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Biophys. J. BioFAST: First Published February 18, 2005. doi:10.1529/biophysj.104.055103
© 2005 by the Biophysical Society.

A more recent version of this article appeared on May 1, 2005.
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PROTEINS

Predicting the signaling state of Photoactive Yellow Protein

Jocelyne Vreede 1, Wim Crielaard 1, Klaas J. Hellingwerf 1 and Peter G. Bolhuis 1*

1 University of Amsterdam

* To whom correspondence should be addressed. E-mail: bolhuis{at}science.uva.nl.

Submitted on October 26, 2004
Revised on January 15, 2005
Accepted on 8 February 2005


  Abstract
As a bacterial blue light sensor the photo-active yellow protein (PYP) undergoes conformational changes upon signal transduction. The absorption of a photon triggers a series of events that are initially localized around the protein chromophore, extend to encompass the whole protein within microseconds, and lead to the formation of the transient pB signaling state. We study the formation of this signaling state pB by molecular simulation and predict its solution structure. Conventional straightforward molecular dynamics is not able to address this formation process due to the long (microsecond) timescales involved, which are (partially) caused by the presence of free energy barriers between the metastable states. To overcome these barriers, we employed the parallel tempering (or replica exchange) method, thus enabling us to predict qualitatively the formation of the PYP signaling state pB. In contrast to the receptor state pG of PYP, the characteristics of this predicted pB structure include a wide open chromophore binding pocket, with the chromophore and Glu46 fully solvent exposed. In addition, loss of alpha-helical structure occurs, caused by the opening motion of the chromophore binding pocket and the disruptive interaction of the negatively charged Glu46 with the backbone atoms in the hydrophobic core of the N-terminal cap. Recent NMR experiments agree very well with these predictions.

Key Words: free energy, molecular dynamics, pB, parallel tempering, photoreceptor, replica exchange




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Copyright © 2005 by the Biophysical Society.