Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes.
Using Intrinsic Surfaces To Calculate the Free-Energy Change When Nanoparticles Adsorb on Membranes.
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DOI：
10.1021/acs.jpcb.8b03661
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发表时间：
2018-05
期刊：
影响因子：
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通讯作者：
Joaquín Klug;Carles Triguero;M. G. Del Pópolo;G. A. Tribello
中科院分区：
文献类型：
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作者：
Joaquín Klug;Carles Triguero;M. G. Del Pópolo;G. A. Tribello
介绍了一种在利用分子动力学研究与动态表面的结合时可以使用的反应坐标。该坐标测量吸附质与密度场中的等密度线之间的距离。此外，该坐标是连续的，因此可以将作为该坐标函数的模拟偏差添加到哈密顿量中，以提高吸附/解吸速率。通过进行元动力学模拟来测量亲水性纳米粒子与脂质双层结合的强度，证明了这种新坐标的有效性。利用该坐标对结合机制进行的研究表明，随着纳米粒子的结合，脂质双层的结构发生了一系列协同变化。
A reaction coordinate that can be used when investigating binding to dynamical surfaces with molecular dynamics is introduced. This coordinate measures the distance between the adsorbate and an isocontour in a density field. Furthermore, the coordinate is continuous so simulation biases that are a function of this coordinate can be added to the Hamiltonian to increase the rate of adsorption/desorption. The efficacy of this new coordinates is demonstrated by performing metadynamics simulations to measure the strength with which a hydrophilic nanoparticle binds to a lipid bilayer. An investigation of the binding mechanism that is performed using the coordinate demonstrates that the lipid bilayer undergoes a series of concerted changes in structure as the nanoparticle binds.