研究者詳細 - 倭　剛久

論文 - 倭　剛久

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

"A. Yamada, T. Ishikura, T. Yamato"

"PROTEINS: Structure, Function and Bioinformatics" 55 巻 ( 4 ) 頁： 1070-1077 2004年6月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Torsion potential works in rhodopsin 査読有り

"A. Yamada, T. Yamato, S. Yamamoto, T. Kakitani"

Photochemistry and Photobiology 79 巻 ( 5 ) 頁： 476-486 2004年5月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Protein driven photoisomerization reaction: Ab initio QM/MM study of photoactive yellow protein

"Yamada A, Ishikura T, Yamato T"

BIOPHYSICAL JOURNAL 84 巻 ( 2 ) 頁： 270A-270A Part 2 Suppl. S 2003年2月

A Computational Study on the stability of the protonated Schiff base of retinal in rhodopsin 査読有り

"A. Yamada, T. Kakitani, S. Yamamoto, and T. Yamato"

Chem. Phys. Lett. 366 巻 ( 5-6 ) 頁： 670-675 2002年12月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Destructive interference in the electron tunneling through protein media 査読有り

"T. Kawatsu, T. Kakitani, T. Yamato"

J. Phys. Chem. B. 106 巻 ( 43 ) 頁： 11356-11366 2002年10月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

On the anomaly of the tunneling matrix element in long-range electron transfer 査読有り

"T. Kawatsu, T. Kakitani, T. Yamato"

J. Phys. Chem. B. 106 巻 ( 19 ) 頁： 5068-5074 2002年5月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Unique mechanism of excitation energy transfer and photoisomerization in biological systems 査読有り

"T. Kakitani, T. Kawatsu, A. Kimura, A. Yamada, T. Yamato, S. Yamamoto"

J. Biol. Phys. 28 巻 ( 3 ) 頁： 367-381 2002年

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Analysis of cis-trans photoisomerization mechanism of rhodopsin based on the tertiary structure of rhodopsin 査読有り

"A. Yamada, T. Yamato, T. Kakitani, S. Yamamoto"

J. Photoscience 9 巻頁： 51-54 2002年

Theory of excitation energy transfer in the intermediate coupling case and its application to the photosynthetic antenna systems 査読有り

"Akihiro Kimura, Toshiaki Kakitani, Takahisa Yamato"

International Journal of Modern Physics B 15 巻 ( 28-30 ) 頁： 3833-3836 2001年12月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Ab initio MO study on the potential energy surfaces for twisting around C15=N bond of protonated Schiff base of retinal 査読有り

"S. Yamamoto, H. Wasada, T. Kakitani, T. Yamato"

THEOCHEM 543 巻頁： 79-87 2001年6月

記述言語：英語掲載種別：研究論文（学術雑誌）

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.

Worm Model for Electron Tunneling in Proteins: Consolidation of the Pathway Model and the Dutton Plot 査読有り

"T. Kawatsu, T. Kakitani, T.Yamato"

J. Phys. Chem. B. 105 巻 ( 19 ) 頁： 4424-4435 2001年5月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Ab initio MO study on potential energy surfaces for twisting around C7=C8 and C4-C7 bonds of coumaric acid 査読有り

"A. Yamada, S. Yamamoto, T. Yamato, T. Kakitani"

THEOCHEM 536 巻 ( 2-3 ) 頁： 195-201 2001年2月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Theory of excitation energy transfer in the intermediate coupling case. II. Criterion for intermediate coupling excitation energy transfer mechanism and application to the photosynthetic antenna system 査読有り

"A. Kimura, T. Kakitani, T. Yamato"

J. Phys. Chem. B. 104 巻 ( 39 ) 頁： 9276-9287 2000年10月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Theory of excitation transfer in the intermediate coupling case 査読有り

"A. Kimura, T. Kakitani, T. Yamato"

J. Luminescence 87-89 巻頁： 815-817 2000年5月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

A novel method for determining electron tunneling pathway in protein 査読有り

"T. Kawatsu, T. Kakitani, T. Yamato"

Inorganica Chimica Acta 300-302 巻頁： 862-868 2000年4月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Monte Carlo simulation study on the structure and reaction at metal-electrolyte interface. II. Mechanism of nonlinear electrode reactions 査読有り

"N. Goto, T. Kakitani, T. Yamato, Y. Hatano"

J. Phys. Soc. Jpn. 68 巻 ( 11 ) 頁： 3729-3737 1999年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Ab initio MO study on the potential energy surfaces for twisting around the C₁₁=C₁₂ bond of the protonated Schiff base of retinal 査読有り

"Yamamoto, S., Wasada, H., Kakitani, T., Yamato, T"

THEOCHEM 461-462 巻頁： 463-471 1999年4月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Molecular Dynamics of a 15-Residue Poly(L-alanine)in Water : Helix Formation and Energetics 査読有り

"M. Takano, T. Yamato, J. Higo, A. Suyama, K. Nagayama"

Journal of the American Chemical Society 121 巻 ( 4 ) 頁： 605-612 1999年2月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

Molecular dynamics simulation of the excited-state dynamics of bacteriorhodopsin

"T. Yamato, T. Kakitani"

"Photosynthesis: Mechanisms and Effects, Vol. III, G. Garab, ed., Kluwer Academic Publishers, Netherlands" 頁： 1771-1774 1999年

Novel method to detect a motif of local structures in different protein conformations 査読有り

"H. Wako, T. Yamato"

Protein Engineering 11 巻 ( 11 ) 頁： 981-990 1998年11月

記述言語：英語掲載種別：研究論文（学術雑誌）

"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."

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