In Silico Mutagenesis Reveals Specific Binding Residues that Regulate KSRP – microRNA Precursor Interactions in Human

Abstract

Aims: The main aim of the study is to identify the key residues involved in interactions of KSRP and microRNAs of human. Study Design: The KH type splicing regulatory protein acronymed as KSRP is a member of the FUSE binding protein family. The FUSE is an AT rich DNA element which is present 1.7kb upstream of the c-Myc oncogene promoter. KSRP also known as FUSE binding protein 2(FBP2). Various activities of KSRP has been reported by many workers over the years, however recent report suggest that KSRP is involved in a crucial step of the microRNA biogenesis pathway – the generation of precursor microRNAs from primary microRNAs. The premise of this work stems from the observation that much micro RNA has been implicated in numerous diseases and though antisense constructs have been projected as possible therapeutic agents against such microRNAs, protein inhibitors or Site directed mutagenesis (SDM) approaches should open up new intervention strategies. Place and Duration: The work was done entirely at the DBT Centre for Bioinformatics, Presidency university, Kolkata for a period from June 2012 – May 2013. Methodology: Comparative modeling followed by molecular dynamic simulation strategies based on flexible and rigid docking approaches were combined with in silico mutagenesis to analyze the interactions of KSRP and human “microRNAs” Results: Results indicate that specific residues of the K type single stranded RNA binding domain play important roles in RNA binding and in their absence the binding affinities are affected. Conclusion: In silico mutagenesis in protein structures can serve as important initial steps to understand the interactions of proteins and their substrates. In context of KSRP the protein active site residues were identified and these could serve as important targets for future experiments.