Takakazu Ishikura

Theoretical study of the prion protein based on the fragment molecular orbital method

We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called “Parallelized ab initio calculation system based on FMO (PAICS)”.

Role of protein in the primary step of the photoreaction of yellow protein

We show the unexpectedly important role of the protein environment in the primary step of the photoreaction of the yellow protein after light illumination. The driving force of the trans‐to‐cis isomerization reaction was analyzed by a computational method. The force was separated into two different components: the term due to the protein‐chromophore interaction and the intrinsic term of the chromophore itself. As a result, we found that the contribution from the interaction term was much greater than that coming from the intrinsic term. This accounts for the efficiency of the isomerization reaction in the protein environment in contrast to that in solution environments. We then analyzed the relaxation process of the chromophore on the excited‐state energy surface and compared the process in the protein environment and that in a vacuum. Based on this analysis, we found that the bond‐selectivity of the isomerization reaction also comes from the interaction between the chromophore and the protein environment. Proteins 2004.

Direct measure of functional importance visualized atom-by-atom for photoactive yellow protein: Application to photoisomerization reaction

Photoreceptor proteins serve as efficient nano‐machines for the photoenergy conversion and the photosignal transduction of living organisms. For instance, the photoactive yellow protein derived from a halophilic bacterium has the p‐coumaric acid chromophore, which undergoes an ultrafast photoisomerization reaction after light illumination. To understand the structure‐function relationship at the atomic level, we used a computational method to find functionally important atoms for the photoisomerization reaction of the photoactive yellow protein. In the present study, a “direct” measure of the functional significance was quantitatively evaluated for each atom by calculating the partial atomic driving force for the photoisomerization reaction. As a result, we revealed the reaction mechanism in which the specific role of each functionally important atom has been well characterized in a systematic manner. In addition, we observed that this mechanism is strongly conserved during the thermal fluctuation of the photoactive yellow protein. We compared the experimental data of fluorescence decay constant of several different mutants and the present analysis. As a result, we found that the reaction rate constant is decreased when a large positive driving force is missing. Proteins 2004.

Energy exchange network of inter‐residue interactions within a thermally fluctuating protein molecule: A computational study

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.

Spectral Tuning of Photoactive Yellow Protein

We report a theoretical study on the optical properties of a small, water‐soluble photosensory receptor, photoactive yellow protein (PYP). A hierarchical ab initio molecular orbital calculation accurately evaluated the optical absorption maximum of the wild‐type, as well as the λmax values of 12 mutants. Electronic excitation of the chromophore directly affects the electronic state of nearby atoms in the protein environment. This effect is explicitly considered in the present study. Furthermore, the spectral tuning mechanism of PYP was investigated at the atomic level.

Theoretical modeling of the O-intermediate structure of bacteriorhodopsin

Bacteriorhodopsin is a prototype of efficient molecular machinery functioning as a light‐activated proton pump. Among the five distinct intermediates (K, L, M, N, and O) of the photocycle, there is less structural information on the later stages compared with the early intermediates. Here, we report the structural modeling of the O‐intermediate for which the determination of experimental structure remains difficult. Hypothetical conformational change of the molecule from the light‐adapted state to the O‐intermediate state was simulated by gradually changing the protonation state of two residues. To achieve accurate molecular modeling, we carefully constructed a realistic system of the native purple membrane. The modeled structure of the O‐intermediate has some implications about proton transfer in the later stages of the photocycle and the structural response of bacteriorhodopsin to the inner charge distribution. Proteins 2009.