Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis

We report a theoretical/computational analysis of the energy flow relevant to the long-range intramolecular crosstalk between different regions in a photosensory receptor, photoactive yellow protein (PYP). To analyze the energy flow in atomic detail, we derived a theoretical expression for the interresidue energy conductivity in terms of the time-correlation function of the interatomic energy flux. The values of energy conductivities were numerically evaluated by using a long molecular dynamics simulation trajectory of the PYP molecule in the aqueous solution environment. As a result, we detected several pathways for energy transfer relevant for the long-range intramolecular signalling of PYP. (c) 2006 Elsevier B.V. All rights reserved.