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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