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鸡蛋清溶菌酶中的水合动力学。

Dynamics of hydration in hen egg white lysozyme.

作者信息

Sterpone F, Ceccarelli M, Marchi M

机构信息

Section de Biophysique des Protéines et des Membranes, DBCM, DSV, CEA, Centre d'Etudes, Saclay, 91191, Gif-sur-Yvette Cedex, France.

出版信息

J Mol Biol. 2001 Aug 10;311(2):409-19. doi: 10.1006/jmbi.2001.4860.

Abstract

We investigate the hydration dynamics of a small globular protein, hen egg-white lysozyme. Extensive simulations (two trajectories of 9 ns each) were carried out to identify the time-scales and mechanism of water attachment to this protein. The location of the surface and integral water molecules in lysozyme was also investigated. Three peculiar temporal scales of the hydration dynamics can be discerned: two among these, with sub-nanosecond mean residence time, tau(w), are characteristic of surface hydration water; the slower time-scale (tau(w) approximately 2/3 ns) is associated with buried water molecules in hydrophilic pores and in superficial clefts. The computed tau(w) values in the two independent runs fall in a similar range and are consistent with each other, thus adding extra weight to our result. The tau(w) of surface water obtained from the two independent trajectories is 20 and 24 ps. In both simulations only three water molecules are bound to lysozyme for the entire length of the trajectories, in agreement with nuclear magnetic relaxation dispersion estimates. Locations other than those identified in the protein crystal are found to be possible for these long-residing water molecules. The dynamics of the hydration water molecules observed in our simulations implies that each water molecule visits a multitude of residues during the lifetime of its bound with the protein. The number of residues seen by a single water molecule increases with the time-scale of its residence time and, on average, is equal to one only for the water molecules with shorter residence time. Thus, tau(w) values obtained from inelastic neutron scattering and based on jump-diffusion models are likely not to account for the contribution of water molecules with longer residence time.

摘要

我们研究了一种小型球状蛋白质——鸡蛋清溶菌酶的水合动力学。进行了大量模拟(每条轨迹9纳秒,共两条轨迹),以确定水与该蛋白质结合的时间尺度和机制。还研究了溶菌酶中表面水分子和整体水分子的位置。水合动力学可识别出三个特殊的时间尺度:其中两个,平均停留时间τ(w) 为亚纳秒级,是表面水合水的特征;较慢的时间尺度(τ(w) 约为2/3纳秒)与亲水性孔隙和表面裂隙中的埋藏水分子有关。两次独立运行中计算得到的τ(w) 值落在相似范围内且相互一致,从而增强了我们结果的可信度。从两条独立轨迹得到的表面水的τ(w) 分别为20皮秒和24皮秒。在两次模拟中,在整个轨迹长度内只有三个水分子与溶菌酶结合,这与核磁共振弛豫色散估计结果一致。发现这些长期存在的水分子可能位于蛋白质晶体中未识别出的位置之外。我们模拟中观察到的水合水分子动力学表明,每个水分子在与蛋白质结合的寿命期间会访问多个残基。单个水分子看到的残基数量随其停留时间的时间尺度增加,平均而言,只有停留时间较短的水分子看到的残基数量才等于一个。因此,从非弹性中子散射获得并基于跳跃扩散模型得到的τ(w) 值可能无法解释停留时间较长的水分子的贡献。

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