含有L-对硝基苯丙氨酸的BAFF改构体的分子动力学模拟与分析

Molecular dynamics simulation and analysis of BAFF which is incorporated with p-nitro-L-phenylalanine

建立含有L-对硝基苯丙氨酸(p-nitro-L-phenylalanine,pNO_2Phe)蛋白的分子动力学模拟方法,分析了含有pNO_2Phe的蛋白具有免疫原性的构效关系,为其他含有非天然氨基酸蛋白的动力学模拟研究提供参考。使用CGenFF-paramchem计算天然氨基酸中不存在的L-对硝基苯丙氨酸的新的成键、键角、二面角信息与能量,将新成键的键长、键角、二面角参数与相应的能量信息写入CHARMM(chemistry at Harvard macromolecular mechanics)力场参数文件中。重新定义L-对硝基苯丙氨酸的CHARMM力场参数后,利用纳米分子动力学(NAMD)成功对含有L-对硝基苯丙氨酸的B淋巴细胞刺激因子(BAFF)进行动力学模拟。统计动力学模拟过程中的每一帧体系的温度,作出的温度分布图符合正态分布,证明了新定义力场参数的稳定性。模拟结果中,蛋白的均方根偏差(RMSD)在趋近于2.5,pNO_2Phe残基的均方根涨落(RMSF)为3.7,显著高于分子的其他部位,表明pNO_2Phe残基运动剧烈,蛋白在该残基附近结构的可变性较大,可能会产生新的构象表位,为含有pNO_2Phe蛋白成为自体疫苗的设计提供了理论上的可行性。

In order to study the structure-function relationship in the protein which is incorporated with p-nitro-L-phenylalanine, the method of MD（Molecular Dynamics）simulation was established and successfully used in the analysis of protein which contains p-nitro-L-phenylalanine. The force field of CHARMM can only stimulate protein with natural amino acid in NAMD. Compared with phenylalanine, p-nitro-L-phenylalanine just has one more group of nitro. If the parameter of group of nitro was defined, the protein containing p-nitro-L-phenylalanine can be simulated. CGenFF-paramchem was used to calculate the energy and topological structure of p-nitro-L-phenylalanine′s new bonds（r）, angles（θ）, dihendrals（φ）and improper angle（ψ）. And then the new defined parameter and topology information was input into the related parameter files and topology files in CHARMM. On the basis of correct parameter, NAMD can successfully simulate the modified BAFF（B lymphocyte stimulator）which contains p-nitro-L-phenylalanine. The changes in structure indicated that there might be new B cell epitopes. The temperature distribution of each frame in the process of dynamics stimulation was in accord with normal distribution, which proved the defined force field parameters was feasible. The RMSD of whole protein solution systemis 2. 5. Calculate each resides′ RMSF in BAFF, the RMSF of p-nitro-L-phenylalanine′s residue is 3. 7, which is obviously higher than that of the other residues in β-pleated sheet, and close to the loop rings, indicate that there might be variation in the area of p-nitro-L-phenylalanine residue and might produce new comformational epitopes. The results of MD stimulation will guide the immunogenicity experiments of p-nitro-L-phenylalanine modified proteins.