A frameshifting stimulatory stem loop destabilizes the hybrid state and impedes ribosomal translocation

• DOI: 10.1073/pnas.1403457111
• Publication Date: 2014-04-01T06:13:03Z
• Authors: Hee-Kyung Kim; Fei Liu; Jingyi Fei; Carlos Bustamante; Ruben L. Gonzalez; Ignacio Tinoco
• Keywords: Models, Molecular; 0301 basic medicine; Multidisciplinary; Models, Genetic; Molecular Conformation; Frameshifting, Ribosomal; 03 medical and health sciences; Bacterial Proteins; Escherichia coli; Fluorescence Resonance Energy Transfer; RNA, Messenger; Ribosomes; DNA Polymerase III

SignificanceA ribosomal frameshift occurs when the ribosome slips by one or more nucleotides on the messenger RNA (mRNA) during translation. Programmed ribosomal frameshifting produces more than one protein from a single mRNA and is tightly regulated by mRNA sequence and structure. Using single-molecule fluorescence resonance energy transfer, we studied the effects of a frameshifting stimulatory mRNA structure on the ribosomal conformational dynamics and translocation rate. Our results show that the structure shifts the conformational equilibrium of ribosomal complexes away from conformations that favor the translocation process, resulting in slowed translocation. We propose that the downstream structure traps ribosomal complexes in the fluctuating conformational states of the translocation process and thus allows more opportunities for frameshifting.