Marchi Massimo, Sterpone Fabio, Ceccarelli Matteo
Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Etudes, Saclay, 91191 Gif-sur-Yvette Cedex, France.
J Am Chem Soc. 2002 Jun 12;124(23):6787-91. doi: 10.1021/ja025905m.
This paper is concerned with the dynamics of water around a small globular protein. Dipolar second-rank relaxation time and diffusion properties of surface water were computed by extensive molecular dynamics simulations of lysozyme in water which lasted a total of 28 ns. Our results indicate that the rotational relaxation of water in the vicinity of lysozyme is 3-7 times slower than that in the bulk depending on how the hydration shell is defined in the calculation. We have also verified that the dynamics of water translational diffusion in the vicinity of lysozyme have retardations similar to rotational relaxation. This is a common assumption in nuclear magnetic relaxation dispersion (NMRD) studies to derive residence times. In contrast to bulk water dynamics, surface water is in a dispersive diffusion regime or subdiffusion. Very good agreement of dipolar second-rank relaxation time with NMRD estimates is obtained by using appropriate dimensions of the hydration shell. Although our computed second-rank dipolar retardations are independent of the water model, SPC/E describes more realistically the time scale of the water dynamics around lysozyme than does TIP3P.
本文关注的是围绕小型球状蛋白质的水的动力学。通过对溶菌酶在水中进行总共28纳秒的广泛分子动力学模拟，计算了表面水的偶极二阶弛豫时间和扩散性质。我们的结果表明，根据计算中如何定义水合壳，溶菌酶附近水的旋转弛豫比本体水慢3至7倍。我们还证实，溶菌酶附近水的平动扩散动力学具有与旋转弛豫类似的延迟。这是在核磁共振弛豫色散（NMRD）研究中推导停留时间的一个常见假设。与本体水动力学不同，表面水处于分散扩散状态或亚扩散状态。通过使用合适的水合壳尺寸，偶极二阶弛豫时间与NMRD估计值取得了非常好的一致性。尽管我们计算的二阶偶极延迟与水模型无关，但与TIP3P相比，SPC/E能更真实地描述溶菌酶周围水动力学的时间尺度。
