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Biophys. J. BioFAST: First Published September 23, 2005. doi:10.1529/biophysj.105.067215
© 2005 by the Biophysical Society.

A more recent version of this article appeared on December 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

{Phi}-value analysis of a linear, sequential reaction mechanism: theory and application to ion channel gating

Yu Zhou 1, Pearson E. John 2 and Anthony L. Auerbach 1*

1 SUNY - Buffalo
2 Los Alamos National Lab

* To whom correspondence should be addressed. E-mail: auerbach{at}buffalo.edu.

Submitted on May 23, 2005
Revised on July 27, 2005
Accepted on 1 August 2005


  Abstract
Allosteric proteins are large, multimeric polymers that alternatively adopt more than one stable conformation. In experiments, such conformational changes often appear to be simple, two-state reactions. However, given the size and complexity of proteins, short-lived intermediate states must exist during the course of a global isomerization. Here we derive the analytical form of a rate-equilibrium free energy relationship (with slope {Phi}) for a bounded, linear chain of coupled reactions having arbitrary connecting rate constants. The results indicate that {Phi}-values reveal the relative heights of the energy barriers between intermediate states but provide no information about the energies of the wells along the reaction path. The equations are applied to experimental {Phi}-values for diliganded acetylcholine receptor channel gating.

Key Words: REFER, acetylcholine receptor, kinetics, linear free energy, single-channel




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Copyright © 2005 by the Biophysical Society.