Authorship：Lead author,　Last author,　Corresponding author   Language：Japanese   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.2142/biophys.60.094

Authorship：Lead author,　Corresponding author   Language：English   Publishing type：Research paper (conference, symposium, etc.)  

DOI： doi.org/10.1007/s12551-020-00625-4

Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.1007/s12551-020-00661-0

DOI： 10.1021/acs.jpcb.8b10489

Web of Science

DOI： 10.2142/biophysico.16.0_322

Web of Science

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.8b07552

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1021/acs.jpcb.8b04333

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Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.cplett.2017.11.025

Web of Science

Language：English   Publishing type：Research paper (scientific journal)  

Web of Science

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1016/j.bpj.2016.09.051

Language：English   Publishing type：Research paper (scientific journal)  

DOI： doi.org/10.1016/j.bpj.2016.09.051

Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)  

Authorship：Lead author   Language：Japanese  

Language：English   Publishing type：Research paper (scientific journal)  

We performed stresstensoranalysis of polypeptides at the atomic level by molecular dynamics simulations. Most of the approaches to stresstensoranalysis of molecules in the literature assume that the interatomic forces are pairwise; however commonly used force-field functions contain multi-body interactions. To address this issue, we derived new mathematical formulae for atomic forces based on force-field functions, in which the total force acting on each atom is expressed as a summation of pairwise interatomic forces. Then, a computer program for stresstensoranalysis was developed, and it successfully characterized the mechanical features of molecules at the atomic level.

DOI： 10.1016/j.cplett.2012.05.005

Language：English   Publishing type：Research paper (scientific journal)  

DOI： 10.1063/1.4704586

Language：English   Publishing type：Research paper (scientific journal)  

The evolution of structural fluctuations of proteins was examined by calculating the isothermal compressibility (beta_T) values of chicken lysozyme and its six evolutionary mutants at Thr40, Ile55, and Ser91 (a ternary mutant corresponding to bobwhite lysozyme) from their X-ray structures by normal-mode analysis at 300 K. The beta_T values of the two extant lysozymes from chicken and bobwhite were 1.61 and 1.59 Mbar^-1, respectively, but five other evolutionary mutants showed larger beta_T values of up to 2.17 Mbar^-1. These results suggest that ancestral lysozymes exhibit larger volume fluctuations than extant ones, and hence that the molecular evolution of lysozymes has followed a nonneutral evolutionary pathway. The evolutionary mutants contained large amount of cavities, although no change was visible in the X-ray structures. There was a linear correlation between βT and total cavity volume, predicting that the cavity volume or atomic packing is an important factor regulating volume fluctuations during the molecular evolution of this protein.

Language：English   Publishing type：Research paper (scientific journal)  

Authorship：Lead author   Language：Japanese  

Authorship：Lead author   Language：Japanese  

Language：English   Publishing type：Research paper (scientific journal)  

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 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 novel method, the continuous illumination of native MbCO 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.

Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)  

DNA photolyase recognizes UV-damaged DNA and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer (CPD) by light-activated electron transfer reaction between the flavin adenine dinucleotide (FADH−), the electron donor, and CPD, the electron acceptor. Theoretical analysis of the electron tunneling pathways of the DNA photolyase derived from Anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. Here, we report the unexpectedly important role of the single methionine residue, Met353, where busy trafficking of electron tunneling currents is observed. The amino acid conservation pattern of Met353 in the homologous sequences perfectly correlates with experimentally verified annotation as photolyases. The bioinformatics sequence analysis also suggests that the residue plays a pivotal role in biological function. Consistent findings from different disciplines of computational biology strongly suggest the pivotal role of Met353 in the biological function of DNA photolyase.

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Immediately after photon absorption, the photoenergy is converted to local stress energy via the ultrafast photoisomerization reaction of the p-coumaric acid (pCA) chromophore in a small water-soluble blue light receptor, photoactive yellow protein (PYP), derived from the halophilic bacterium, Halorhodospira halophila. A series of conformational changes are then induced, which are intimately related with the relaxation process on the energy landscape of PYP. In order to understand the signaling function of PYP in atomic detail, the characterization of the physical mechanism of the protein quake of PYP is important as well as the atomic description of the series of conformational changes associated with the photocycle is important. Here, we report a theoretical/computational study for the analysis of the intramolecular stress tensor for the dark state and three intermediate states, pR, pB1 and pB2, of PYP. As a result, we found that the magnitude of the stress released during the change from pR to pB1 state is significantly large at the hydroxyl oxygen atom of Tyr42 suggesting that this atom is the focus of the proteinquake of PYP. This is consistent with previous experimental observations.

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"Vision begins when light is absorbed by visual pigments. It is commonly believed that the absorption spectra of visual pigments are modulated by interactions between the retinal and amino acids within or near 4.5 angstrom of the retinal in the transmembrane (TM) segments. However, this dogma has not been rigorously tested. Here, we show that the retinal-opsin interactions extend well beyond the retinal binding pocket. We found that, although it is positioned outside of TM segments, the C-terminus of the rhodopsin in the rockfish longspine thornyhead (Sebastolobus altivelis) modulates its by interacting mainly with the last TM segment. Our results illustrate how amino acids in the C-terminus are likely to interact with the retinal. We anticipate our analyses to be a starting point for viewing the spectral tuning of visual pigments as interactions between the retinal and key amino acid residues that are distributed throughout the entire pigment."

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

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 lambda_max 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.The static disorder of a protein molecule is intimately related to the complex nature of its energy landscape. By using molecular dynamics simulation and quantum mechanical structure optimization, we obtained multiple minimum energy conformations of PYP. The statistical distribution of electronic excitation energies of these minima was compared with the hole-burning experiment [Masciangioli, T. (2000) Photochem. Photobiol. 72, 639-644], a direct observation of the distribution of excitation energies.

Language：English   Publishing type：Research paper (bulletin of university, research institution)  

Language：English   Publishing type：Research paper (scientific journal)  

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.

Language：English   Publishing type：Research paper (scientific journal)  

We found a linear correlation between the theoretically predicted shifts and experimentally observed absorption spectra for various mutants of photoactive yellow protein (PYP), a photosensory receptor. Excitation energies of mutants were evaluated by the combination of the high level ab initio calculation for the chromophore inside and the low level ab initio calculation for the surrounding protein environment. Importantly, the electronic states of these two regions were treated both as variables and they are solved consistently to each other. The protein-chromophore interaction has been accurately reproduced by this method.

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"The property of the anomalous inverted region in the energy gap law which was found in the recent non-Condon theory of the electron transfer (ET) in protein media is investigated in more detail in relation to the inelastic electron tunneling. The physical aspect of the inelastic electron tunneling is theoretically discussed and schematically explained. Since it was previously shown that the inelastic electron tunneling mechanism worked significantly due to an exponential-like decay of the autocorrelation function of the electron tunneling matrix element with a small correlation function is obtained or not and how the correlation time is changed at low temperatures. For this purpose, numerical calculations for the electron tunneling matrix element in the ET at 77 K from bacteriopheophytin anion to the primary quinine in the reaction center of photosynthetic bacteria Rhodobactor sphaerhoides are made. The results are that almost exponential-like decay of the autocorrelation function was obtained even at 77 K and the half decay time was of the similar magnitude to that at 300 K. Physical meaning of this temperature dependence is discussed."

Language：English  

Language：English   Publishing type：Research paper (scientific journal)  

"Developing the quantum transition rate theory of Prezhdo and Rossky (J. Chem. Phys. 1997, 107, 5863), we produced a new non-Condon theory of the rate of electron transfer (ET) which happens through a protein medium with conformational fluctuation. The new theory is expressed by a convolution form of the power spectrum for the autocorrelation function of the electronic tunneling matrix element T-DA(t) with quantum correction and the ordinary Franck-Condon factor. The new theory satisfies the detailed balance condition for the forward and backward ET rates. The ET rate formula is divided into two terms of elastic and inelastic tunneling mechanisms on the mathematical basis. The present theory is applied to the ET from Bph(-) to Q(A) in the reaction center of Rhodobacter sphaeroides. Numerical calculations of T-DA(t) were made by a combined method of molecular dynamics simulations and quantum chemistry calculations. We showed that the normalized autocorrelation function of TDA(t) is almost expressed by exponential forms. The calculated energy gap law of the ET rate is nearly Marcus' parabola in most of the normal region and around the maximum region, but it does not decay substantially in the inverted region, which is called the anomalous inverted region. We also showed that the energy gap law at the high uphill energy gap in the normal region is elevated considerably from the Marcus' parabola, which is called the anomalous normal region. Those anomalous energy gap laws are due to the inelastic tunneling mechanism which works actively at the energy gap far from zero. We presented an empirical formula for easily calculating the non-Condon ET rate, which is usable by many researchers. We provided experimental evidence for the anomalous inverted region which was basically reproduced by the present theory. The present theory was extensively compared with the previous non-Condon theories."

Language：English   Publishing type：Research paper (scientific journal)  

"Electron tunneling routes for the electron transfer from the bacteriopheophytin anion to the primary quinone in the bacterial photosynthetic reaction center of Rhodobactor sphaeroides are investigated by a combined method of molecular dynamics simulations for the protein conformation fluctuation and quantum chemical calculations for the electronic states of the donor, acceptor, and protein medium. The analysis of the tunneling route is made by mapping interatomic electron tunneling currents for each protein conformation. We found that there are two dominant routes mainly passing through TrpM252 (Trp route) or mainly passing through MetM218 (Met route). Actual electron tunneling pathways alternate between the two routes, depending on the protein conformation which varies with time. When either the Trp route or the Met route dominates, the electron tunneling matrix element TDA becomes large. When both the Trp route and the Met route dominate, TDA becomes very small due to the destructive interference of the electron tunneling currents between the two routes. We found that a linear relationship exists between the value of TDA and the inverse of the degree of destructive interference Q for a wide range of values (ca. 3-103 for Q). A similar relationship was also found previously for electron transfer in ruthenium-modified azurins (Kawatsu, T.; Kakitani, T.; Yamato, T. J. Phys. Chem. B 2002, 106, 11356), suggesting that this relationship holds true in general. From these results, we are led to the conclusion that TDA cannot exceed a maximum value at Q = 1, even if much variation of TDA happens due to the fluctuation of protein conformation. We also conclude that the property of the electron transfer alternates between constructive and destructive interference, due to the fluctuation of protein conformation. It is impossible to keep a system in either constructive or destructive interference because thermal fluctuation of protein conformation takes place."

Language：English  

Language：English   Publishing type：Research paper (bulletin of university, research institution)  

Language：English   Publishing type：Research paper (scientific journal)  

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.

Language：English   Publishing type：Research paper (scientific journal)  

"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."

Language：English   Publishing type：Research paper (scientific journal)  

"We investigate the role of protein environment of rhodopsin and the intramolecular interaction of the chromophore in the cis-trans photoisomerization of rhodopsin by means of a newly developed theoretical method. We theoretically produce modified rhodopsins in which a force field of arbitrarily chosen part of the chromophore or the binding pocket of rhodopsin is altered. We compare the equilibrium conformation of the chromophore and the energy stored in the chromophore of modified rhodopsins with those of native rhodopsins. This method is called site-specific force field switch (SFS). We show that this method is most successfully applied to the torsion potential of rhodopsin. Namely, by reducing the twisting force constant of the C11=C12 of 11-cis retinal chromophore of rhodopsin to zero, we found that the equilibrium value of the twisting angle of the C11=C12 bond is twisted in the negative direction down to about -80degrees. The relaxation energy obtained by this change amounts to an order of 10 kcal/mol. In the case that the twisting force constant of the other double bond is reduced to zero, no such large twisting of the bond happens. From these results we conclude that a certain torsion potential is applied specifically to the C11=C12 bond of the chromophore in the ground state of rhodopsin. This torsion potential facilitates the bond-specific cis-trans photoisomerization of rhodopsin. This kind of the mechanism is consistent with our torsion model proposed by us more than a quarter of century ago. The origin of the torsion potential is analyzed in detail on the basis of the chromophore structure and protein conformation, by applying the SFS method extensively."

Language：English  

Language：English   Publishing type：Research paper (scientific journal)  

"We investigated the effect of amino acids in rhodopsin on the protonation state of the Schiff base (SB) retinal. We constructed a model system consisting of SB retinal, Glul 13 (counterion), and eight residues. For this model, we considered two states of the SB retinal, namely, the protonated/deprotonated state. We then performed ab initio, MO calculations at the RHF/6-31g* level. As a result, the protonated state was stabler than the deprotonated state. Interestingly, we observed an additive rule for the contribution to the stabilization energy due to each amino acid. Above all, it turned out that Ser186 and Cys187 play a significant role in the stability."

Language：English   Publishing type：Research paper (scientific journal)  

"We investigated the origin of the very rapid and large fluctuation of the electron tunneling matrix element TDA due to the thermal fluctuation of protein conformation which was recently observed by the simulation study (Daizadeh, L; Medvedev, E. S.; Stuchebrukhov, A. A. Proc. Natl. Acad. Sci. U.S.A. 1997, 94, 3703). We made analysis of this phenomena by using the interatomic tunneling current map of Ru-modified azurins. We defined a new index, degree of destructive interference Q, by making an average of the intermediate level for the interatomic tunneling currents. We found an empirical relation that \T-DA] is proportional to Q(-1) holds true in the course of thermal fluctuation of protein conformation. Comparing maps of the interatomic tunneling currents with different values of Q, we found that the very rapid (in much less than 1 ps) and large amount (maximally 2 orders of magnitude) of fluctuations in T-DA are caused by the reconnection and the change in the direction of interatomic tunneling currents with considerable amplitudes. By taking the statistical average for the dynamics effect of log \T-DA\, we found that the range of the averaged dynamic modification of electron transfer rate amounts to more than 2 orders of magnitude in the Ru-modified azurins. In the systems with a large range of dynamic modification, this nuclear dynamics effect contributes to enhance the thermally averaged electron transfer rate considerably."

Language：English   Publishing type：Research paper (scientific journal)  

"The electron tunneling matrix element of long-range electron transfer has usually been calculated by the two-state model. This model is useful when couplings between a donor and mediator and between an acceptor and mediator are weak. In the resent paper, we make correction for this electron tunneling matrix element on the basis of the diabatic picture so that the element can be used when the couplings are not necessarily weak. This correction is due to the normalization factors for the electronic wave functions of the initial and final states. We prove that these normalization factors are equivalent to the ""dilution factors"" derived by Katz and Stuchebrukhov (J. Chem. Phys. 1998, 109, 4960) on the basis of the adiabatic picture by adopting the truncation of Taylor expansion. We find that the normalized tunneling matrix element for the electron transfer in protein has a dip when the tunneling energy approaches the energy of the localized state whose group is close to either the donor or acceptor. This dip can be eliminated by choosing a combined system of the molecular group corresponding to the localized state with the original donor or acceptor as a new donor or acceptor. Making use of this anomaly, we can determine the proper size of the donor or acceptor in any long-range electron-transfer reaction."

Language：English   Publishing type：Research paper (scientific journal)  

Language：English   Publishing type：Research paper (scientific journal)  

"We discuss unique mechanisms typical in the elementary processes of biological functions. We focus on three topics. Excitation energy transfer in the light-harvesting antenna systems of photosynthetic bacteria is unique in its structure and the energy transfer mechanism. In the case of LH2 of Rhodopseudomonas acidophila, the B850 intra-ring energy transfer and the inter-ring energy transfer between B800 and B850 take place by the intermediate coupling mechanism of energy transfer. The excitonic coherent domain shows a wave-like movement along the ring, and this property is expected to play a significant role in the inter-ring energy transfer between LH2's. The electron transfer in biological systems is mostly long-range electron transfer that occurs by the electron tunneling through the protein media. There is a long-standing problem that which part of protein media is used for the electron tunneling root. As a result of our detailed analysis, we found that the global electron tunneling root is a little winded with a width of a few angstrom, reflecting the property of tertiary and secondary structures of the protein and it is affected by the thermal fluctuation of protein structure. Photoisomerization of rhodopsin is very unique: The cis-trans photoisomerization of rhodopsin occurs only around the C11 = C12 bond in the counterclockwise direction. Its molecular mechanism is resolved by our MD simulation study using the structure of rhodopsin which was recently obtained by the X-ray crystallographic analysis."

Language：English   Publishing type：Research paper (scientific journal)  

"We developed the theory of excitation energy transfer (EET) in the intermediate coupling case using the decoupling procedure. We succeeded in treating the theory analytically by assuming that the two-time correlation function is represented as an exponential function. We examined the validity of its approximation. We calculated the time dependent probability n(a)(t) of the EET, in which the acceptor molecule is in the excited state by making alternative calculation of the cumulant expansion method. Applying this calculation by this method to the photosynthetic antenna systems and comparing its result with the analytical formula, we found that these results coincide well with each other in the due time region of the approximation."

Language：English   Publishing type：Research paper (scientific journal)  

We have calculated the potential energy surfaces for the twisting around the C-15=N bond of protonated Schiff base of retinal (PSBR) with and without a negative point charge or a water molecule in the vicinity of the Schiff base by means of the state-average complete active space self-consistent field (sa-CASSCF) method. We have found that the S-1 potential energy surface has a large energy barrier for twisting from -180 to -90 degrees for PSBR in vacuum and for PSBR with a water molecule. These results are quite different from the S-1 potential energy surface for the twisting around the C-11=C-12 and C-13=C-14 bonds where very small energy barriers exist in the above molecular systems.

Language：English   Publishing type：Research paper (scientific journal)  

"We present a novel method for selecting important electron tunneling pathways in proteins by connecting important interatomic tunneling currents. Then, we constituted an electron tunneling route, called a ""worm"", which is formed by averaging over all of the interatomic tunneling currents. The method is applied to six kinds of Ru-modified azurins where the electron transfer takes place from the copper ion to the ruthenium ion linked to the surface of the azurin. We found that the worm is not straight but winds, reflecting the specific role of the microenvironment of the protein structure and ligands in the electron tunneling pathway and rather narrow radius of the worm, ca. 1.5 Angstrom at most. The donor-acceptor distance dependence of the electron-transfer rate k(e) is examined by taking into account the one-dimensional atomic density in the worm. We found that the Dutton plot, in which the logarithm of k(e) is in a linear relation with the donor-acceptor distance, which, in turn, depends somewhat an the one-dimensional atom density, is reproduced for a certain level of analysis by the worm model. Thus, we can consolidate the electron tunneling pathway model with the Dutton plot by using the worm model."

Language：English   Publishing type：Research paper (scientific journal)  

"We have calculated potential energy surfaces (PESs) for the twisting around C7=C8 and C4-C7 bonds of anionic form of coumaric acid with and without hydrogen bonds between its phenorate part and hydroxyl groups nearby. modeling the active sits of Photoactive Yellow Protein. The calculation is made by means of the state-average complete active space self-consistent field theory. We revealed that the PESs of the ground and first excited states as a function of twisting angle around C7=C8 are of strongly crt,sing type. and the crossing tendency becomes more prominent in the presence of the hydrogen bonds. We found that the PESs of the ground and first excited states as: a function of twisting angle around C4-C7 bond are also of crossing type, representing double bond character."

Language：English   Publishing type：Research paper (scientific journal)  

"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 Forster mechanisms. We exploited a novel method for determining the EET rate applicable to all the mechanisms from Forster 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."

Language：English   Publishing type：Research paper (scientific journal)  

"Theory of excitation energy transfer (EET) between donor and acceptor molecules in the intermediate coupling case is constructed. This theory interpolates theories of exciton and Forster mechanism. We also derived formulas of criterion among exciton, intermediate coupling and Forster mechanisms. The theory was applied to the light-harvesting system LH2 of photosynthetic bacteria."

Language：English   Publishing type：Research paper (scientific journal)  

"A novel method for determining the electron tunneling pathway in protein is proposed. The pathway is constructed connecting vectors of important interatomic currents of the tunneling electron. The method is applied to some ruthenium-modified azurins. From this analysis, we found that the through-space is very often used as well as the through-bond, while the hydrogen-bond is scarcely used in the important interatomic currents."

Language：English   Publishing type：Research paper (scientific journal)  

"Using the two-dimensional free energy surfaces which were obtained previously by the Monte Carlo simulations for metal-electrolyte interfaces by allowing the movement of reactant [N. Goto et al.: J. Phys, Sec. Jpn. 66 (1997) 1825], we have analyzed the mechanism of nonlinearity in the electrode reaction in detail. The nonlinearity was defined as a square of ratio between widths of the energy gap laws for the neutralization and ionization reactions. We developed a method to derive the nonlinearity due to only fluctuations of motion of solvent molecules and electrolyte ions for each distance of the reactant from the metal surface. We found that the nonlinearity was the largest (4.8) at the distance 6 Angstrom of the reactant from the metal surface, and was the smallest (2.2) at the distance 2 Angstrom where the reactant is in contact with the metal surface and at the distance larger than 9 Angstrom where Gouy-Chapman diffuse layer ends. We also found that the movement of the ions and solvents directly adsorbed to the metal-surface is strongly restricted, showing a feature of dielectric saturation. Combining these facts, we conclude that the strongly adsorbed layer of ions and solvent molecules (Helmholtz double layer) causes a large nonlinear phenomenon of the electrode reaction due to breakdown of the central limit theorem especially for the reactant contacting the adsorbed layer."

Language：English   Publishing type：Research paper (scientific journal)  

"We have calculated potential energy surfaces for the twisting around the C-11=C-12 bond of the protonated Schiff base of retinal without and with a negative point charge or a water molecule in the vicinity of the Schiff base by means of the state-average complete active space self-consistent field (sa-CASSCF) method. We find that the potential energy surfaces obtained in this study are qualitatively similar to, but quantitatively different from those for the twisting around the C-13=C-14 bond of the protonated Schiff base which were obtained previously."

Language：English   Publishing type：Research paper (scientific journal)  

"We present a molecular dynamics study of the alpha-helix formation in a system consisting of a 15-residue poly(L-alanine) and surrounding water molecules. By applying a relatively high temperature, we observed the alpha-helix formation several times during a 17-ns run, and reversible helix-coil transitions were also observed. The alpha-helix formations were usually initiated by the beta-tum structures. A crank-shaft-like motion of the peptide was included in the folding process. In the formed alpha-helical domains, substantial 3(10)-helix formations were found especially at the termini, as observed by the NMR study. The folding time scale at room temperature estimated from our simulation was found to lie in the range of 100ns, which is in accord with the time scale of the T-jump experiments. The total energy of the whole system was lower in the alpha-helix state than in the random-coil state by 20.4 +/- 4.8 kcal/mol, which is consistent with the experimental value obtained by calorimetry. This energy decrease in forming the alpha-helix was mainly caused by the Coulombic energy and the torsional energy."

Authorship：Lead author   Language：English   Publishing type：Research paper (bulletin of university, research institution)  

Language：English   Publishing type：Research paper (scientific journal)  

"In order to detect a motif of local structures in different protein conformations, the Delaunay tessellation is applied to protein structures represented by C-alpha atoms only. By the Delaunay tessellation the interior space of the protein is uniquely divided up into Delaunay tetrahedra whose vertices are the C-alpha atom positions. Some edges of the tetrahedra are virtual bonds connecting adjacent residues' C-alpha atoms along the polypeptide chain and others indicate interactions between residues nearest neighbouring in space. The rules are proposed to assign a code, i.e., a string of digits, to each tetrahedron to characterize the local structure constructed by the vertex residues of one relevant tetrahedron and four surrounding it. Many sets comprised of the local structures with the same code are obtained from 293 proteins, each of which has relatively low sequence similarity with the others, The local structures in each set are similar enough to each other to represent a motif, Some of them are parts of secondary or supersecondary structures, and others are irregular, but definite structures. The method proposed here can find motifs of local structures in the Protein Data Bank much more easily and rapidly than other conventional methods, because they are represented by codes. The motifs detected in this method can provide more detailed information about specific interactions between residues in the local structures, because the edges of the Delaunay tetrahedra are regarded to express interactions between residues nearest neighbouring in space."

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

"Molecular dynamics simulations were carried out to study what happens in a photoreceptor protein, photoactive yellow protein (PYP), immediately after the vertical transition of the chromophore from the ground to the excited state. A photon absorption simulation was performed to investigate the movement of amino acid residues upon photoexcitation, To calculate the excited state of the chromophore, SCF-CI calculation was carried out with INDO/S Hamiltonian, We observed that some amino acid residues have strong interactions with the chromophore, Most of these amino acid residues are conserved in PYPs from three different species of bacteria. This observation indicates the biological importance of these residues. Proteins 32:268-275, 1998."

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

"The excited-state dynamics of bacteriorhodopsin was studied by molecular dynamics simulation. For the purpose of suppressing large displacement of amino acid residues on the surface of bacteriorhodopsin, positional restraints were imposed on these residues. A new method was developed to investigate the movement of amino acid residues upon photoexcitation and their role on the ultrafast photoisomerization of the chromophore. The structural change of bacteriorhodopsin was then traced up to 200 fs, i.e. until the formation of the intermediate I. We found that when all the conjugated bonds of the chromophore were allowed to twist freely in the excited state, many bonds including the C13=C14 bond twist in large scale within 100 fs. When only the C13=C14 bond and the single bonds were allowed to twist freely, the twisting took place at most 20 degrees within 200 fs. From these results, it is claimed that a special potential surface is provided for the C13=C14 bond twisting by the protein environment in the course of the isomerization reaction, giving rise to the specific, ultrafast photoisomerization of bacteriorhodopsin. As a trace of such a mechanism, we observed that several functionally important residues incuding Asp85, Asp212 and Tyr185 responded quickly to the photoexcitation of the chromophore."

Language：English   Publishing type：Research paper (scientific journal)  

"The mechanical response of a TIM-barrel protein to an applied pressure has been studied. We generated structures under an applied pressure by assuming the volume change to be a Linear function of normal mode variables. By Delaunay tessellation, the space occupied by protein atoms is divided uniquely into tetrahedra, whose four vertices correspond to atomic positions. Based on the atoms that define them, the resulting Delaunay tetrahedra are classified as belonging to various secondary structures in the protein. The compressibility of various regions identified with respect to secondary structural elements in this protein is obtained from volume changes of respective regions in two structures with and without an applied pressure. We found that the beta barrel region located at the core of the protein is quite soft. The interior of the beta barrel, occupied by side chains of beta strands, is the softest. The helix, strand, and loop segments themselves are extremely rigid, while the regions existing between these secondary structural elements are soft. These results suggest that the regions between secondary structural elements play an important role in protein dynamics, Another aspect of tetrahedra, referred to as bond distance, is introduced to account for rigidities of the tetrahedra. Bond distance is a measure of separation of the atoms of a tetrahedron in terms of number of bonds along the polypeptide chain or side chains. Tetrahedra with longer bond distances are found to be softer on average. From this behavior, we derive a simple empirical equation, which well describes the compressibilities of various regions."

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

"The tensor fields of pressure strain imposed on protein molecules have been visualized by computer graphics and computational geometry. The pressure-induced deformations of lysozyme and myoglobin were analyzed by the present method, which regards each molecule as a patchwork of microscopic continuous bodies of Delaunay tetrahedra. The strain tensor describes the deformation of each tetrahedron. The illustrated deformations turned out to be complex and inhomogeneous ones in which local expansions and contractions concomitantly occurred. Not only the pressure deformation but also any other type of moderate deformation can be analyzed by this method."

Authorship：Lead author   Language：English   Publishing type：Research paper (bulletin of university, research institution)  

Molecular dynamics simulations of the S-peptide of ribonuclease S in water at 1 atm and 10 k atm were conducted. Conformational clusters were found in these dynamics trajectories. Pressure effects on peptide structures were investigated using a strain tensor analysis with Delaunay tessellation. A computer graphics technique was employed in the analysis. The whole structure of the S-peptide was divided into core parts in which atom packings were conserved and surrounding flexible parts.

Authorship：Lead author   Language：Japanese  

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

"A new topographical metric has been introduced for measuring the topographical difference between the three-dimensional instantaneous conformations of a protein which is thermally fluctuating at room temperature. Delaunay tetrahedra were employed for defining topographical structures and the metric. An 18.6 ps trajectory at 300 K, obtained from a precise molecular dynamics simulation of human lysozyme in aqueous solution, was analyzed using the topographical metric. The time series of the protein conformations exhibited both topographical clusters and topographical transitions between the clusters."

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Authorship：Lead author   Language：Japanese  

Authorship：Lead author   Language：English   Publishing type：Research paper (scientific journal)  

"Pressure effect on the equilibrium conformation in sperm whale deoxymyoglobin and its volume fluctuation are studied by the normal mode analysis and strain tensor analysis. The pressure-induced deformation of interhelix regions are found to be remarkably more compressed than the other parts of the molecule. The intrahelix compressibility is shown to be relatively small. We also calculate the compressibility of the three hydrophobic clusters, located at the bottom, distal, and proximal side of the heme. Its value is found to decrease in the indicated order. The average compressibility of these hydrophobic clusters is less than the average interhelix compressibility, even though there are large cavities in these clusters. In order to study overall deformation, we define a linear compressibility and calculate it for all pairs of Catoms. The pressure-induced deformation is observed to be heterogeneous also in this analysis. The calculated root-mean-square displacement of the constituent atoms in the equilibrium conformation at 1,000 atm from those at 0 atm is 0.12 Å, which is much smaller in magnitude than the average value of the atomic fluctuations at room temperature. In the water solvent, the volume excluded by the protein molecule in the equilibrium conformation is reduced by 0.9%, when the pressure is raised from 0 to 1,000 atm. The calculated magnitude of the root-mean-square volume fluctuation is 0.3% of the excluded volume at room temperature. The square of the volume fluctuation is given as a sum of contributions from individual normal modes. Contributions from low frequency normal modes are found to dominate over those from higher frequency normal modes. The estimated value of the isothermal compressibility of deoxymyoglobin is 9.37 ラ 10-12 cm2/dyn."

Authorship：Lead author   Language：English   Publishing type：Research paper (bulletin of university, research institution)  

"Pressure effects on the structure of sperm whale deoxymyoglobin have been studied by the normal mode analysis (NMA) and the strain tensor analysis (STA). Inhomogeneous mechanical construction of the molecule is revealed in the microscopic detail. The pressure-induced deformations of inter-helix regions are remarkably larger than those of the other parts. On the other hand, the intra-helix compressibility is shown to be relatively small."

Authorship：Lead author   Language：Japanese   Publishing type：Research paper (bulletin of university, research institution)  

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