Microscopic dynamics of water around unfolded structures of barstar at room temperature.
Microscopic dynamics of water around unfolded structures of barstar at room temperature.
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室温下 Barstar 展开结构周围水的微观动力学。
DOI：
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发表时间：
2015
影响因子：
4.4
通讯作者：
S. Bandyopadhyay
中科院分区：
文献类型：
--
作者：
S. Pal;K. Chakraborty;Prabir Khatua;S. Bandyopadhyay
蛋白质天然结构的破坏及其对周围溶剂动态响应的影响是蛋白质折叠中的一个重要问题。在这项工作中，我们进行了原子分子动力学模拟，以在两种不同的温度（400 K 和 450 K）下展开蛋白质 barstar。在室温下进一步研究在如此高的温度下获得的两种展开形式，以探索蛋白质二级结构沿着两种不同途径的不均匀展开对表面水分子微观动力学性质的影响。研究表明，虽然蛋白质的结构转变通常会导致其片段周围的水运动受到较少的限制，但有证据表明，随着周围环境的日益受限，在展开时会形成新的构象基序，从而导致其水化层中的水流动性进一步受到限制。此外，值得注意的是，蛋白质片段的不均匀展开对蛋白质-水（PW）和水-水（WW）氢键的弛豫时间的影响与受阻的水合水运动相关。然而，发现这种氢键的断裂和重组动力学在界面处受到不同的影响。据观察，虽然解折叠对 PW 氢键动力学的影响似乎最小，但涉及蛋白质片段周围 WW 氢键的动力学表现出明显的异质特征。我们相信，这是一个重要的观察，它可以为蛋白质解折叠对其水合水微观性质的异质影响的起源提供有价值的见解。
The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein-water (PW) and the water-water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.
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Barstar 具有高度动态的疏水核心：来自分子动力学模拟和核磁共振弛豫数据的证据。
DOI：
10.1021/bi980552i
发表时间：
1998
期刊：
Biochemistry.
影响因子：
--
作者：
Wong,KB;Daggett,V
通讯作者：
Daggett,V
DOI：
10.1021/jp046711r
发表时间：
2004-12
期刊：
The journal of physical chemistry. A
影响因子：
--
作者：
T. Steinel;J. Asbury;Junrong Zheng;M. Fayer
通讯作者：
T. Steinel;J. Asbury;Junrong Zheng;M. Fayer
影响因子：
56.9
作者：
Duan, Y;Kollman, PA
通讯作者：
Kollman, PA
DOI：
10.1073/pnas.0307851100
发表时间：
2004-03-09
影响因子：
11.1
作者：
Papoian, GA;Ulander, J;Wolynes, PG
通讯作者：
Wolynes, PG
影响因子：
15
作者：
MacKerell, AD;Feig, M;Brooks, CL
通讯作者：
Brooks, CL