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Journal Articles

Intensity of diffracted X-rays from biomolecules with radiation damage caused by strong X-ray pulses

Kai, Takeshi; Tokuhisa, Atsushi*; Moribayashi, Kengo; Fukuda, Yuji; Kono, Hidetoshi; Go, Nobuhiro*

Journal of the Physical Society of Japan, 83(9), p.094301_1 - 094301_5, 2014/09

 Times Cited Count:1 Percentile:13.18(Physics, Multidisciplinary)

no abstracts in English

Journal Articles

High-speed classification of coherent X-ray diffraction Patterns on the K computer for high-resolution single biomolecule imaging

Tokuhisa, Atsushi*; Arai, Junya*; Jochi, Yasumasa*; Ono, Yoshiyuki*; Kameyama, Toyohisa*; Yamamoto, Keiji*; Hatanaka, Masayuki*; Gerofi, B.*; Shimada, Akio*; Kurokawa, Motoyoshi*; et al.

Journal of Synchrotron Radiation, 20(6), p.899 - 904, 2013/11

 Times Cited Count:4 Percentile:27.21(Instruments & Instrumentation)

Journal Articles

Calculation of molecular-structure-based damage caused by short-pulse high-intensity X-ray lasers

Kai, Takeshi; Tokuhisa, Atsushi*; Kono, Hidetoshi

Journal of the Physical Society of Japan, 82(11), p.114301_1 - 114301_5, 2013/11

 Times Cited Count:1 Percentile:12.72(Physics, Multidisciplinary)

no abstracts in English

Journal Articles

Classifying and assembling two-dimensional X-ray laser diffraction patterns of a single particle to reconstruct the three-dimensional diffraction intensity function; Resolution limit due to the quantum noise

Tokuhisa, Atsushi*; Taka, Junichiro*; Kono, Hidetoshi; Go, Nobuhiro*

Acta Crystallographica Section A, 68(3), p.366 - 381, 2012/05

 Times Cited Count:18 Percentile:82.22(Chemistry, Multidisciplinary)

Journal Articles

Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation

Tokuhisa, Atsushi; Jochi, Yasumasa*; Nakagawa, Hiroshi; Kitao, Akio*; Kataoka, Mikio

Physical Review E, 75(4), p.041912_1 - 041912_8, 2007/05

 Times Cited Count:20 Percentile:69.76(Physics, Fluids & Plasmas)

Elastic incoherent neutron scattering (EINS) data can be approximated with a Gaussian function of q in a low q region. However, in a higher q region the deviation from a Gaussian function becomes non-negligible. Protein dynamic properties can be derived from the analyses of the non-Gaussian behavior, which has been experimentally investigated. To evaluate the origins of the non-Gaussian behavior of protein dynamics, we conducted a molecular dynamics (MD) simulation of Staphylococcal nuclease. Instead of the ordinary cumulant expansion, we decomposed the non-Gaussian terms into three components: (1) the component originating from the heterogeneity of the mean-square fluctuation, (2) that from the anisotropy, and (3) that from higher order terms such as anharmonicity. The MD simulation revealed various dynamics for each atom. The atomic motions are classified into three types: (1) "harmonic", (2) "anisotropic", and (3) "anharmonic". However, each atom has a different degree of anisotropy. The contribution of the anisotropy to the total scattering function averages out due to these differences. Anharmonic motion is described as the jump among multiple minima. The jump distance and the probability of the residence at one site vary from atom to atom. Each anharmonic component oscillates between positive and negative values. Thus, the contribution of the anharmonicity to the total scattering is canceled due to the variations in the anharmonicity. Consequently, the non-Gaussian behavior of the total EINS from a protein can be analyzed by the dynamical heterogeneity.

Journal Articles

Dynamical heterogeneity of protein dynamics studied by elastic incoherent neutron scattering and molecular simulations

Nakagawa, Hiroshi; Tokuhisa, Atsushi*; Kamikubo, Hironari*; Jochi, Yasumasa*; Kitao, Akio*; Kataoka, Mikio*

Materials Science & Engineering A, 442(1-2), p.356 - 360, 2006/12

 Times Cited Count:4 Percentile:36.15(Nanoscience & Nanotechnology)

The dynamical heterogeneity of a globular soluble protein was studied by elastic incoherent neutron scattering and molecular simulations. The q-dependence of the elastic incoherent neutron scattering shows a non-Gaussianity, a deviation from Gaussian approximation. We determined that the dynamical heterogeneity explains the non-Gaussianity, although the anharmonicity is also plausible origin. Molecular dynamics simulations confirmed that the non-Gaussianity is mainly due to the dynamical heterogeneity at a lower energy resolution, $$Delta$$$$omega$$=1meV. On the other hand, the contribution from the anharmonicities to the non-Gaussianity became substantial at a higher resolution, $$Delta$$$$omega$$=10$$mu$$eV. Regardless, the dynamical heterogeneity is the dominant factor for the non-Gaussianity.

Journal Articles

Hydration-coupled protein boson peak measured by incoherent neutron scattering

Nakagawa, Hiroshi; Kataoka, Mikio*; Jochi, Yasumasa*; Kitao, Akio*; Shibata, Kaoru; Tokuhisa, Atsushi*; Tsukushi, Itaru*; Go, Nobuhiro

Physica B; Condensed Matter, 385-386(2), p.871 - 873, 2006/11

 Times Cited Count:13 Percentile:53.84(Physics, Condensed Matter)

The boson peak of a protein was examined in relation to hydration using staphylococcal nuclease. Although the boson peak is commonly observed in synthetic polymers, glassy materials and amorphous materials, the origin of the boson peak is not fully understood. The motions that contribute to the peak are harmonic vibrations. Upon hydration the peak frequency shifts to a higher frequency and the effective force constant of the vibration increases at low temperatures, suggesting that the protein energy surface is modified. Hydration of the protein leads to a more rugged surface and the vibrational motions are trapped within the local minimum at cryogenic temperatures. The origin of the protein boson peak may be related to this rugged energy surface.

Oral presentation

Hydration and temperature dependence of protein dynamics studied by incoherent inelastic neutron scattering

Nakagawa, Hiroshi; Shibata, Kaoru; Jochi, Yasumasa*; Tokuhisa, Atsushi*; Kataoka, Mikio*; Go, Nobuhiro

no journal, , 

Protein dynamics is essential for the protein function. In order to understand the dynamical properties of protein, the effects of hydration and temperature on the dynamics of staphylococcal nuclease were intensively examined by incoherent inelastic neutron scattering with LAM-40 instrument in KENS, Japan. Inelastic neutron scattering of dry, D$$_{2}$$O-hydrated and H$$_{2}$$O-hydrated protein were measured at various temperatures between 100 and 300K. The spectra of dry protein at low temperatures shows the peak at around 3 meV, which was shifted to around 4meV with D$$_{2}$$O-hydrated protein. This indicates that the vibrational frequency distribution was changed by the hydration. The anomalous decrease in the Debye-Waller factor at high temperatures is corresponding to an increase of the mean-square displacement, which is called the dynamical transition. This is accompanied by the appearance of a quasielastic scattering. The natures of the motions above the dynamical transition temperature were characterized by the analysis of the quasielastic scattering. The dynamical transition was striking with the hydrated protein. This suggests that the hydration water has strongly effects on the protein dynamics. The scattering profile of the hydration water was calculated by the subtraction of the scattering profiles of a D2O-hydrated protein from that of a H$$_{2}$$O-hydrated protein. We will discuss the relation between hydration water dynamics and the protein dynamics.

Oral presentation

Hydration dependent protein dynamics by incoherent neutron scattering

Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Shibata, Kaoru; Tokuhisa, Atsushi*; Go, Nobuhiro; Kataoka, Mikio

no journal, , 

Protein dynamics in a solvated sample are strongly coupled to their environment. The dynamical transition and boson peak of a protein were examined in relation to hydration using staphylococcal nuclease. A dynamical transition of protein around 230K is observed only for the hydrated protein. It is demonstrated that the functions of some proteins are suppressed with the loss of anharmonic dynamics as the proteins are cooled down below the dynamical transition temperature. Hydration level dependence of the dynamical transition was examined. The dynamical transition was observed at higher hydration level, 0.26gwater/gprotein. The previous work reported that about 0.2 gwater/gprotein hydration is necessary for the protein function. This suggests that dynamical transition is important for protein function. On the other hand, below the 150K, even low hydration affects the harmonic vibration of protein. At low temperature the protein boson peak was observed. Although the boson peak is commonly observed in synthetic polymers, glassy materials and amorphous materials, the origin of the boson peak has not been fully understood. The motions that contribute to the peak are harmonic vibrations. Upon hydration the peak frequency shifts to a higher frequency and the effective force constant of the vibration increases at low temperatures, suggesting that the protein energy surface is modified. Hydration of the protein leads to a more rugged potential surface and the vibrational motions are trapped within a local minimum at cryogenic temperatures. The origin of the protein boson peak is related to this rugged energy surface and the distribution of low-energy vibrations.

Oral presentation

Development of a computational method for single-molecule X-ray structure determination

Tokuhisa, Atsushi; Ishida, Hisashi; Matsumoto, Atsushi; Kono, Hidetoshi; Go, Nobuhiro

no journal, , 

In the present, the determination of biomolecular structures is mainly on the basis of the Braggs law, where the crystallization of the sample is inevitable. However, only a part of biomolecules can be crystallized. A promising 3D structure determination method without crystallization is proposed just using single-molecule sample with X-ray free electron lasers which are under construction in Europe, USA and Japan. Our final goal is to develop computational method for single-molecule X-ray structure determination. At this meeting, I will report on the outline of our method to construct a 3D structure from the speckle patterns, considering the molecular orientation and the influence of thermal fluctuation.

Oral presentation

Molecular dynamics simulation study on the differences between specific and non-specific protein-DNA interactions

Tokuhisa, Atsushi; Kono, Hidetoshi

no journal, , 

no abstracts in English

Oral presentation

Theoretical approach for solving 3D structures of biomolecules with single-molecule X-ray diffraction patterns

Tokuhisa, Atsushi; Taka, Junichiro; Moribayashi, Kengo; Otobe, Tomohito; Kai, Takeshi; Nakamura, Tatsufumi; Fukuda, Yuji; Kono, Hidetoshi; Go, Nobuhiro

no journal, , 

Oral presentation

Theory of single molecule imaging by X-ray free-electron laser

Tokuhisa, Atsushi; Taka, Junichiro; Kono, Hidetoshi; Go, Nobuhiro*

no journal, , 

Oral presentation

Estimation of attainable structural resolution by computer simulation for single biomolecule imaging with X-ray Free Electron Laser

Tokuhisa, Atsushi*; Kai, Takeshi; Taka, Junichiro*; Kono, Hidetoshi; Go, Nobuhiro*

no journal, , 

Oral presentation

Phase retrieval from noisy X-ray diffraction patterns of single molecules

Kono, Hidetoshi; Ikeda, Shiro*; Tokuhisa, Atsushi*

no journal, , 

Oral presentation

Protein conformation and its dynamics in solution by molecular dynamics simulation for small-angle neutron scattering data analysis

Putra, E. G. R.*; Kono, Hidetoshi; Tokuhisa, Atsushi*; Bahrum, E. S.*; Patriati, A.*

no journal, , 

Oral presentation

Automatic similarity identification of 2D diffraction patterns with noisy background for 3D coherent X-ray diffractive imaging

Tokuhisa, Atsushi*; Jochi, Yasumasa*; Kono, Hidetoshi; Go, Nobuhiro*

no journal, , 

18 (Records 1-18 displayed on this page)
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