Ribosome as a molecular machine

Abstract 

General principles of structure and function of the ribosome are surveyed, and the translating ribosome is regarded as a molecular conveying machine. Two coupled conveying processes, the passing of compact tRNA globules and the drawing of linear mRNA chain through intraribosomal channel, are considered driven by discrete acts of translocation during translation. Instead of mechanical transmission mechanisms and power-stroke ‘motors’, thermal motion and chemically induced changes in affinities of ribosomal binding sites for their ligands (tRNAs, mRNA, elongation factors) are proposed to underlie all the directional movements within the ribosomal complex. The GTP-dependent catalysis of conformational transitions by elongation factors during translation is also discussed.

Keywords:  Ribosomal translocation, Conformational movement, Thermal ratchet mechanism, Locked and unlocked conformation, Elongation factor, GTP-dependent catalysis

Abbreviations:  Aa-tRNA, aminoacyl-tRNA, Pept-tRNA, peptidyl-tRNA, PTC, peptidyl transferase center, EF-Tu, elongation factor Tu, EF-G, elongation factor G, GMPPCP, 5′-guanylyl methylene diphosphonate, GMPPNP, 5′-guanylyl imidodiphosphate, colons (:) in molecular complexes, such as Aa-tRNA:EF-Tu:GTP, EF-Tu:GDP and EF-G:GMPPNP, designate non-covalent multi-center bonding