全α蛋白质体系能量转变的分子动力学模拟

A Study on the Energy Transition of All-α Proteins by Molecular Dynamics Simulation

采用简化的NHP模型并考虑蛋白质链的二级结构信息,对全α型蛋白质链进行构建.利用分子动力学模拟研究全α蛋白质体系势能的变化情况,得出键伸缩和弯曲能量随蛋白质的链长线性增加;单键的伸缩能和弯曲能随着温度的升高而线性增加,且伸缩能比弯曲能随温度的增加更为明显的结论.键扭转能随二级结构α螺旋数目的增加而线性降低,随温度的上升,扭转能变化呈现先增加后减少的趋势.非键能的大小随疏水残基在蛋白质组分中的比例增加而降低,但线性关系不明显.键扭转能和非键能都存在转变温度.蛋白质链的结构是由多种势能协同作用的结果,键能和非键能的相互竞争以及组成蛋白质链的氨基酸亲疏水性和二级结构组分都会影响蛋白质体系的能量,这些结果对深入理解蛋白质的结构提供理论依据.

Abstract All-α proteins simplified by NHP model with its secondary structure information were studied by molecular dynamics simulation. The transitions of potential energy in 50 all-α proteins under different temperatures were well discussed in this paper. It is concluded that the bond-stretching and bending energies increase linearly with the chain length. The bond-stretching and bending energies of each bond also increase linearly with the temperature due to more obvious bond vibration under high temperatures. The slope of the linear relationship between bond-stretching energy and temperature is larger than the one of bond-bending energy as the function of T＊ . The bond-torsional energy decreases linearly with the number of α-helix in each protein chain, instead of the chain length. It increases with the temperature when the temperature is lower than 0.3. And then it decreases with the temperature increasing. Non-bond energy is mainly dependent on hydrophobic-hydrophobic interactions. It doesn＇t show obvious linear relationship due to the mutual interactions between hydrophilic, hydrophobic, or neutral residues. The transition temperatures are shown in bond-torsional and non-bond potential energies. The native structure is related to the mutual effect of bond and non-bond potential energies, which compete with each other for lower potential energy. These conclusions provide a natural realization of understanding the structure of proteins.