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Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Yamamuro, Osamu*; Kataoka, Mikio*
Biophysical Journal, 117(2), p.229 - 238, 2019/07
Times Cited Count：5 Percentile：20.74(Biophysics)Softness and rigidity of proteins are reflected in the structural dynamics, which are in turn affected by the environment. The characteristic low-frequency vibrational spectrum of a protein, known as boson peak, is an indication of the structural rigidity of the protein at cryogenic temperature or dehydrated conditions. In this paper, the effect of hydration, temperature, and pressure on the boson peak and volumetric properties of a globular protein are evaluated by using inelastic neutron scattering and molecular dynamics simulation. Hydration, pressurization, and cooling shift the boson peak position to higher energy and depress the peak intensity and decreases the protein and cavity volumes, although pressure hardly affects the boson peak of the fully hydrated protein. A decrease of each volume means the increase of rigidity, which is the origin of the boson peak shift. The boson peak profile can be predicted by the total cavity volume. This prediction is effective for the evaluation of the net quasielastic scattering of incoherent neutron scattering spectra when the boson peak cannot be distinguished experimentally because of a strong contribution from quasielastic scattering.
Yang, L.-W.*; Kitao, Akio*; Huang, B.-C.*; Go, Nobuhiro*
Biophysical Journal, 107(6), p.1415 - 1425, 2014/09
Times Cited Count：21 Percentile：57.94(Biophysics)Higuchi, Mariko; Fujii, Jumpei*; Yonetani, Yoshiteru; Kitao, Akio*; Go, Nobuhiro*
Journal of Structural Biology, 173(1), p.20 - 28, 2011/01
Times Cited Count：2 Percentile：5.96(Biochemistry & Molecular Biology)MutT distinguishes substrate 8-oxo-dGTP from dGTP and also 8-oxo-dGMP from dGMP despite small differences of chemical structures between them. In this paper we show by the method of molecular dynamics simulation that the transition between conformational substates of MutT is a key mechanism for a high resolution molecular recognition of the differences between the very similar chemical compounds. The native state MutT has two conformational substates with similar free energies, each characterized by either open or close of two loops surrounding the substrate binding active site. Between the two substates, the open substate is more stable in free MutT and in dGMP-MutT complex, and the closed substate is more stable in 8-oxo-dGMP-MutT complex. A hydrogen bond between H7 atom of 8-oxo-dGMP and the sidechain of Asn119 plays a crucial role for maintaining the closed substate in 8-oxo-dGMP-MutT complex.
Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Kataoka, Mikio
Biophysical Journal, 95(6), p.2916 - 2923, 2008/09
Times Cited Count：51 Percentile：78.54(Biophysics)Jochi, Yasumasa*; Nakagawa, Hiroshi; Kataoka, Mikio; Kitao, Akio*
Biophysical Journal, 94(11), p.4435 - 4443, 2008/06
Times Cited Count：24 Percentile：52.44(Biophysics)Hydration effects on protein dynamics were investigated by comparing the frequency dependence of the calculated neutron scattering spectra between full and minimal hydration states at temperatures between 100 and 300 K. The protein boson peak is observed in the frequency range 1-4 meV at 100 K in both states. The peak frequency in the minimal hydration state shifts to lower than that in the full hydration state. Protein motions with frequency higher than 4 meV were shown to undergo almost harmonic motion in both states at all temperatures simulated, whereas those with frequency lower than 1 meV dominate the total fluctuations above 220 K and contribute to the origin of the glass-like transition. At 300 K, the boson peak becomes buried in the quasi-elastic contributions in the full hydration state, but is still observed in the minimal hydration state. The boson peak is observed when protein dynamics are trapped within a local minimum of its energy surface. Protein motions, which contribute to the boson peak, are distributed throughout the whole protein. Fine structure of the dynamics structure factor is expected to be detected by the experiment if a high resolution instrument is developed in the near future.
Jochi, Yasumasa*; Nakagawa, Hiroshi; Kataoka, Mikio; Kitao, Akio*
Journal of Physical Chemistry B, 112(11), p.3522 - 3528, 2008/03
Times Cited Count：11 Percentile：27.10(Chemistry, Physical)Molecular dynamics simulations of crystalline Staphylococcal nuclease in full and minimal hydration states were performed to study hydration effects on protein dynamics at temperatures ranging from 100 to 300 K. In a full hydration state (hydration ratio in weight, h = 0.49), gaps are fully filled with water molecules, whereas only crystal waters are included in a minimal hydration state (h = 0.09). The inflection of the atomic mean-square fluctuation of protein as a function of temperature, known as the glass-like transition, is observed at 220 K in both cases, which is more significant in the full hydration state. By examining the temperature dependence of residual fluctuation, we found that the increase of fluctuations in the loop and terminal regions, which are exposed to water, is much greater than in other regions in the full hydration state, but the mobility of the corresponding regions are relatively restricted in the minimal hydration state by inter-molecular contact. The atomic mean-square fluctuation of water molecules in the full hydration state at 300 K is one order of magnitude greater than that in the minimal hydration state. Above the transition temperature, most water molecules in the full hydration state behave like bulk water, and act as a lubricant for protein dynamics. In contrast, water molecules in the minimal hydration state tend to form more hydrogen bonds with the protein, restricting the fluctuation of these water molecules to the level of the protein. Thus, inter-molecular interaction and solvent mobility are important to understand the glass-like transition in proteins.
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：21 Percentile：67.64(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.
Ishida, Hisashi; Higuchi, Mariko; Yonetani, Yoshiteru*; Kano, Takuma; Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro
Annual Report of the Earth Simulator Center April 2005 - March 2006, p.237 - 240, 2007/01
no abstracts in English
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：33.48(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, 
=1meV. On the other hand, the contribution from the anharmonicities to the non-Gaussianity became substantial at a higher resolution, =10
eV. Regardless, the dynamical heterogeneity is the dominant factor for the non-Gaussianity.
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：14 Percentile：53.31(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.
Kitao, Akio*; Yonekura, Koji*; Yonekura, Saori*; Samatey, F.*; Imada, Katsumi*; Namba, Keiichi*; Go, Nobuhiro
Proceedings of the National Academy of Sciences of the United States of America, 103(13), p.4894 - 4899, 2006/03
Times Cited Count：46 Percentile：63.18(Multidisciplinary Sciences)no abstracts in English
Ishida, Hisashi; Higuchi, Mariko; Yonetani, Yoshiteru*; Kano, Takuma; Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro
Annual Report of the Earth Simulator Center April 2004 - March 2005, p.241 - 246, 2005/12
no abstracts in English
Jochi, Yasumasa*; Kitao, Akio*; Go, Nobuhiro
Journal of the American Chemical Society, 127(24), p.8705 - 8709, 2005/06
Times Cited Count：27 Percentile：60.76(Chemistry, Multidisciplinary)no abstracts in English
Ishida, Hisashi; Jochi, Yasumasa*; Higuchi, Mariko; Kano, Takuma; Kitao, Akio*; Go, Nobuhiro
Annual Report of the Earth Simulator Center April 2003 - March 2004, p.175 - 179, 2004/07
no abstracts in English
Kitao, Akio
Hamon, 12(2), p.80 - 83, 2002/04
no abstracts in English
Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Shibata, Kaoru; Go, Nobuhiro; Kataoka, Mikio
no journal, ,
no abstracts in English
Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Kataoka, Mikio
no journal, ,
Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Kataoka, Mikio
no journal, ,
Most globular proteins work in an aqueous milieu and water molecules located at the protein surface strongly affects the protein stability and function. Structure and dynamics of hydration water on the protein, staphylococcal nuclease, were examined at various hydration levels to study the hydration effect on dynamics. We found that the hydration dependent protein dynamical transition around 240 K shows the threshold hydration level between 0.30 and 0.42 (g water/g protein). Below the threshold, hydration water is localized to form several independent clusters on the surface, while above the threshold level the hydration water encircles the protein via hydrogen bond, suggesting the percolation transition. The MD simulations at various hydration indicate that the size of the cluster of hydrogen bonded hydration water dramatically increased above the threshold level of the hydration level. We concluded that the dynamics of hydration water is coupled with the protein dynamics via hydrogen-bond network on the protein-water interface. Such a dynamical coupling drives the hydration dependent protein dynamical transition.
Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Kataoka, Mikio
no journal, ,
Nakagawa, Hiroshi; Jochi, Yasumasa*; Kitao, Akio*; Kataoka, Mikio
no journal, ,
To understand the effect of hydration on protein dynamics, inelastic neutron scattering experiments were carried out on Staphylococcal nuclease samples at differing hydration levels: dehydrated, partially hydrated and hydrated. At cryogenic temperatures, hydration affected the collective motions with energies lower than 5 meV, while the high energy localized motions were independent of hydration. The prominent change was a shift of boson peak toward higher energy by hydration, suggesting hardening of harmonic potential at local minima on the energy landscape. The 240 K transition was observed only for the hydrated protein. Significant quasi-elastic scattering at 300 K was observed only for the hydrated sample, indicating that the origin of the transition is the motion activated by hydration water. The neutron scattering profile of the partially hydrated sample was quite similar to that of the hydrated sample at 100 and 200 K, while it was close to the dehydrated sample at 300 K, indicating that partial hydration is sufficient to affect the harmonic nature of protein dynamics, and that there is a threshold hydration level to activate the anharmonic motions. Thus, hydration water controls both the harmonic and anharmonic protein dynamics, by differing means.
