BIOPHYSICAL THEORY AND MODELING |
Simple models for extracting mechanical work from the
ATP hydrolysis cycle
Jonathan L Eide 1, Arup K Chakraborty 2 and George F Oster 3*
1 Department of Chemical Engineering, University of California, Berkeley, California 94720
2 Department of Chemistry and Biophysics Graduate Group, University of California, Berkeley, CA 94720
3 University of California, Departments of Molecular & Cell Biology and ESPM, Berkeley, CA 94720-31
* To whom correspondence should be addressed. E-mail: goster{at}nature.berkeley.edu.
Submitted on August 30, 2005
Revised on November 11, 2005
Accepted on 23 February 2006
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Abstract |
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According to the Binding Zipper model, the RecA class of ATPase motors convert chemical energy into mechanical force by the progressive annealing of hydrogen bonds between the nucleotide and the catalytic pocket (1-3). The role of hydrolysis is to weaken the binding of products allowing them to be released so that the cycle can repeat. Molecular dynamics can be used to study the unbinding process (2), but the binding process is more complex, so that inferences about it are made indirectly from structural, mutation, and biochemical studies. Here we present a series of 'toy' models of varying complexity that illustrate the basic processes involved in force production during ATP binding. These models reveal the role of solvent and geometry in determining the amount of mechanical work that can be extracted from the binding process.
Key Words:
ATP hydrolysis, biniding zipper, mathematical model, mechanochemistry
