Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme
Stochastic Analysis of Molecular Dynamics Reveals the Rotation Dynamics Distribution of Water around Lysozyme
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DOI：
10.1021/acs.jpcb.2c00970
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发表时间：
2022-06-23
影响因子：
3.3
通讯作者：
Shirakashi, Ryo
中科院分区：
文献类型：
--
作者：
Hu, Kang;Matsuura, Hiroaki;Shirakashi, Ryo
水动力学是必不可少的生化过程，介导所有这些反应，包括生物分子在溶液中的退化。为了解开周围的溶质生物分子的水动力学的分子尺度分布，我们在这里研究的旋转动力学的水周围的溶菌酶结合分子动力学（MD）模拟和宽带介电谱（BDS）。提出了一种利用每个水分子的弛豫时间和运动轨迹进行统计分析的方法，并给出了水分子在离溶菌酶表面一定距离处随旋转弛豫时间的二维概率分布.对于所观察到的34-284 mg/mL的溶菌酶溶液，我们发现从该分布获得的介电弛豫时间与测量的γ弛豫时间吻合得很好，这表明水分子的旋转自相关是介电谱的千兆赫域的基础。无论蛋白质浓度如何，水旋转弛豫时间与离溶菌酶表面的距离的关系表明，水旋转在离溶菌酶表面3 A内严重受阻，并且当远离10 A时几乎与纯水相当。随后确定的第一水化层的尺寸在水旋转的加速度和距离蛋白质表面之间的关系。
Water dynamics is essential to biochemical processes by mediating all such reactions, including biomolecular degeneration in solutions. To disentangle the molecular-scale distribution of water dynamics around a solute biomolecule, we investigated here the rotational dynamics of water around lysozyme by combining molecular dynamics (MD) simulations and broadband dielectric spectroscopy (BDS). A statistical analysis using the relaxation times and trajectories of every single water molecule was proposed, and the two-dimensional probability distribution of water at a distance from the lysozyme surface with a rotational relaxation time was given. For the observed lysozyme solutions of 34-284 mg/mL, we discovered that the dielectric relaxation time obtained from this distribution agrees well with the measured gamma relaxation time, which suggests that rotational self-correlation of water molecules underlies the gigahertz domain of the dielectric spectra. Regardless of protein concentration, water rotational relaxation time versus the distance from the lysozyme surface revealed that the water rotation is severely retarded within 3 A from the lysozyme surface and is nearly comparable to pure water when farther than 10 A. The dimension of the first hydration layer was subsequently identified in terms of the relationship between the acceleration of water rotation and the distance from the protein surface.