白蛋白和石墨烯的结构及其相互作用的分子动力学模拟  

Molecular dynamics simulations of albumin and graphene structures and their interaction

作　　者：孙颖[1,2] 丁佳丽[1,2] 宗皓 王健丹[1] 吕晓迎[1] 

机构地区：[1]东南大学生物电子学国家重点实验室,南京210096 [2]东南大学江苏省生物材料与器件重点实验室,南京210009 [3]东南大学软件学院,南京211189

出　　处：《东南大学学报（自然科学版）》2014年第1期123-128,共6页Journal of Southeast University：Natural Science Edition

基　　金：国家自然科学基金资助项目(31271012)

摘　　要：采用分子动力学模拟的方法分析研究了白蛋白与石墨烯表面的相互作用．分子模拟过程采用Gromacs软件进行运算及数据采集分析，并采用VMD软件实现结构的可视化．首先，建立周期边界条件，在边长为9nm的有限空间中采用恒温恒压系综，对ffgmx力场条件下的白蛋白原始真空构象进行优化，使其在水相中达到平衡态．然后，以水相中得到的稳定的白蛋白作为模型，构建与石墨烯相互作用的总体构象及界面．最后，在周期性边界条件下，经过500ps的动态过程，完成了白蛋白在石墨烯表面的吸附．对能量、残基轨迹、扭转角等数据进行分析总结，确定了白蛋白在石墨烯表面的吸附位点为白蛋白序列中90～97号肽段90ALA-91GLY-92ILE一93THR_94SER_95ASP_q6PHE．97TYR．Molecular dynamics simulations were used to study the interaction between albumin and graphene surface. During the simulation, Gromacs software was used to collect and analyze data, and VMD software was used to realize visualization of structures. First, the periodic boundary condi- tion was established. The constant temperature and pressure ensemble was adopted in a limited space with the side length of 9 nm, and the original vacuum conformation of albumin was optimized under the force field ffgmx, so that equilibrium in the aqueous phase was reached. Then, the optimized stable albumin in the aqueous phase was used as a model to build the overall conformation and inter- action interface with graphene. Finally, after 500 ps of the dynamic process under periodic boundary conditions, the adsorption of albumin onto the graphene surface was completed. The energy, trajec- tory of residues, torsion angle and other data were analyzed, and the adsorption sites of albumin on the graphene surface were determined to be 90 to 97 peptide 90ALA-91GLY-92ILE-93THR-94SER- 95ASP-96PHE-97TYR.

关 键 词：分子动力学模拟 白蛋白 石墨烯 相互作用机制 

分 类 号：R318.08[医药卫生—生物医学工程]