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Stochastic kinetics of ribosomes: Single motor properties and collective behavior

Cornell Affiliated Author(s)

Author

Debanjan Chowdhury
A. Garai
Debanjan Chowdhury
T.V. Ramakrishnan

Abstract

Syntheses of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an exact analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a "Michaelis-Menten-type" equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechanochemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes simultaneously move on the same mRNA track, while each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in three-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions. © 2009 The American Physical Society.

Date Published

Journal

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volume

80

Issue

1

URL

https://www.scopus.com/inward/record.uri?eid=2-s2.0-68949085318&doi=10.1103%2fPhysRevE.80.011908&partnerID=40&md5=d430e8c50e6b41aff662673148dcc0c2

DOI

10.1103/PhysRevE.80.011908

Group (Lab)

Debanjan Chowdhury Group

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