The ribosome as an RNA-based molecular machine

Abstract

The ribosome is a protein-synthesizing ribonucleoprotein particle where RNA forms its structural and functional core. Compact self-folding of ribosomal RNA resulting in its specific tertiary structure and its conformational mobility underlie the functional behavior of the ribosome. In addition to the functions of ligand recognition (binding of mRNA, tRNA and translation factors) and catalysis (peptidyltransferase activity), the ribosomal RNA with its movable blocks principally contributes to the construction of the ribosome as a molecular machine. The oscillations between open (unlocked) and closed (locked) conformations are proposed to be necessary events in the processes of aminoacyl-tRNA binding, transpeptidation and translocation. Elongation factors EF-Tu and EF-G with GTP are considered as catalysts of conformational transitions during aminoacyl-tRNA binding and translocation, and the theory of NTP-dependent conformational catalysis via conformational intermediates is discussed. Thermal fluctuations are assumed to serve as the main "motive force" to move RNA parts and ligands in the translating ribosome. The binding of functional ligands, such as aminoacyl-tRNA and an elongation factor with GTP, and the chemical reactions of transpeptidation and GTP hydrolysis play the role of a Maxwell's Demon: they rectify the random fluctuations to produce the unidirectional conveyance process and translation ("thermal ratchet" model).