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Nakagawa, Hiroshi; Yonetani, Yoshiteru*; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya*; Inamura, Yasuhiro; Kataoka, Mikio*; Kono, Hidetoshi*
JPS Conference Proceedings (Internet), 33, p.011101_1 - 011101_6, 2021/03
Hydration water dynamics were measured by quasi-elastic neutron scattering with HnO/DO contrast for two DNA dodecamers, 5'CGCGCGCG'3 and 5'CGCGCGCG'3, which have been computationally shown to be structurally rigid and flexible, respectively. The dynamical transitions of the hydration water as well as DNA were observed for both sequences at approximately 240 K. Above the transition temperature, the mean square displacements of the hydration water for the rigid sequence were smaller than those for the flexible one. Furthermore, the relaxation time of the hydration water was longer in the rigid DNA than in the flexible DNA. We suggest that hydration water dynamics on the picosecond timescale are associated with sequence-dependent deformability of DNA.
Yonetani, Yoshiteru*; Nakagawa, Hiroshi
Chemical Physics Letters, 749, p.137441_1 - 137441_5, 2020/06
Times Cited Count:2 Percentile:4.20(Chemistry, Physical)We calculated solvent accessibility of DNA backbone hydrogen sites, H1'-H5' by using molecular dynamics simulation of DNA. The result of accessibility is well correlated with the site-dependent reactivity with OH radicals experimentally reported, indicating that the different DNA-radical reactivity is mainly caused by the difference in the solvent accessibility of each hydrogen site. Compared with the previous calculation with solvent-accessible surface area, the present MD-based counting of molecular access provided a slightly improved result, which suggests importance of more realistic molecular components such as electrostatic interactions and DNA conformational fluctuation.
Yonetani, Yoshiteru
Journal of Chemical Physics, 143(4), p.044506_1 - 044506_9, 2015/07
Times Cited Count:15 Percentile:52.01(Chemistry, Physical)Nakagawa, Hiroshi; Yonetani, Yoshiteru; Nakajima, Kenji; Kawamura, Seiko; Kikuchi, Tatsuya; Inamura, Yasuhiro; Kataoka, Mikio; Kono, Hidetoshi
Physical Review E, 90(2), p.022723_1 - 022723_11, 2014/08
Times Cited Count:10 Percentile:53.99(Physics, Fluids & Plasmas)Molecular dynamics (MD) simulations and Quasi-Elastic Neutron Scattering (QENS) experiments were conducted on hydrated two DNA dodecamers with distinct deformability; 5'CGCGAATTCGCG3' and 5'CGCGTTAACGCG3'. The former is known to be rigid and the latter to be flexible. The mean-square displacements (MSDs) of DNA dodecamers exhibit so-called dynamical transition around 200-240 K for both sequences. To investigate the DNA sequence dependent dynamics, the dynamics of DNA and hydration water above the transition temperature were examined using both MD simulations and QENS experiments. The fluctuation amplitude of the AATT central tetramer is smaller, and its relaxation time is longer, than that observed in TTAA, suggesting that the AT step is kinetically more stable than TA. The sequence-dependent local base pair step dynamics correlate with the kinetics of breaking the hydrogen bond between DNA and hydration water. The sequence dependent DNA base pair step fluctuations appear above the dynamical transition temperature. Together with these results, we conclude that DNA deformability is related to the local dynamics of base pair step, themselves coupled to hydration water in the minor groove.
Yonetani, Yoshiteru; Kono, Hidetoshi
Journal of Physical Chemistry B, 117(25), p.7535 - 7545, 2013/06
Times Cited Count:15 Percentile:36.39(Chemistry, Physical)Yonetani, Yoshiteru; Kono, Hidetoshi
Ansanburu, 14(4), p.182 - 186, 2012/10
no abstracts in English
Yonetani, Yoshiteru; Kono, Hidetoshi
Biophysical Chemistry, 160(1), p.54 - 61, 2012/01
Times Cited Count:21 Percentile:52.96(Biochemistry & Molecular Biology)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:6.02(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.
Yonetani, Yoshiteru; Kono, Hidetoshi
Yuragi To Seitai Kino, p.66 - 71, 2010/10
no abstracts in English
Oikawa, Masataka; Yonetani, Yoshiteru
Biophysical Journal, 98(12), p.2974 - 2983, 2010/06
Times Cited Count:9 Percentile:23.04(Biophysics)Yonetani, Yoshiteru; Kono, Hidetoshi
Biophysical Journal, 97(4), p.1138 - 1147, 2009/08
Times Cited Count:31 Percentile:61.55(Biophysics)Yonetani, Yoshiteru*; Maruyama, Yutaka*; Hirata, Fumio*; Kono, Hidetoshi
Journal of Chemical Physics, 128(18), p.185102_1 - 185102_9, 2008/05
Times Cited Count:20 Percentile:57.48(Chemistry, Physical)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
Yonetani, Yoshiteru*; Kono, Hidetoshi; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro
Molecular Simulation, 33(1-2), p.103 - 107, 2007/01
Times Cited Count:5 Percentile:16.38(Chemistry, Physical)DNA tetramer sequences AATT and TTAA are known to be conformationally more rigid and flexible, respectively. In this study, we carry out molecular dynamics simulations of these two sequences, and investigate the characteristic hydration pattern. The rigid AATT is found to be more likely to construct the hydration spine in the minor groove than the flexible TTAA. The result suggests that the hydration water molecules play a critical role for determining the sequence dependent deformability of DNA conformation.
Yonetani, Yoshiteru*
Journal of Chemical Physics, 124(20), p.204501_1 - 204501_11, 2006/05
Times Cited Count:60 Percentile:88.33(Chemistry, Physical)Cutoff treatment is the simplest approach for evaluating intermolecular interactions in molecular dynamics simulations. It has been believed that increasing cutoff length makes simulation results better. On the contrary, our results of the bulk water simulations studied within the range of cutoff length, 9-18 showed an opposite tendency: the artifact was enhanced by increasing the cutoff length. Especially, in terms of the distance dependent Kirkwood factor G(r), it was clearly shown that the orientational behavior of water molecules becomes gradually worse as the cutoff length becomes longer. The artifact enhanced by the increased cutoff length led to a reported spurious artifact, i.e., phase transition [Y. Yonetani, Chem. Phys. Lett. 406, 49 (2005)]. Though the cutoff artifact was largely reduced by adopting a force switching technique, it did not completely remove the anomalous cutoff length dependence of the artifact. These results suggest that increasing cutoff should not be attempted, regardless of whether the switching force is adopted or not.
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
Go, Nobuhiro; Yonetani, Yoshiteru*
Seitai No Kagaku, 56(6), p.626 - 631, 2005/12
no abstracts in English
Yonetani, Yoshiteru
Chemical Physics Letters, 406(1-3), p.49 - 53, 2005/04
Times Cited Count:52 Percentile:84.28(Chemistry, Physical)We report that a severe artifact appeared in molecular dynamics simulation of bulk water using the long cut-off length 18 AA ; Our result shows that increasing the cut-off length does not always improve the simulation result. Moreover, the use of the long cut-off length can lead to a spurious result. It is suggested that the simulation of solvated biomolecules using such a long cut-off length, which has been often performed, may contain an unexpected artifact.
Yonetani, Yoshiteru; Kono, Hidetoshi
no journal, ,
no abstracts in English
Yonetani, Yoshiteru; Maruyama, Yutaka*; Hirata, Fumio*; Kono, Hidetoshi
no journal, ,