We developed a theory of excitation energy transfer (EET) which is applicable to all the values of the coupling strength U in the presence of homogeneous and inhomogeneous broadening. In constructing the theory, we adopted a decoupling procedure corresponding to the factorization by a two-time correlation function of the excitation transfer interaction in the integro-differential equation of a renormalized propagator. We also assumed that the two-time correlation function decreases exponentially with time. Under these assumptions, we could handle our theory nonperturbatively and analytically. We derived formulas of criteria among exciton, intermediate coupling, and Förster mechanisms. We exploited a novel method for determining the EET rate applicable to all the mechanisms from Förster to exciton. Then, we obtained compact formulas for the EET rate and the degree of coherency involved in the EET. We demonstrated how the exciton state is destabilized by the presence of inhomogeneity in the excitation energy of the constituents. The theory was applied to a light-harvesting system LH2 of photosynthetic bacteria.

Proteins harbor a number of cavities of relatively small volume. Although these packing defects are associated with the thermodynamic instability of the proteins, the cavities also play specific roles in controlling protein functions, e.g., ligand migration and binding. This issue has been extensively studied in a well-known protein, myoglobin (Mb). Mb reversibly binds gas ligands at the heme site buried in the protein matrix and possesses several internal cavities in which ligand molecules can reside. It is still an open question as to how a ligand finds its migration pathways between the internal cavities. Here, we report on the dynamic and sequential structural deformation of internal cavities during the ligand migration process in Mb. Our method, the continuous illumination of native carbonmonoxy Mb crystals with pulsed laser at cryogenic temperatures, has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino acid residues around the cavity, which results in the expansion of the cavity with a breathing motion. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand migration channel arising by induced fit, which is further supported by computational geometry analysis by the Delaunay tessellation method. This result suggests a crucial role of the breathing motion of internal cavities as a general mechanism of ligand migration in a protein matrix.hydrophobic cavity ͉ molecular movie ͉ protein dynamics ͉ time-resolved crystallography L ocalized electronic excitation by photons often induces largescale structural modulations and novel physical properties in condensed matter (1, 2). Myoglobin (Mb), often referred to as the hydrogen atom of biology and a paradigm of complexity (3), has played a central role in research on the photo-induced response of proteins and migration of gases, solvents, and ligands in the protein matrix (3, 4). Despite the large number of details known about Mb dynamics, it remains unclear how a ligand molecule escapes from the protein matrix to the solvent and how the protein matrix responds to the ligand migration at the atomic level. A number of time-resolved spectroscopic measurements of Mb photoproducts have revealed a complex ligand-binding reaction with multiple kinetic intermediates (4-8). After dissociation from the heme iron atom, ligand gas molecules either rebind internally from the distal pocket (DP) (Fig. 1) or escape into the solvent. It has been deduced that the escape of the ligand is assisted by the thermal f luctuations that transiently open exit channels. Lowering the temperature slows down the thermal f luctuations, and the internal binding process becomes dominant (4, 5).The multiple kinetic intermediates scheme of Mb has motivated researchers to characterize the structural features of the the intermediates by using both time-resolved (9-14) and cryogenic crystallographic measurements (15)(16)(17)(18)(19)(20)(21)(22). A general picture emerging from these experiments is that Mb...

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Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD-95, and the results were used to illustrate the energy exchange network of inter-residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21-fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph.