磷脂膜表面附近质子传输的分子动力学模拟
Molecular dynamics simulation of proton transport near the surface of a phospholipid membrane.
作者信息
Smondyrev Alexander M, Voth Gregory A
机构信息
Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112-0850, USA.
出版信息
Biophys J. 2002 Mar;82(3):1460-8. doi: 10.1016/S0006-3495(02)75500-8.
Abstract
The structural and dynamical properties of a hydrated proton near the surface of DMPC membrane were studied using a molecular dynamics simulation. The proton transport between water molecules was modeled using the second generation multistate empirical valence bond model. The proton diffusion was found to be inhibited at the membrane surface. The potential of mean force for the proton adsorption to the membrane surface and its release back into the bulk water was also determined, yielding a small barrier in each direction. An efficient algorithm for Ewald summation calculations for the multistate empirical valence bond model is also introduced.
摘要
利用分子动力学模拟研究了DMPC膜表面附近水合质子的结构和动力学性质。使用第二代多态经验价键模型对水分子间的质子传输进行了建模。发现质子在膜表面的扩散受到抑制。还确定了质子吸附到膜表面及其释放回 bulk 水的平均力势，在每个方向上都产生了一个小的势垒。还介绍了一种用于多态经验价键模型的Ewald求和计算的高效算法。
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本文引用的文献
1
Dynamic studies of proton diffusion in mesoscopic heterogeneous matrix: II. The interbilayer space between phospholipid membranes.
Biophys J. 1992 Jul;63(1):281-90. doi: 10.1016/S0006-3495(92)81585-0.
2
The formation and dynamics of proton wires in channel environments.
Biophys J. 2001 Apr;80(4):1691-702. doi: 10.1016/S0006-3495(01)76140-1.
3
Framework model for single proton conduction through gramicidin.
Biophys J. 2001 Jan;80(1):12-30. doi: 10.1016/S0006-3495(01)75992-9.
4
A combined molecular dynamics and diffusion model of single proton conduction through gramicidin.
Biophys J. 2000 Dec;79(6):2840-57. doi: 10.1016/S0006-3495(00)76522-2.
5
Structure of lipid bilayers.
Biochim Biophys Acta. 2000 Nov 10;1469(3):159-95. doi: 10.1016/s0304-4157(00)00016-2.
6
Proton transfer reactions across bacteriorhodopsin and along the membrane.
Biochim Biophys Acta. 2000 May 12;1458(1):135-47. doi: 10.1016/s0005-2728(00)00064-5.
7
Biophysical aspects of intra-protein proton transfer.
Biochim Biophys Acta. 2000 May 12;1458(1):120-34. doi: 10.1016/s0005-2728(00)00063-3.
8
Unified approach for molecular dynamics and density-functional theory.
Phys Rev Lett. 1985 Nov 25;55(22):2471-2474. doi: 10.1103/PhysRevLett.55.2471.
9
Canonical dynamics: Equilibrium phase-space distributions.
Phys Rev A Gen Phys. 1985 Mar;31(3):1695-1697. doi: 10.1103/physreva.31.1695.
10
Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations.
Biophys J. 1996 Aug;71(2):632-47. doi: 10.1016/S0006-3495(96)79264-0.
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