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Simulating activity of the bacterial ribosome

Published online by Cambridge University Press:  10 May 2010

Joanna Trylska
Joanna Trylska*
Affiliation:
Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Warsaw, Poland
*
*Author for correspondence: J. Trylska, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Zwirki i Wigury 93, 02-089Warsaw, Poland. Tel.: 48-22-5540-843; Fax: 48-22-5540-801; Email: joanna@icm.edu.pl
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Abstract

Computational modeling studies that investigate activity of the bacterial ribosome were reviewed. Computational approaches became possible with the availability of three-dimensional atomic resolution structures of the ribosomal subunits. However, due to the enormous size of the system, theoretical efforts to study the ribosome are few and challenging. For example, to extend the simulation timescales to biologically relevant ones, often, reduced models that require tedious parameterizations need to be applied. To that end, modeling of the ribosome focused on its internal dynamics, electrostatic properties, inhibition by antibiotics, polypeptide folding in the ribosome tunnel and assembly mechanisms driving the formation of the small ribosomal subunit.

Type
Review Article
Information
Quarterly Reviews of Biophysics , Volume 42 , Issue 4 , November 2009 , pp. 301 - 316
Copyright
Copyright © Cambridge University Press 2010

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