Coupling of functioning and folding: photoactive yellow protein as an example system

It has been recognized recently that a significant amount of proteins have partially or entirely disordered conformations in their functional state. Photoactive yellow protein (PYP), which is a model protein of photoreceptor and is a prototype of PAS domain superfamily, has the unfolded N-terminal domain in its signaling state. Using a simple coarse-grained model, we illustrate the free energy surface of the photocycle of PYP. The result implies the importance of cooperative effects between the local structural disturbance around the chromophore and the global loosening of the structure associated with unfolding of the N-terminal domain. This example offers a new scenario of photochemistry in which the photochemical kinetics is controlled by the designed energy landscape of protein folding. (C) 2004 Elsevier B.V. All rights reserved.