布朗运动理论在分子动力学计算的膜通道离子轨迹分析中的应用。
Application of Brownian motion theory to the analysis of membrane channel ionic trajectories calculated by molecular dynamics.
作者信息
Jakobsson E, Chiu S W
机构信息
Department of Physiology and Biophysics, University of Illinois, Urbana 61801.
出版信息
Biophys J. 1988 Oct;54(4):751-6. doi: 10.1016/S0006-3495(88)83012-1.
Abstract
This paper shows how Brownian motion theory can be used to analyze features of individual ion trajectories in channels as calculated by molecular dynamics, and that its use permits more precise determinations of diffusion coefficients than would otherwise be possible. We also show how a consideration of trajectories of single particles can distinguish between effects due to the magnitude of the diffusion coefficient and effects due to barriers and wells in the potential profile, effects which can not be distinguished by consideration of average fluxes.
摘要
本文展示了布朗运动理论如何用于分析通过分子动力学计算得到的通道中单个离子轨迹的特征，并且其应用使得扩散系数的测定比其他方法更精确。我们还展示了如何通过考虑单个粒子的轨迹来区分由于扩散系数大小引起的效应和由于势垒和势阱在势能分布中引起的效应，而这些效应通过考虑平均通量是无法区分的。
相似文献
1
Application of Brownian motion theory to the analysis of membrane channel ionic trajectories calculated by molecular dynamics.布朗运动理论在分子动力学计算的膜通道离子轨迹分析中的应用。
Biophys J. 1988 Oct;54(4):751-6. doi: 10.1016/S0006-3495(88)83012-1.
2
Ion permeation through the gramicidin channel: atomically detailed modeling by the Stochastic Difference Equation.离子通过短杆菌肽通道的渗透：基于随机差分方程的原子级详细建模。
Proteins. 2003 Jan 1;50(1):63-80. doi: 10.1002/prot.10256.
3
Stochastic theory of ion movement in channels with single-ion occupancy. Application to sodium permeation of gramicidin channels.单离子占据通道中离子运动的随机理论。应用于短杆菌肽通道的钠渗透。
Biophys J. 1987 Jul;52(1):33-45. doi: 10.1016/S0006-3495(87)83186-7.
4
Simulation of voltage-driven hydrated cation transport through narrow transmembrane channels.通过狭窄跨膜通道的电压驱动水合阳离子运输的模拟。
Biophys J. 1987 Jun;51(6):977-83. doi: 10.1016/S0006-3495(87)83425-2.
5
Boundary conditions for- single-ion diffusion.单离子扩散的边界条件。
Biophys J. 1996 Oct;71(4):1723-42. doi: 10.1016/S0006-3495(96)79374-8.
6
The nature of ion and water barrier crossings in a simulated ion channel.模拟离子通道中离子与水屏障穿越的性质
Biophys J. 1993 Jan;64(1):98-109. doi: 10.1016/S0006-3495(93)81344-4.
7
The role of the dielectric barrier in narrow biological channels: a novel composite approach to modeling single-channel currents.介电势垒在狭窄生物通道中的作用：一种模拟单通道电流的新型复合方法。
Biophys J. 2003 Jun;84(6):3646-61. doi: 10.1016/S0006-3495(03)75095-4.
8
Ion fluxes through nanopores and transmembrane channels.离子通过纳米孔和跨膜通道的通量。
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Mar;85(3 Pt 1):031914. doi: 10.1103/PhysRevE.85.031914. Epub 2012 Mar 26.
9
A stochastic simulation of direct ion passage through a sodium channel.
Membr Cell Biol. 1997;11(1):101-13.
10
Memoryless control of boundary concentrations of diffusing particles.扩散粒子边界浓度的无记忆控制
Phys Rev E Stat Nonlin Soft Matter Phys. 2004 Dec;70(6 Pt 1):061106. doi: 10.1103/PhysRevE.70.061106. Epub 2004 Dec 22.
引用本文的文献
1
Electrostatics of a simple membrane model using Green's functions formalism.使用格林函数形式的简单膜模型的静电学
Biophys J. 1996 Aug;71(2):795-810. doi: 10.1016/S0006-3495(96)79281-0.
2
The nature of ion and water barrier crossings in a simulated ion channel.模拟离子通道中离子与水屏障穿越的性质
Biophys J. 1993 Jan;64(1):98-109. doi: 10.1016/S0006-3495(93)81344-4.
3
Brownian dynamics study of a multiply-occupied cation channel: application to understanding permeation in potassium channels.多占据阳离子通道的布朗动力学研究：应用于理解钾通道中的渗透作用
Biophys J. 1994 Apr;66(4):1028-38. doi: 10.1016/S0006-3495(94)80884-7.
4
Stochastic theory of singly occupied ion channels. II. Effects of access resistance and potential gradients extending into the bath.单占据离子通道的随机理论。II. 延伸至浴槽中的接入电阻和电位梯度的影响。
Biophys J. 1989 Jan;55(1):147-57. doi: 10.1016/S0006-3495(89)82786-9.
5
Time-correlation analysis of simulated water motion in flexible and rigid gramicidin channels.柔性和刚性短杆菌肽通道中模拟水运动的时间相关性分析
Biophys J. 1991 Jul;60(1):273-85. doi: 10.1016/S0006-3495(91)82049-5.
本文引用的文献
1
Structure and dynamics of ion transport through gramicidin A.离子通过短杆菌肽A的转运结构与动力学
Biophys J. 1984 Aug;46(2):229-48. doi: 10.1016/S0006-3495(84)84016-3.
2
Water transport and ion-water interaction in the gramicidin channel.短杆菌肽通道中的水运输及离子-水相互作用
Biophys J. 1981 Aug;35(2):501-8. doi: 10.1016/S0006-3495(81)84805-9.
3
Molecular dynamics simulation of cation motion in water-filled gramicidinlike pores.充满水的类短杆菌肽孔中阳离子运动的分子动力学模拟
Biophys J. 1984 Dec;46(6):805-19. doi: 10.1016/S0006-3495(84)84079-5.
4
Rate theories and puzzles of hemeprotein kinetics.血红素蛋白动力学的速率理论与谜题。
Science. 1985 Jul 26;229(4711):337-45. doi: 10.1126/science.4012322.
5
Diffusion in a rough potential.在粗糙势场中的扩散。
Proc Natl Acad Sci U S A. 1988 Apr;85(7):2029-30. doi: 10.1073/pnas.85.7.2029.
6
Possible allosteric significance of water structures in proteins.蛋白质中水分子结构可能具有的别构意义。
J Biomol Struct Dyn. 1986 Dec;4(3):491-500. doi: 10.1080/07391102.1986.10506364.
7
Stochastic theory of ion movement in channels with single-ion occupancy. Application to sodium permeation of gramicidin channels.单离子占据通道中离子运动的随机理论。应用于短杆菌肽通道的钠渗透。
Biophys J. 1987 Jul;52(1):33-45. doi: 10.1016/S0006-3495(87)83186-7.
8
Simulation of voltage-driven hydrated cation transport through narrow transmembrane channels.通过狭窄跨膜通道的电压驱动水合阳离子运输的模拟。
Biophys J. 1987 Jun;51(6):977-83. doi: 10.1016/S0006-3495(87)83425-2.
9
Structure and dynamics of one-dimensional ionic solutions in biological transmembrane channels.生物跨膜通道中一维离子溶液的结构与动力学
Biophys J. 1987 Jun;51(6):969-76. doi: 10.1016/S0006-3495(87)83424-0.
10
Single-channel studies on linear gramicidins with altered amino acid side chains. Effects of altering the polarity of the side chain at position 1 in gramicidin A.对具有改变氨基酸侧链的线性短杆菌肽的单通道研究。改变短杆菌肽A中第1位侧链极性的影响。
Biophys J. 1986 Mar;49(3):673-86. doi: 10.1016/S0006-3495(86)83694-3.
Zotero 插件