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Originally published as Biophys J. BioFAST on February 18, 2005.
doi:10.1529/biophysj.104.055103
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Biophysical Journal 88:3525-3535 (2005)
© 2005 The Biophysical Society

Predicting the Signaling State of Photoactive Yellow Protein

Jocelyne Vreede *, Wim Crielaard *, Klaas J. Hellingwerf * and Peter G. Bolhuis {dagger}

* Swammerdam Institute for Life Sciences, and {dagger} van 't Hoff Institute of Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands

Correspondence: Address reprint requests to Peter Bolhuis, Tel.: 0-20-525-6447; E-mail: bolhuis{at}science.uva.nl.

As a bacterial blue light sensor the photoactive 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, extends to encompass the whole protein within microseconds, and leads 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.




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