含锌蛋白结构的电荷分布及蛋白质片段的结构优化

Charge distribution and optimization of structure for zinc protein

在PDB数据库中选取一系列的含锌蛋白模型分子并采用B3LYP/6-31+G*方法对氢原子进行部分优化,以Mulliken电荷为基准,利用线性回归和最小二乘法进行电荷分布计算,拟合出一套适用于含锌蛋白分子电荷计算的ABEEMσπ模型电荷参数.通过测试分子的检验,说明参数具有很好的可转移性.将拟合好的电荷参数融入ABEEMσπ浮动电荷极化力场,对3个蛋白质片段进行了力场优化并与PDB结构进行对比,得到相应键长和键角的偏差并统计了均方根偏差.键长均方根偏差最大值为0.005 6nm,键角均方根偏差最大值为3.75°.从优化结果来看,ABEEMσπ浮动电荷极化力场的参数是合理的,可以应用到更大的含锌蛋白体系中.

A series of molecular models were obtained from PDB database and hydrogen atoms were optimized at the B3LYP/6-31＋G＊level,then the charge parameters of ABEEMσπmodel were fitted by linear regression and the least square method based on Mulliken charge.The parameters are suitable for zinc proteins.It has a good parameter transferability by examining test molecules.The fitted parameters were integrated into ABEEMσπfluctuating charge polarizable force filed and then three zinc protein fragments were minimized.Compared the minimized structures with PDB structures,we got an exciting result that the maximum RMSD value of bond lengths and bond angles was 0.005 6nm and 3.75°,respectively.The results show that the parameters are reasonable and can be applied to the complex zinc proteins.