Helix formation is a dynamical bottleneck in the recovery reaction of Photoactive Yellow Protein.
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 did observe transient interactions between residues of the CBP occurring when the chromophore is in a trans configuration. Using simulations that sample anomalous exposure of the chromophore in the receptor state, we were able to sample chromophore re-entry into its binding pocket. While the involved time scales prohibit drawing definitive conclusions even when using parallel tempering, we nevertheless propose that the formation of a helix in the CBP is essential for a successful recovery of the receptor state, and forms a kinetic barrier in this process.
Vreede
Jocelyne
J
van't Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands. vreede@science.uva.nl
Hellingwerf
Klaas J
KJ
Bolhuis
Peter G
PG
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D003198:Computer Simulation; D050505:Mutant Proteins / Q000737:chemistry; D020283:Photoreceptors, Microbial / Q000737:chemistry*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D015398:Signal Transduction; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D001426:Bacterial Proteins; D050505:Mutant Proteins; D020283:Photoreceptors, Microbial; C050162:photoactive yellow protein, Bacteria