ABEEMσπ/MM模型对蛋白质G_A88/G_B88水溶液动力学性质的研究

应用ABEEMσπ/MM（σπ水平的原子与键电负性均衡方法融合进分子力学）浮动电荷模型以及显性ABEEM-7P水模型,对GA88和GB88两个蛋白质分子进行了分子动力学模拟.分析了2个蛋白质的动力学性质,包括蛋白质的回旋半径、疏水表面积和亲水表面积、各类原子位置的均方根偏差以及氢键分布.通过对比水溶液和真空下2个蛋白质的回旋半径,表明该模型很好地体现了蛋白质的＂电致紧缩＂现象;对疏水表面积和亲水表面积的计算表明,GB88中残基与溶剂的相互作用更强一些;非氢原子位置的均方根偏差及氢键分布情况与实验结构相比较表明,ABEEMσπ/MM浮动电荷模型模拟的GA88和GB88的结构与实验结构有很好的一致性,进而说明该模型的合理性和参数的可转移性.

The dynamic property investigation of G_A88 and G_B88 aqueous solution by means of ABEEMσπ/MM model

The dynamic behaviors of proteins GA88 and GB88 have been investigated,using molecular dynamics by means of ABEEMσπ/MM（Atom-Bond Electronegativity Equalization Method at σπ level fused into Molecular Mechanics） and the explicit ABEEM-7P water solvent models.Analyze the dynamic properties of these proteins,including radius of gyration,the distribution of hydrophobic and hydrophilic surface area,root mean square deviations of diverse non-hydrogen atoms,as well as the distribution of hydrogen bonds.The radius of gyration in aqueous solution and in vacuum showed that this model has properly embodied the ＂electrostatic compactness＂ phenomenon.Those calculations on hydrophobic and hydrophilic surface area display that the interaction between the residue of GB88 and solution is stronger.Those results,that is,the root mean square deviations of diverse non-hydrogen atoms between the structure of ABEEMσπ/MM model and experimental data and the distribution of hydrogen bond,demonstrate that the simulated structures of GA88 and GB88 by ABEEMσπ/MM fluctuating charge model are in good agreement with the experimental structures,and then explain the rationality of our model and transferability of the parameters.