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Journal Articles

Sequence-dependent hydration water dynamics of dodecameric DNA

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 Hn$$_{2}$$O/D$$_{2}$$O contrast for two DNA dodecamers, 5'CGCG$$underline{rm AATT}$$CGCG'3 and 5'CGCG$$underline{rm TTAA}$$CGCG'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.

Journal Articles

H3 histone tail conformation within the nucleosome and the impact of K14 acetylation studied using enhanced sampling simulation

Ikebe, Kimiyoshi; Sakuraba, Shun*; Kono, Hidetoshi

PLOS Computational Biology, 12(3), p.e1004788_1 - e1004788_13, 2016/03

 Times Cited Count:31 Percentile:91.07(Biochemical Research Methods)

Journal Articles

Two arginine residues suppress the flexibility of nucleosomal DNA in the canonical nucleosome core

Kono, Hidetoshi; Shirayama, Kazuyoshi*; Arimura, Yasuhiro*; Tachiwana, Hiroaki*; Kurumizaka, Hitoshi*

PLOS ONE (Internet), 10(3), p.e0120635_1 - e0120635_15, 2015/03

 Times Cited Count:21 Percentile:63.66(Multidisciplinary Sciences)

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

Local dynamics coupled to hydration water determines DNA-sequence-dependent deformability

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:7 Percentile:50.1(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.

Journal Articles

Adaptive lambda square dynamics simulation; An Efficient conformational sampling method for biomolecules

Ikebe, Kimiyoshi; Sakuraba, Shun; Kono, Hidetoshi

Journal of Computational Chemistry, 35(1), p.39 - 50, 2014/01

 Times Cited Count:14 Percentile:45.64(Chemistry, Multidisciplinary)

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

Dissociation free-energy profiles of specific and nonspecific DNA-protein complexes

Yonetani, Yoshiteru; Kono, Hidetoshi

Journal of Physical Chemistry B, 117(25), p.7535 - 7545, 2013/06

 Times Cited Count:13 Percentile:38.08(Chemistry, Physical)

Journal Articles

Journal Articles

Local conformational changes in the DNA interfaces of proteins

Sunami, Tomoko; Kono, Hidetoshi

PLOS ONE (Internet), 8(2), p.e56080_1 - e56080_12, 2013/02

 Times Cited Count:8 Percentile:24.34(Multidisciplinary Sciences)

Journal Articles

Phase retrieval from a sparse scattering pattern for single molecular structural analysis

Kono, Hidetoshi; Ikeda, Shiro*

Hoshako, 26(1), p.38 - 43, 2013/01

A new strong, short-pulse and coherent X-ray light source, which has been built at SPring8, is expected to achieve a single molecular imaging. With this 109 times brighter light than that of the current synchrotrons, we have to measure the diffraction within a few femto-second before the molecule is destroyed due to the radiation damage. Thus, the obtained diffraction pattern will be very sparse. We have recently developed a phase retrieval method based on the Bayesian statistics that is applicable for such a sparse diffraction pattern. In this article, we introduce the method.

Journal Articles

What determines the residence time of water molecules hydrating on biomolecules ?

Yonetani, Yoshiteru; Kono, Hidetoshi

Ansanburu, 14(4), p.182 - 186, 2012/10

no abstracts in English

Journal Articles

A New method for evaluating the specificity of indirect readout in protein-DNA recognition

Yamasaki, Satoshi*; Terada, Toru*; Kono, Hidetoshi; Shimizu, Kentaro*; Sarai, Akinori*

Nucleic Acids Research, 40(17), p.e129_1 - e129_7, 2012/09

 Times Cited Count:18 Percentile:49.11(Biochemistry & Molecular Biology)

Journal Articles

Molecular structure of isolated MvspI, a variable surface protein of the fish pathogen ${it Mycoplasma mobile}$

Adan, J.*; Yoshii, Shuhei*; Kono, Hidetoshi; Miyata, Makoto*

Journal of Bacteriology, 194(12), p.3050 - 3057, 2012/06

 Times Cited Count:7 Percentile:22.41(Microbiology)

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

Rational design of DNA sequence-specific zinc fingers

Kono, Hidetoshi; Imanishi, Miki*; Negi, Shigeru*; Tatsutani, Kazuya*; Sakaeda, Yui*; Hashimoto, Ayaka*; Nakayama, Chie*; Futaki, Shiro*; Sugiura, Yukio*

FEBS Letters, 586(6), p.918 - 923, 2012/03

 Times Cited Count:5 Percentile:17.5(Biochemistry & Molecular Biology)

Journal Articles

Phase retrieval from single biomolecule diffraction pattern

Ikeda, Shiro*; Kono, Hidetoshi

Optics Express (Internet), 20(4), p.3375 - 3387, 2012/02

 Times Cited Count:9 Percentile:47.42(Optics)

Journal Articles

What determines water-bridge lifetimes at the surface of DNA? Insight from systematic molecular dynamics analysis of water kinetics for various DNA sequences

Yonetani, Yoshiteru; Kono, Hidetoshi

Biophysical Chemistry, 160(1), p.54 - 61, 2012/01

 Times Cited Count:20 Percentile:60.26(Biochemistry & Molecular Biology)

Journal Articles

Sequence dependencies of DNA strucutural dynamics and hydration; Torwards understanding the molecular recognition of DNA

Yonetani, Yoshiteru; Kono, Hidetoshi

Yuragi To Seitai Kino, p.66 - 71, 2010/10

no abstracts in English

Journal Articles

Discovery of proteinaceous N-modification in lysine biosynthesis of ${it Thermus thermophilus}$

Horie, Akira*; Tomita, Takeo*; Saiki, Asako*; Kono, Hidetoshi; Taka, Hikari*; Mineki, Reiko*; Fujimura, Tsutomu*; Nishiyama, Chiharu*; Kuzuyama, Tomohisa*; Nishiyama, Makoto*

Nature Chemical Biology, 5(9), p.673 - 679, 2009/09

 Times Cited Count:36 Percentile:65.43(Biochemistry & Molecular Biology)

182 (Records 1-20 displayed on this page)