5 - RNA—Protein Recognition during RNA Processing and Maturation

Abstract

This chapter reviews the molecular basis of Ribonucleic acid (RNA)-protein recognition events that occur during post-transcriptional RNA processing. Understanding the molecular basis of RNA-protein recognition, requires a rationalization of the physical origin of the absolute binding energy (affinity) and relative energy differences for different substrates (specificity). The analysis of the relatively few existing structures of RNA-protein complexes determined at atomic resolution reveals that affinity and specificity do not depend in a simple way on simple physical chemical properties such as protein charge or size of intermolecular interface area. Gene expression in eukaryotes is regulated after transcription through messenger RNA (mRNA) stability, transport, localization and through the excision of non-coding regions (splicing). During these maturation events, messenger RNA (mRNAs) are complexed in ribonucleoprotein particles with proteins that recognize specific RNA sequences to affect different regulatory steps. The assembly of large ribonucleoproteins perfoming RNA splicing (spliceosome) and translation (ribosome) also depends on recognition of spliceosomal small nuclear RNAs (snRNAs) and ribosomal RNA, respectively, by constitutive and auxiliary protein factors. Understanding the molecular basis of RNA-protein recognition is necessary to understand these regulatory events and to learn how to exogeneously regulate gene-expression at the post-transcriptional stage.