TCB Publications - Abstract

James Gumbart, Eduard Schreiner, Leonardo G. Trabuco, Kwok-Yan Chan, and Klaus Schulten. Viewing the mechanisms of translation through the computational microscope. In Joachim Frank, editor, Molecular Machines in Biology, chapter 8, pp. 142-157. Cambridge University Press, 2011.

GUMB2011 Molecular machines carry out a vast array of functions in the living cell, such as transport of cargo, synthesis of chemical energy, and replication of DNA. The ribosome, a large macromolecular complex composed of over 50 proteins and RNA strands, is an example of such a machine. The ribosome is responsible for translating the genetic information carried by mRNA into proteins, a process which occurs in multiple stages, each regulated through interactions with additional factors. Understanding how the ribosome connects the behavior of the its smallest components to its large-scale functioning is a challenge being met by many different techniques, including molecular dynamics simulations. In this chapter, we describe in detail three examples of how molecular dynamics has been utilized to addressed different aspects of translation by the ribosome, and present an overview of the numerous other contributions from simulations.

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