Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.
Quantum dynamics in continuum for proton transport II: Variational solvent-solute interface.
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DOI：
10.1002/cnm.1458
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发表时间：
2012-01
影响因子：
2.1
通讯作者：
Wei GW
中科院分区：
文献类型：
--
作者：
Chen D;Chen Z;Wei GW
质子转运在生物能量传递和感觉系统中起着重要的作用。因此，在过去的几十年里，它引起了生物科学和生物医学工程的广泛关注。目前的工作提出了一个多尺度/多物理模型的理解质子跨膜蛋白的分子机制，涉及连续，原子和量子的描述，辅助膜通道表面的演变，形成和可视化。我们描述质子动力学量子力学通过一个新的密度泛函理论的基础上的玻尔兹曼统计，而隐含的模型众多的溶剂分子作为一个介电连续，以减少自由度的数量。假设溶剂中所有其他离子的密度以动态方式服从玻尔兹曼分布。蛋白质分子结构及其电荷极化对质子输运的影响被认为是明确在原子尺度上。变分溶质-溶剂界面的设计，以分离显式分子和隐式溶剂区域。我们制定了一个总的自由能功能，把质子的动能和势能，所有其他离子的自由能，整个系统的极性和非极性能量在平等的基础上。利用变分原理导出了质子输运系统的耦合控制方程。在此变分框架下得到了广义Laplace-Beltrami方程、广义Poisson-Boltzmann方程和广义Kohn-Sham方程。变分的溶剂-溶质界面生成和可视化，以方便多尺度离散/连续/量子描述。质子密度和电导的理论公式的基础上构建的基本物理定律。一些数学算法，包括狄利克雷到诺依曼映射（DNM），匹配接口和边界（MIB）的方法，Gummel迭代，Krylov空间技术被用来实现所提出的模型在计算上有效的方式。短杆菌肽A（GA）通道被用来验证所提出的质子传输模型的性能，并证明所提出的数学算法的效率。质子通道电导的研究超过了一些施加的电压和参考浓度。与实验数据的比较验证了本模型的预测，并证实了所提出的模型。
Proton transport plays an important role in biological energy transduction and sensory systems. Therefore it has attracted much attention in biological science and biomedical engineering in the past few decades. The present work proposes a multiscale/multiphysics model for the understanding of the molecular mechanism of proton transport in transmembrane proteins involving continuum, atomic and quantum descriptions, assisted with the evolution, formation and visualization of membrane channel surfaces. We describe proton dynamics quantum mechanically via a new density functional theory based on the Boltzmann statistics, while implicitly model numerous solvent molecules as a dielectric continuum to reduce the number of degrees of freedom. The density of all other ions in the solvent is assumed to obey the Boltzmann distribution in a dynamic manner. The impact of protein molecular structure and its charge polarization on the proton transport is considered explicitly at the atomic scale. A variational solute-solvent interface is designed to separate the explicit molecule and implicit solvent regions. We formulate a total free energy functional to put proton kinetic and potential energies, the free energy of all other ions, the polar and nonpolar energies of the whole system on an equal footing. The variational principle is employed to derive coupled governing equations for the proton transport system. Generalized Laplace-Beltrami equation, generalized Poisson-Boltzmann equation and generalized Kohn-Sham equation are obtained from the present variational framework. The variational solvent-solute interface is generated and visualized to facilitate the multiscale discrete/continuum/quantum descriptions. Theoretical formulations for the proton density and conductance are constructed based on fundamental laws of physics. A number of mathematical algorithms, including the Dirichlet to Neumann mapping (DNM), matched interface and boundary (MIB) method, Gummel iteration, and Krylov space techniques are utilized to implement the proposed model in a computationally efficient manner. The Gramicidin A (GA) channel is used to validate the performance of the proposed proton transport model and demonstrate the efficiency of the proposed mathematical algorithms. The proton channel conductances are studied over a number of applied voltages and reference concentrations. A comparison with experimental data verifies the present model predictions and confirms the proposed model.
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影响因子：
3.3
作者：
Bothma, Jacques P.;Gilmore, Joel B.;McKenzie, Ross H.
通讯作者：
McKenzie, Ross H.
影响因子：
4.1
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影响因子：
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