Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China.
PLoS One. 2018 May 24;13(5):e0198049. doi: 10.1371/journal.pone.0198049. eCollection 2018.
A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a coarse-grained elementary bead based on functional group. The effective hybrid potential between any pair of beads is composed of a short-range repulsive soft-core potential that directly adopts the form of an explicit-solvent DPD model and a long-range attractive hydrophobic potential. The parameters of the attractive potentials for lipid molecules were obtained by fitting the explicit-solvent DPD simulation of one bead of any type in a water box, then finely tuning it until the bilayer membrane properties obtained in the explicit-solvent model were matched. These parameters were further extended to amino acids according to bead type. The structural and elastic properties of bilayer membranes, free energy profiles for a lipid flip-flop and amino acid analogues translocating across the membrane, and membrane pore formation induced by antimicrobial peptides obtained from this solvent-free DPD force field considerably agreed with the explicit-solvent DPD results. Importantly, the efficiency of this method is guaranteed to accelerate the assembly of vesicles composed of several thousand lipids by up to 50-fold, rendering the experimental liposome dynamics as well as membrane-peptide interactions feasible at accessible computational expense.
一组新的高效无溶剂耗散粒子动力学（DPD）力场被开发用于磷脂和肽。为了增强可转移性，该模型基于官能团将大约四个重原子及其连接的氢原子映射到一个粗粒的基本珠上。任意两个珠之间的有效混合势能由短程排斥软核势组成，该势直接采用显式溶剂 DPD 模型的形式，以及长程吸引疏水性势。脂质分子的吸引势能参数是通过拟合水盒中任意类型的单个珠的显式溶剂 DPD 模拟获得的，然后进行微调，直到在显式溶剂模型中获得的双层膜性质得到匹配。根据珠的类型，这些参数进一步扩展到氨基酸。从这个无溶剂 DPD 力场获得的双层膜的结构和弹性性质、脂质翻转的自由能曲线以及穿过膜的氨基酸类似物的转运、抗菌肽诱导的膜孔形成与显式溶剂 DPD 结果相当吻合。重要的是，这种方法的效率保证了组装由数千个脂质组成的囊泡的速度提高了 50 倍，使得实验脂质体动力学以及膜-肽相互作用在可访问的计算成本下成为可行的。
