Faculty Profiles - YAMATO, Takahisa

Papers - YAMATO, Takahisa

Division display 21 - 40 of about 73 ／ All the affair displays >>

Nonneutral evolution of volume fluctuation in lysozymes revealed by normal-mode analysis Reviewed

Shigefumi Miura, Takahisa Yamato, Tadashi Kamiyama, Kunihiko Gekko

Biophysical Chemistry Vol. 161 page： 39-45 2012.2

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.

Molecular mechanism of long-range synergetic color tuning between multiple amino acid residues in conger rhodopsin Reviewed

Biophysics Vol. 6 page： 67-78 2010.12

Proteins at work: Computational biopolymer science of energy, electron, proton transfer and ligand migration Invited Reviewed

Vol. 67 ( 3 ) page： 179-186 2010.3

*Visualizing breathing motion of internal cavities in concert with ligand migration in myoglobin Reviewed

Ayana Tomita, Tokushi Sato, Kouhei Ichiyanagi, Shunsuke Nozawa, Hirohiko Ichikawa, Matthieu Chollet, Fumihiro Kawai, Sam-Yong Park, Takayuki Tsuduki, Takahisa Yamato, Shin-ya Koshihara, and Shin-ichi Adachi

Proceedings of the National Academy of Sciences of U.S.A Vol. 106 ( 8 ) page： 2612-2616 2009

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.

Theoretical modeling of the O-intermediate structure of bacteriorhodopsin Reviewed

Hiroshi C. Watanabe, Takakazu Ishikura, and Takahisa Yamato

PROTEINS: Structure, Function, and Bioinformatics Vol. 75 ( 1 ) page： 53-61 2009

Identification of Functional Residues of DNA Photolyase by BiophysicalComputation and Bioinformatics Invited Reviewed

Vol. 49 ( 4 ) page： 196-197 2009

*Discrimination of class I CPD photolyase from blue light photoreceptors by single methionine residue Reviewed

Yuji Miyazawa, Hirotaka Nishioka, Kei Yura, and Takahisa Yamato

Biophysical Journal Vol. 94 page： 2194-2203 2008.3

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.

Stress tensor analysis of the proteinquake of photoactive yellow protein Reviewed

Kana Koike, Kazutomo Kawaguchi, and Takahisa Yamato

Phys. Chem. Chem. Phys. Vol. 10 ( 10 ) page： 1400-1405 2008

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

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.

Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus Invited Reviewed

"S. Yokoyama, T. Tada, T. Yamato"

Photochemistry and Photobiology Vol. 83 ( 2 ) page： 236-241 2007.3

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

"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."

Spectral tuning of photoactive yellow protein Invited Reviewed

"T. Yamato, T. Ishikura, T. Kakitani, K. Kawaguchi, H. Watanabe"

Photochemistry and Photobiology Vol. 83 ( 2 ) page： 323-327 2007.3

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.

Non-Condon theory for the energy gap dependence of electron transfer rate

"H. Nishioka, T. Yamato, T. Kakitani"

Frontiers of Computational Science. Proceedings of the International Symposium on Frontiers of Computational Science 2005, Y. Kaneda, H. Kawamura, M. Sasai, Eds., Springer page： 293-297 2007

*Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis Reviewed

T. Ishikura, T. Yamato

Chemical Physics Letters Vol. 432 ( 4-6 ) page： 533-537 2006.12

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.

Theoretical prediction of optical absorption maxima for photosensory receptor mutants Reviewed

"Kazutomo Kawaguchi, and Takahisa Yamato"

Chemical Physics Letters Vol. 430 ( 4-6 ) page： 386-390 2006.10

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.

Temperature dependence of the inelastic electron tunneling Reviewed

"Hirotaka Nishioka, Takahisa Yamato, and Toshiaki Kakitani"

Molecular Simulation Vol. 32 ( 9 ) page： 727-734 2006.8

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

"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."

Photochemical reaction of cyanobacterial BLUF domain protein PixD

"Fukushima Y, Murai Y, Okajima K, Shibata Y, Ikeuchi M, Yamato T, Itoh S"

PLANT AND CELL PHYSIOLOGY Vol. 47 page： S158-S158 Supple. S 2006

"Interference, fluctuation, and alternation of electron tunneling in protein media. 2. Non-Condon theory for the energy gap dependence of electron transfer rate" Reviewed

"H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu, T. Kakitani"

J. Phys. Chem. B. Vol. 109 page： 15621-15635 2005.8

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."

"Interference, fluctuation, and alternation of electron tunneling in protein media. 1. Two tunneling routes in photosynthetic reaction center alternate due to thermal fluctuation of protein conformation" Reviewed

"H. Nishioka, A. Kimura, T. Yamato, T. Kawatsu, T. Kakitani"

J. Phys. Chem. B. Vol. 109 ( 5 ) page： 1978-1987 2005.2

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."

Spectral tuning in photoactive yellow protein

"Kawaguchi K, Yamato T"

BIOPHYSICAL JOURNAL Vol. 88 ( 1 ) page： 508A-509A Part 2 Suppl. S 2005.1

Prediction of Inelastic Tunneling Mechanism from Bacteriopheophytin to the Primary Quinone in Modified Bacterial Photosynthetic Reaction Centers

"H. Nishioka, T. Kawatsu, A. Kimura, T. Yamato, T. Kakitani"

"Photosynthesis: Fundamental Aspects to Global Perspectives, Proceedings of the 13th International Congress on Photosynthesis" Vol. 1 page： 327-328 2005

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

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

"PROTEINS: Structure, Function and Bioinformatics" Vol. 55 ( 5 ) page： 1063-1069 2004.6

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.

　 PREV - NEXT 　

<YAMATO, Takahisa>

Papers - YAMATO, Takahisa