Validating a new proton shuttle reaction pathway for formation of the peptide bond in ribosomes: A theoretical investigation

Abstract

A ribosome is a large RNA–protein machine that catalyzes protein synthesis. RNA plays a crucial role in catalyzing peptide bond formation. In this Letter, we focus on the catalytic role of the A76 2′-OH of the P site in tRNA. Three possible reaction schemes were compared using the same reaction model and theoretical level. By comparison of the potential energy surface and optimized geometries of transition states, a new favorable reaction pathway is shown. The activation energy is 24 kcal/mol. This work will provide a foundation for further theoretical and experimental study of ribosome mechanisms.