Using computer simulations to study decoding by the ribosome

Abstract

The ribosome is the central information-processing unit of the cell. Decoding is the step during protein synthesis where information is transferred from protein to nucleic acid. The decoding problem is reviewed, including recent kinetic, X-ray and cryo-EM data. Molecular dynamics simulations are described which investigate the role of hydrogen bond networks, "baseflipping" events, and changes in the conformation of transfer RNA. © 2006 Springer.