2 by using site finder tools of Molecular Operation Environment (MOE). Furthermore, the results also predicted two conserved regions, both 45AA long, having 100.0% similarity with the crystal structure of Calmodium-Dependent Protein Kinase I (CaM kinase I) from rat (Q63450). This is the first report that deals with the Arabian camelOGG1protein structure prediction along with functional motifs and binding sites identification.