Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization
Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization
复制标题
蛋白质内氢键通过电子极化动态稳定
DOI：
10.1063/1.3089723
复制
发表时间：
2009-03-21
影响因子：
4.4
通讯作者：
Zhang, John Z. H.
中科院分区：
文献类型：
--
作者：
Duan, Li L.;Mei, Ye;Zhang, John Z. H.
采用分子动力学（MD）模拟方法研究了蛋白质内氢键的动力学稳定性。后者是来自量子力学计算的蛋白质在溶液中使用最近开发的分子分馏共轭帽泊松玻尔兹曼（MFCC-PB）的方法，因此包括在天然结构的蛋白质的电子极化效应。对含有螺旋和/或β折叠二级结构的许多基准蛋白进行MD模拟。计算结果表明，在模拟时间内平均的氢键占据百分比，以及作为模拟时间的函数的氢键的数量，是一贯的PPC下高于AMBER电荷。特别是，一些蛋白质内的氢键被发现在MD模拟使用琥珀色电荷，但他们是稳定的使用PPC。AMBER模拟中蛋白质内部氢键的断裂是导致分子动力学模拟中蛋白质局部结构变形或变性的主要原因。目前的研究提供了强有力的证据表明，氢键是动态更稳定的PPC比琥珀色电荷，突出了电子极化对蛋白质结构的稳定作用。
Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived from quantum mechanical calculation for protein in solution using a recently developed molecular fractionation with conjugate caps-Poisson-Boltzmann (MFCC-PB) approach and therefore includes electronic polarization effect of the protein at native structure. MD simulations are performed for a number of benchmark proteins containing helix and/or beta sheet secondary structures. The computational result shows that occupancy percentage of hydrogen bonds averaged over simulation time, as well as the number of hydrogen bonds as a function of simulation time, is consistently higher under PPC than AMBER charge. In particular, some intra-protein hydrogen bonds are found broken during MD simulation using AMBER charge but they are stable using PPC. The breaking of some intra-protein hydrogen bonds in AMBER simulation is responsible for deformation or denaturing of some local structures of proteins during MD simulation. The current study provides strong evidence that hydrogen bonding is dynamically more stable using PPC than AMBER charge, highlighting the stabilizing effect of electronic polarization on protein structure.