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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

Understanding water-mediated DNA damage production by molecular dynamics calculation of solvent accessibility

Yonetani, Yoshiteru*; Nakagawa, Hiroshi

Chemical Physics Letters, 749, p.137441_1 - 137441_5, 2020/06

 Times Cited Count:0 Percentile:0.01(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.

Journal Articles

Distinct dissociation kinetics between ion pairs; Solvent-coordinate free-energy landscape analysis

Yonetani, Yoshiteru

Journal of Chemical Physics, 143(4), p.044506_1 - 044506_9, 2015/07

 Times Cited Count:13 Percentile:56.96(Chemistry, Physical)

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

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

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

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

Enhanced resolution of molecular recognition to distinguish structurally similar molecules by different conformational responses of a protein upon ligand binding

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:6.99(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.

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

Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities

Oikawa, Masataka; Yonetani, Yoshiteru

Biophysical Journal, 98(12), p.2974 - 2983, 2010/06

 Times Cited Count:9 Percentile:26.63(Biophysics)

Journal Articles

Sequence dependencies of DNA deformability and hydration in the minor groove

Yonetani, Yoshiteru; Kono, Hidetoshi

Biophysical Journal, 97(4), p.1138 - 1147, 2009/08

 Times Cited Count:24 Percentile:59.4(Biophysics)

Journal Articles

Comparison of DNA hydration patterns obtained using two distinct computational methods, molecular dynamics simulation and three-dimensional reference interaction site model theory

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:61.22(Chemistry, Physical)

Journal Articles

Analysis of the function of a large-scale supra-biomolecule system by molecular dynamics simulation system, SCUBA (Simulation Codes for hUge Biomolecular Assembly)

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

Journal Articles

DNA deformability and hydration studied by molecular dynamics simulation

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:17.86(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.

Journal Articles

Liquid water simulation; A Critical examination of cutoff length

Yonetani, Yoshiteru*

Journal of Chemical Physics, 124(20), p.204501_1 - 204501_11, 2006/05

 Times Cited Count:52 Percentile:87.45(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 ${AA}$ showed an opposite tendency: the artifact was enhanced by increasing the cutoff length. Especially, in terms of the distance dependent Kirkwood factor G$$_{k}$$(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.

Journal Articles

Development of molecular dynamics simulation system for large-scale supra-biomolecules, PABIOS (PArallel BIOmolecular Simulator)

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

Journal Articles

Role of theory and computation for "understanding protein"

Go, Nobuhiro; Yonetani, Yoshiteru*

Seitai No Kagaku, 56(6), p.626 - 631, 2005/12

no abstracts in English

Journal Articles

A Severe artifact in simulation of liquid water using a long cut-off length; Appearance of a strange layer structure

Yonetani, Yoshiteru

Chemical Physics Letters, 406(1-3), p.49 - 53, 2005/04

 Times Cited Count:49 Percentile:84.98(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.

Oral presentation

Sequence-dependent DNA conformation and flexibility characterized by hydration pattern

Yonetani, Yoshiteru*; Kono, Hidetoshi; Go, Nobuhiro

no journal, , 

no abstracts in English

Oral presentation

DNA sequence-dependent deformability associated with hydration; Implication for indirect readout in protein-DNA interactions

Kono, Hidetoshi; Yonetani, Yoshiteru*; Fujii, Satoshi*; Sarai, Akinori*; Go, Nobuhiro

no journal, , 

Proteins recognize specific DNA sequences not only through direct contact between amino acids and base-pairs, but also indirectly based on the sequence-dependent conformation and deformability of the DNA (indirect readout). We used molecular dynamics simulations to analyze the sequence-dependent DNA conformations of all 136 possible tetramericsequences sandwiched between CGCG sequences. We found that the average conformation and deformability of the tetramers can be highly sequence dependent. Even the tetrameric sequences having the same dimeric sequence at the center showed the distinct deformabilities dependent on the bases on either end of the tetramers. Such conformations of tetramers were found to be associated with hydration. The tetrameric sequences with AT at their center, for instance, generally were rigid and highly hydrated. The rigidity among the tetramers was affected by the flanking bases and also correlated with the amount of hydration which we defined as number of water molecules bridging two bases belonging to different chains in minor groove. These results suggest that hydration of DNA is responsible for the mechanism of indirect readout during protein-DNA recognition. We also show that the sequence dependence of DNA conformation and deformability may be used to estimate the contribution of indirect readout to the specificity of protein-DNA recognition as well as nucleosome positioning and large-scale behavior of nucleic acids.

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