Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein

Proteins
Jocelyne VreedePeter G Bolhuis

Abstract

The bacterial sensor Photoactive Yellow Protein (PYP) signals the presence of blue light by undergoing a series of conformational changes. We present atomistic Parallel Tempering (Replica Exchange Molecular Dynamics) simulations of conformational changes occurring during the photo-cycle of PYP. First, we study the signaling state formation of PYP in detail. Our previous simulations have shown that the formation of the signaling state is characterized by the solvent exposure of both the chromophore and Glu46 (Vreede J, Crielaard W, Hellingwerf KJ, Bolhuis PG. Biophys J, 2005;8:3525-3535). Subsequent NMR results agreed with this prediction, but as these experiments were performed on an N-terminally truncated mutant, a simulation of this mutant would further substantiate our previous results. Here, we compare simulations of the truncated PYP to the NMR structures, as well as to the wild type predictions. This comparison also gives some insight into the role of the N-terminal domain of PYP, which restricts the movement of the chromophore binding pocket (CBP) in the wild type. Second, we report simulations of the recovery of the receptor state from the signaling state. While we did not observe complete refolding of the protein, we d...Continue Reading

References

May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J L PellequerE D Getzoff
Feb 28, 2002·Biophysical Journal·Johnny HendriksJasper J van Thor
Apr 25, 2002·Annual Review of Physical Chemistry·Peter G BolhuisPhillip L Geissler
Jan 28, 2003·Biophysical Journal·Johnny HendriksKlaas J Hellingwerf
Mar 18, 2003·The Journal of Biological Chemistry·Jocelyne VreedeDaan M F van Aalten
Nov 2, 2004·Biophysical Journal·Peter G Bolhuis
Dec 14, 2004·Proceedings of the National Academy of Sciences of the United States of America·Daan Frenkel
Jan 12, 2005·Structure·Sudarshan RajagopalKeith Moffat
Feb 22, 2005·Biophysical Journal·Jocelyne VreedePeter G Bolhuis
Aug 20, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Ivan Coluzza, Daan Frenkel
Oct 13, 2006·Journal of the American Chemical Society·Giovanni BussiMichele Parrinello
Oct 13, 2006·Proceedings of the National Academy of Sciences of the United States of America·J Juraszek, P G Bolhuis
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Dec 7, 2005·Physical Chemistry Chemical Physics : PCCP·David J Earl, Michael W Deem

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Citations

Feb 6, 2010·Proceedings of the National Academy of Sciences of the United States of America·Jocelyne VreedePeter G Bolhuis
Sep 8, 2012·The Journal of Physical Chemistry. B·Kristen A Marino, Peter G Bolhuis
Oct 31, 2014·PLoS Computational Biology·Mary A RohrdanzCecilia Clementi

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