※ 半角英数字
 年 ~ 
検索結果: 74 件中 1件目~20件目を表示


Initialising ...



Initialising ...


Initialising ...


Initialising ...


Initialising ...


Initialising ...


Initialising ...


Initialising ...



Sequence-dependent hydration water dynamics of dodecameric DNA

中川 洋; 米谷 佳晃*; 中島 健次; 河村 聖子; 菊地 龍弥*; 稲村 泰弘; 片岡 幹雄*; 河野 秀俊*

JPS Conference Proceedings (Internet), 33, p.011101_1 - 011101_6, 2021/03

5'CGCG$$underline{rm AATT}$$CGCG'3 and 5'CGCG$$underline{rm TTAA}$$CGCG'3のDNAについて、軽水と重水のコントラストを利用した中性子準弾性散乱による水和水ダイナミクスを測定した。この2つのDNAは計算機によってそれぞれ硬い分子と柔らかい分子であることが分かっている。どちらの配列も約240KにDNAと水和水のどちらも動力学転移が観測された。転移温度以上では、水和水の平均自乗変位は硬い配列の方が小さかった。また水和水の緩和時間は硬いほうが長かった。ピコ秒時間スケールの水和水ダイナミクスは配列依存的なDNAの硬さと関係していることを示唆した。


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

米谷 佳晃*; 中川 洋

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

 被引用回数:0 パーセンタイル:0.01(Chemistry, Physical)



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

米谷 佳晃

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

 被引用回数:15 パーセンタイル:55.57(Chemistry, Physical)

Different ion pairs exhibit different dissociation kinetics: however, while the nature of this process is vital for understanding various molecular systems, the underlying mechanism remains unclear. In this study, to examine the origin of different kinetic rate constants for this process, molecular dynamics simulations were conducted for LiCl, NaCl, KCl, and CsCl in water. The results showed substantial differences in dissociation rate constant. Analysis of the free-energy landscape with a solvent reaction coordinate and subsequent rate component analysis showed that the differences in these rate constants arose predominantly from the variation in solvent-state distribution between the ion pairs. The formation of a water-bridging configuration, in which the water molecule binds to an anion and a cation simultaneously, was identified as a key step in this process: water-bridge formation lowers the related dissociation free-energy barrier, thereby increasing the probability of ion-pair dissociation. Consequently, a higher probability of water-bridge formation leads to a higher ion-pair dissociation rate.


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

中川 洋; 米谷 佳晃; 中島 健次; 河村 聖子; 菊地 龍弥; 稲村 泰弘; 片岡 幹雄; 河野 秀俊

Physical Review E, 90(2), p.022723_1 - 022723_11, 2014/08

 被引用回数:10 パーセンタイル:56.64(Physics, Fluids & Plasmas)



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

米谷 佳晃; 河野 秀俊

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

 被引用回数:13 パーセンタイル:34(Chemistry, Physical)

DNA-binding proteins recognize DNA sequences with at least two different binding modes, specific and nonspecific. Experimental structures of such complexes provide us a static view of the bindings. However, it is difficult to reveal further mechanisms of their target-site search and recognition only from static information because the transition process between the bound and unbound states is not clarified by static information. What is the difference between specific and nonspecific bindings? Here we performed adaptive biasing force molecular dynamics simulations with the specific and nonspecific structures of DNA-Lac repressor complexes to investigate the dissociation process. The resultant free-energy profiles showed that the specific complex has a sharp, deep well consistent with tight binding, whereas the non-specific complex has a broad, shallow well consistent with loose binding. The difference in the well depth, 5 kcal/mol, was in fair agreement with the experimentally obtained value and was found to mainly come from the protein conformational difference, particularly in the C-terminal tail. Comparison of the free-energy barrier for sliding, $$sim$$8.7 kcal/mol, and that for dissociation (at least $$sim$$16 kcal/mol) calculated in this study suggests that sliding is much preferred to dissociation.



米谷 佳晃; 河野 秀俊

アンサンブル, 14(4), p.182 - 186, 2012/10



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

米谷 佳晃; 河野 秀俊

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

 被引用回数:20 パーセンタイル:55.5(Biochemistry & Molecular Biology)

The lifetime during which a water molecule resides at the surface of a biomolecule varies according to the hydration site. What determines this variety of lifetimes? Despite many previous studies, there is still no uniform picture quantitatively explaining this phenomenon. Here we calculate the lifetime for a particular hydration pattern in the DNA minor groove, the water bridge, for various DNA sequences to show that the water-bridge lifetime varies from 1 to 300 ps in a sequence-dependent manner. We find that it follows 1/k ($$V$$$$_{step}$$)$$P$$$$_{m}$$, where $$P$$$$_{m}$$ and $$V$$$$_{step}$$ are two crucial factors, namely the probability of forming a specific hydrogen bond in which more than one donor atom participates, and the structural fluctuation of DNA, respectively. This relationship provides a picture of the water kinetics with atomistic detail and shows that water dissociation occurs when a particular hydrogen-bonding pattern appears.


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

樋口 真理子; 藤井 淳平*; 米谷 佳晃; 北尾 彰朗*; 郷 信広*

Journal of Structural Biology, 173(1), p.20 - 28, 2011/01

 被引用回数:2 パーセンタイル:6.31(Biochemistry & Molecular Biology)



DNAの水和とダイナミクスの塩基配列依存性; DNA-タンパク質,DNA-低分子認識の理解に向けて

米谷 佳晃; 河野 秀俊

揺らぎと生体機能, p.66 - 71, 2010/10



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

及川 雅隆; 米谷 佳晃

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

 被引用回数:9 パーセンタイル:24.13(Biophysics)

Are protein nonpolar cavities filled with water molecules ? Though many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1$$beta$$, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of four protein nonpolar cavities by means of the molecular dynamics thermodynamic integration method. Besides the IL-1$$beta$$ cavity, we selected the three largest nonpolar cavities from the structural database, in view of the simulation result of Vaitheeswaran et al. [Proc. Natl. Acad. Sci. (2004)] showing that larger nonpolar cavities are more expected to be hydrated. The calculated free energy changes were all positive; hydration of the nonpolar cavities was energetically unfavorable for all four cases. Because hydration of smaller cavities should happen more rarely, we conclude that existing protein nonpolar cavities are not likely to be hydrated. Although a possibility remains for much larger nonpolar cavities, such cases are not found experimentally. We present a hypothesis to explain this: hydrated nonpolar cavities are quite unstable and the conformation could not be maintained.


Sequence dependencies of DNA deformability and hydration in the minor groove

米谷 佳晃; 河野 秀俊

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

 被引用回数:27 パーセンタイル:60.51(Biophysics)

DNA deformability and hydration are both sequence dependent and are essential in specific DNA sequence recognition by proteins. However, their relationship is not well understood. Here, systematic molecular dynamics simulations of the 136 DNA sequences that differ from each other in the central tetramer revealed that sequence dependence of hydration is clearly correlated with that of deformability. We show that the feature of this correlation can be explained by the following four typical cases. Most of rigid base-pair steps are highly likely to form an ordered hydration pattern composed of one water molecule bridging between the bases of distinct strands, but there are a few exceptions which favor another ordered hydration composed of two water molecules participating in the bridge construction. Steps with medium deformability can make both of the hydration patterns with frequent transition. Highly flexible steps do not have any stable hydration pattern. The detailed picture of this correlation demonstrated that motions of hydration water molecules and of DNA bases were tightly coupled with each other at the atomic level. These results are helpful to understand the entropic contribution from water molecules in protein or drug binding and could be applied for predicting the binding sites.


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

米谷 佳晃*; 丸山 豊*; 平田 文男*; 河野 秀俊

Journal of Chemical Physics, 128(18), p.185102_1 - 185102_9, 2008/05

 被引用回数:20 パーセンタイル:58.64(Chemistry, Physical)

Although high-resolution, crystal structure analyses have given us a view of tightly bound water molecules on their surface, the structural data is still insufficient to capture the detailed configurations of water molecules around the surface of these biomolecules. Thanks to the invention of various computational algorithms, computer simulations can now provide an atomic view of hydration. Here we describe the apparent patterns of DNA hydration calculated using two different computational methods, MD simulation and 3D-RISM theory. This rigorous comparison showed that MD and 3D-RISM provide essentially similar hydration patterns when there is sufficient sampling time for MD and a sufficient number of conformations to describe molecular flexibility for 3D-RISM. This suggests that these two computational methods can be used to complement one another when evaluating the reliability of calculated hydration patterns.


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

石田 恒; 樋口 真理子; 米谷 佳晃*; 叶野 琢磨; 城地 保昌*; 北尾 彰朗*; 郷 信広

Annual Report of the Earth Simulator Center April 2005 - March 2006, p.237 - 240, 2007/01



DNA deformability and hydration studied by molecular dynamics simulation

米谷 佳晃*; 河野 秀俊; 藤井 聡*; 皿井 明倫*; 郷 信広

Molecular Simulation, 33(1-2), p.103 - 107, 2007/01

 被引用回数:5 パーセンタイル:16.87(Chemistry, Physical)



Liquid water simulation; A Critical examination of cutoff length

米谷 佳晃*

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

 被引用回数:56 パーセンタイル:87.7(Chemistry, Physical)



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

石田 恒; 樋口 真理子; 米谷 佳晃*; 叶野 琢磨; 城地 保昌*; 北尾 彰朗*; 郷 信広

Annual Report of the Earth Simulator Center April 2004 - March 2005, p.241 - 246, 2005/12

地球シミュレータは従来にはない大規模超分子系の分子動力学シミュレーションを可能とする計算能力を持つ。そこで、われわれは数百万原子のシステムを扱う大規模な分子シミュレーション(PABIOS)を開発している。PABIOSは空間分割法を用いており高い並列化効率を持つ。PABIOSは系のエネルギー,温度,圧力を一定に保つさまざまな時間積分アルゴリズム,原子結合長を固定することにより時間ステップの増大を可能とするSHAKE, RATTLEアルゴリズムなどの高精度アルゴリズムを採用した計算性能に優れたシミュレーションシステムである。今回、系の原子分布の異方性による並列化効率の悪化がおこらないように、動的ロードバランスを開発した。ホリデイ分岐DNAとDNA結合蛋白質RuvA4量体の複合体が水中に存在する系(全系16万6千原子)について分子動力学シミュレーションを実行した結果、地球シミュレータで120個のプロセッサを用いてもPABIOSはベクトル化率95%以上,並列化効率50%以上の優れた性能を達成することに成功した。そして計算速度も昨年度と比べて約2倍程度向上した。



郷 信広; 米谷 佳晃*

生体の科学, 56(6), p.626 - 631, 2005/12



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

米谷 佳晃

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

 被引用回数:50 パーセンタイル:84.25(Chemistry, Physical)

18$AA $の長いカットオフ距離を用いて水の分子動力学シミュレーションを行ったところ、水の挙動に著しいアーティファクトが現れた。この結果から、カットオフ距離の増加によりシミュレーション結果が改善されるとは限らないことが判明した。さらに、これまでに長いカットオフ距離を用いて行われてきた水を含む生体分子系のシミュレーションにも予想外に大きいアーティファクトが存在していた可能性が示唆されている。


Sequence-dependent DNA conformation and flexibility characterized by hydration pattern

米谷 佳晃*; 河野 秀俊; 郷 信広

no journal, , 



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

河野 秀俊; 米谷 佳晃*; 藤井 聡*; 皿井 明倫*; 郷 信広

no journal, , 


74 件中 1件目~20件目を表示