中国药科大学学报2017，Vol.48Issue(2)：227-232,6.DOI:10.11665/j.issn.1000-5048.20170215
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
摘要
Abstract
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.关键词
纳米分子动力学(NAMD)/可视化分子动力学(VMD)/分子动力学模似/CHARMM/L-对硝基苯丙氨酸/B淋巴细胞刺激因子Key words
nanoscale molecular dynamics (NAMD)/visual molecular dynamics (VMD)/molecular dynamics simulation/chemistry at Harvard macromolecular mechanics (CHARMM)/p-nitro-L-phenylalanine/B lymphocyte stimulator分类
生物科学引用本文复制引用
蔡棣,田浤,姚文兵..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[J].中国药科大学学报,2017,48(2):227-232,6.基金项目
国家教育部博士点基金资助项目(No.20120096110007) （No.20120096110007）
国家自然科学基金资助项目(No.81273426)This study was supported by the Ph.D Programs Foundation of Ministry of Education of China (No.20120096110007)and the National Natural Science Foundation of China(No.81273426) （No.81273426）
