摘要
本文通过全原子分子动力学研究了典型的自组装芳香二肽分子(z-FF)自组装过程的微观结构演化,探索了肽分子间以及肽分子与溶剂水分子的微观作用力在自组装各个阶段的作用.模拟结果显示,尽管π-π堆积作用占分子间作用能的比重不高,但其在自组装初期对分子聚集起到的驱动力的贡献大于非π-π堆积作用力.肽分子与溶剂水分子形成的氢键数量随着组装进程而减少,总体呈现去溶剂化效应,但同时伴随着多次再溶剂化过程.水化层中的水分子存在两种特殊的“水桥”形式,即“单分子水桥”和“水团簇水桥”,其在水化层水分子中占比在30%~70%之间涨落.水桥的涨落伴随着肽分子结构重排,在自组装各个阶段(相分离、成核、生长和纤维交联)起着重要作用.
The microscopic structural evolution of a typical self-assembling aromatic dipeptide(z-FF) during selfassembly process was studied by performing all-atom molecular dynamics,in which the role of the microscopic forces between peptide molecules,as well as between peptide and solvent(water) molecules in each stage of self-assembly process was explored in detail.The simulation results show that,although the proportion of π-π interaction in the intermolecular interaction energy is not high,its contribution to the driving force of molecular aggregation at the initial stage of self-assembly is greater than that of non-π-π interaction.The number of hydrogen bonds(H-bonds) formed between peptides and solvents decreases with the development of the assembly process,but the number of water molecules in the hydration layer(defined as the water molecules forming hydrogen bonds with peptide molecules)remains basically unchanged.There are two special states of “water bridge” among the water molecules,defined as“single water bridge” and “water bridge cluster”,which fluctuate between 30% and 70% of all water molecules in the hydration layer.The fluctuation of water bridge is accompanied by the rearrangement of peptide molecules,which plays important roles in each stage of self-assembly such as phase separation,nucleation,fibril growth and cross-linking.
作者
周鹏
袁成前
闫学海
Peng Zhou;Chengqian Yuan;Xuehai Yan(State Key Laboratory of Biochemical Engineering,Institute of Process Engineering,Chinese Academy of Sciences,Beijing 100190,China;School of Chemical Engineering,University of Chinese Academy of Sciences,Beijing 100049,China)
出处
《中国科学：化学》
CAS
CSCD
北大核心
2023年第7期1227-1235,共9页
SCIENTIA SINICA Chimica
基金
国家杰出青年科学基金(编号:22025207)
国家自然科学基金(编号:51904322,22172172,22232006)资助项目。
关键词
自组装
肽
微观作用力
分子动力学模拟
Π-Π堆积作用
水桥
self-assembly
peptide
microscopic interaction
molecular dynamics simulation
π-πinteraction
water bridge
