Faculty Profiles - YAMATO, Takahisa

Papers - YAMATO, Takahisa

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Molecular Dynamics Study of Femtosecond Events in Photoactive Yellow Protein After Photocexcitation of the Chromophore Reviewed

"T. Yamato, N. Niimura, N. Go"

"PROTEINS : Structure, Function, and Genetics" Vol. 32 ( 3 ) page： 268-275 1998.8

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."

Molecular Dynamics Simulation of the Excited-State Dynamics of Bacteriorhodopsin Reviewed

"T. Yamato, T. Kakitani"

Photochemistry and Photobiology Vol. 66 ( 6 ) page： 735-740 1997.12

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."

Mechanical Property of a TIM-Barrel Protein Reviewed

"N. Kobayashi, T. Yamato, N. Go"

"Proteins : Structure, Function, and Genetics" Vol. 28 page： 109-116 1997

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."

Strain Tensor Field in Proteins Reviewed

T. Yamato

Journal of Molecular Graphics Vol. 14 page： 105-107 1996

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."

Finite element study of protein structure under high pressure

T. Yamato

"High Pressure Bioscience and Biotechnology Progress in Biotechnology, 13. Elsevier, Amsterdam," page： 157-162 1996

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.

Computer simulation approach

"T. Yamato, N. Go"

( 24 ) page： 25-29 1995

Topographical metric to analyze the theumal flucfuations of protein conformation Reviewed

"T. Yamato, M. Saito, J. Higo"

Chemical Physics Lelters Vol. 219 page： 155-159 1994

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."

Dynamical properties of a beta-sheet in a tim barrel

"N. Kobayashi, T. Yamato, N. Go"

Protein Eng. Vol. 7 ( 9 ) page： 1163-1164 1994

有限要素と歪みテンソル解析を用いた球状蛋白質の圧力変形の研究(共著)

第45回タンパク質構造討論会大阪 1994

Computational Study of Mechanical Constructions of Protein

T. Yamato

BUTSURI Vol. 49 ( 4 ) page： 305-307 1994

Conformational Deformation in Deoxymyoglobin by Hydrostafic Pressure Reviewed

"T. Yamato, J. Higo, Y. Seno, and N. Go"

"Proteins : Structure, Function and Gentics" Vol. 16 ( 4 ) page： 327-340 1993.8

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."

Conformational Deformation in Deoxymyoglobin by Hydrostafic Pressure

T.Yamato and N. Go

"Computer Aided innovation of New Materials II, Elsevier Science Publishers B. V." page： 1215-1218 1993

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."

Glass state of Proteins

"T. Yamato, N. Go"

BUSSEI KENKYU Vol. 59 ( 5 ) page： 672-677 1993

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Papers - YAMATO, Takahisa