※ 半角英数字
 年 ~ 
検索結果: 15 件中 1件目~15件目を表示
  • 1


Initialising ...



Initialising ...


Initialising ...


Initialising ...


Initialising ...


Initialising ...


Initialising ...


Initialising ...



Effect of water activity on the mechanical glass transition and dynamical transition of bacteria

曽我部 知史*; 中川 洋; 山田 武*; 小関 成樹*; 川井 清司*

Biophysical Journal, 121(20), p.3874 - 3882, 2022/10

 被引用回数:0 パーセンタイル:0.01(Biophysics)

本研究の目的は、バクテリア($$Cronobacter sakazakii$$)のガラス転移挙動を水分活性($$a_{rm w}$$)の関数として明らかにすることである。298Kでの機械的緩和を調べ、機械的$$a_{rm wc}$$(298Kで機械的ガラス転移が起こる$$a_{rm w}$$)を0.667と決定した。平均二乗変位の温度依存性は、中性子非弾性散乱により調べた。フィッティングにより、2つの動的転移温度(low $$T_{rm ds}$$とhigh $$T_{rm ds}$$)が決定された。乾燥試料を除いて、低Tdに対する$$a_{rm w}$$の影響はわずかであった。高$$T_{rm d}$$$$a_{rm w}$$の減少に伴い大きく上昇した。高$$T_{rm d}$$で決定された動的$$a_{rm wc}$$(0.688)は、測定時間スケールが異なるため、機械的$$a_{rm wc}$$よりもわずかに高い値であった。高$$T_{rm d}$$をガラス転移温度($$T_{rm g}$$)に変換し、無水$$T_{rm g}$$は411Kと推定された。


Nanosecond structural dynamics of intrinsically disordered $$beta$$-casein micelles by neutron spectroscopy

中川 洋; Appavou, M.-S.*; Wuttke, J.*; Zamponi, M.*; Holderer, O.*; Schrader, T. E.*; Richter, D.*; Doster, W.*

Biophysical Journal, 120(23), p.5408 - 5420, 2021/12

 被引用回数:0 パーセンタイル:0.01(Biophysics)



Conformational dynamics of a multidomain protein by neutron scattering and computational analysis

中川 洋; 齋尾 智英*; 長尾 道弘*; 井上 倫太郎*; 杉山 正明*; 味戸 聡志; 富永 大輝*; 川北 至信

Biophysical Journal, 120(16), p.3341 - 3354, 2021/08

 被引用回数:1 パーセンタイル:15(Biophysics)



Conformational ensemble of a multidomain protein explored by Gd$$^{3+}$$ electron paramagnetic resonance

齋尾 智英*; 平松 蒼野*; 浅田 瑞枝*; 中川 洋; 清水 和美*; 久米田 博之*; 中村 敏和*; 石森 浩一郎*

Biophysical Journal, 120(15), p.2943 - 2951, 2021/08

 被引用回数:0 パーセンタイル:0.01(Biophysics)



Universality and structural implications of the Boson peak in Proteins

中川 洋; 城地 保昌*; 北尾 彰朗*; 山室 修*; 片岡 幹雄*

Biophysical Journal, 117(2), p.229 - 238, 2019/07

 被引用回数:3 パーセンタイル:16.76(Biophysics)



Ligand-induced protein responses and mechanical signal propagation described by linear response theories

Yang, L.-W.*; 北尾 彰朗*; Huang, B.-C.*; 郷 信広*

Biophysical Journal, 107(6), p.1415 - 1425, 2014/09

 被引用回数:17 パーセンタイル:52.28(Biophysics)

In this study, a general linear response theory (LRT) is formulated to describe time-dependent and -independent protein conformational changes upon CO binding with myoglobin. Using the theory, we are able to monitor protein relaxation in two stages. The slower relaxation is found to occur from 4.4 to 81.2 picoseconds and the time constants characterized for a couple of aromatic residues agree with those observed by UV Resonance Raman (UVRR) spectrometry and time resolved X-ray crystallography. The faster "early responses", triggered as early as 400 femtoseconds, can be best described by the theory when impulse forces are used. The newly formulated theory describes the mechanical propagation following ligand-binding as a function of time, space and types of the perturbation forces. The "disseminators", defined as the residues that propagate signals throughout the molecule the fastest among all the residues in protein when perturbed, are found evolutionarily conserved and the mutations of which have been shown to largely change the CO rebinding kinetics in myoglobin.


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:24.29(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:60.94(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.


Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome

石田 恒; Hayward, S.*

Biophysical Journal, 95(12), p.5962 - 5973, 2008/12

 被引用回数:29 パーセンタイル:61.68(Biophysics)

Molecular dynamics simulations were performed on ${it Thermus thermophilus }$ 70S ribosome with and without the nascent polypeptide inside the exit tunnel. Modeling of the polypeptide in the tunnel revealed two possible paths: one over Arg$$^{92}$$ of L22 and one under (from the viewpoint of 50S on top of 30S). A strong interaction between L4 and Arg$$^{92}$$ was observed without the polypeptide and when it passed over Arg$$^{92}$$. However, when the polypeptide passed under, Arg$$^{92}$$ repositioned to interact with Ade$$^{2059}$$ of 23S rRNA. Using steered molecular dynamics the polypeptide could be pulled through the L4-L22 constriction when situated under Arg$$^{92}$$, but did not move when over. These results suggest that the tunnel is closed by the Arg$$^{92}$$-L4 interaction before elongation of the polypeptide and the tunnel leads the entering polypeptide from the peptidyl transferase center to the passage under Arg$$^{92}$$, causing Arg$$^{92}$$ to switch to an open position. It is possible, therefore, that Arg$$^{92}$$ plays the role of a gate, opening and closing the tunnel at L4-L22. There is controversy over whether the tunnel is dynamics or rigid. At least within the time-scale of our simulations conformational analysis showed that global motions mainly involve relative movement of the 50S and 30S subunits and appear not to affect the conformation of the tunnel.


Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal-mode analysis

松本 淳; 鎌田 徹治*; 高木 淳一*; 岩崎 憲治*; 由良 敬

Biophysical Journal, 95(6), p.2895 - 2908, 2008/09

 被引用回数:17 パーセンタイル:41.5(Biophysics)



Hydration affects both harmonic and anharmonic nature of protein dynamics

中川 洋; 城地 保昌*; 北尾 彰朗*; 片岡 幹雄

Biophysical Journal, 95(6), p.2916 - 2923, 2008/09

 被引用回数:49 パーセンタイル:79.24(Biophysics)

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.


Hydration effect on low-frequency protein dynamics observed in simulated neutron scattering spectra

城地 保昌*; 中川 洋; 片岡 幹雄; 北尾 彰朗*

Biophysical Journal, 94(11), p.4435 - 4443, 2008/06

 被引用回数:24 パーセンタイル:54.58(Biophysics)



Differences in internal dynamics of actin under different structural states detected by neutron scattering

藤原 悟; Plazanet, M.*; 松本 富美子; 小田 俊郎*

Biophysical Journal, 94(12), p.4880 - 4889, 2008/06

 被引用回数:9 パーセンタイル:22.08(Biophysics)



Discrimination of class I cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue

宮沢 祐司*; 西岡 宏隆*; 由良 敬; 倭 剛久*

Biophysical Journal, 94(6), p.2194 - 2203, 2008/03

 被引用回数:22 パーセンタイル:51.26(Biophysics)



Novel approach for the effective determination of DNA scission site using the Sanger method

坂本 文徳; 鈴木 英治*; 藤井 有起*

Journal of Biochemical and Biophysical Methods, 52(2), p.97 - 109, 2002/07

 被引用回数:4 パーセンタイル:9.84(Biochemical Research Methods)


15 件中 1件目~15件目を表示
  • 1