Molecular dynamic simulations and calibration of the RNA-PPR interactions

Abstract

Pentatricopeptide proteins (PPR) are a group of helical repeat proteins which mediate several aspects of RNA metabolism in eukaryotes. The protein binds specifically, in a modular and base-specific manner, to a single stranded RNA. This unique mode of identification has made it an attractive molecule for designing proteins that bind to desired RNAs. However, effective protein design relies on understanding in detail the factors that contribute to the affinity and specificity of PPR-RNA interactions.