Department of Physics, National Central University, Jhongli 32001, Taiwan.
J Chem Phys. 2013 May 21;138(19):195101. doi: 10.1063/1.4803507.
A coarse-grain method for simulations of the dynamics of active protein inclusions in lipid bilayers is described. It combines the previously proposed hybrid simulations of bilayers [M.-J. Huang, R. Kapral, A. S. Mikhailov, and H.-Y. Chen, J. Chem. Phys. 137, 055101 (2012)], based on molecular dynamics for the lipids and multi-particle collision dynamics for the solvent, with an elastic-network description of active proteins. The method is implemented for a model molecular machine which performs active conformational motions induced by ligand binding and its release after reaction. The situation characteristic for peripheral membrane proteins is considered. Statistical investigations of the effects of single active or passive inclusions on the shape of the membrane are carried out. The results show that the peripheral machine produces asymmetric perturbations of the thickness of two leaflets of the membrane. It also produces a local saddle in the midplane height of the bilayer. Analysis of the power spectrum of the fluctuations of the membrane midplane shows that the conformational motion of the machine perturbs these membrane fluctuations. The hydrodynamic lipid flows induced by cyclic conformational changes in the machine are analyzed. It is shown that such flows are long-ranged and should provide an additional important mechanism for interactions between active inclusions in biological membranes.
一种用于模拟脂质双层中活性蛋白包含物动力学的粗粒度方法被描述。它结合了之前提出的双层混合模拟[M.-J. Huang、R. Kapral、A. S. Mikhailov 和 H.-Y. Chen，J. Chem. Phys. 137，055101（2012）]，基于分子动力学用于脂质和多粒子碰撞动力学用于溶剂，以及活性蛋白的弹性网络描述。该方法针对一种模型分子机器进行了实现，该机器通过配体结合及其反应后释放来执行主动构象运动。考虑了外周膜蛋白的特征情况。对单个活性或被动包含物对膜形状的影响进行了统计研究。结果表明，外围机器会对膜的两个叶层的厚度产生不对称的干扰。它还会在双层的中间平面高度产生局部鞍点。对膜中间平面波动的功率谱分析表明，机器的构象运动会干扰这些膜波动。对机器周期性构象变化引起的流体动力学脂质流进行了分析。结果表明，这种流动具有长程性，应该为生物膜中活性包含物之间的相互作用提供另一个重要机制。
