Effect of microscopic interactions on the evolution of structures in peptide self-assembly process: A molecular dynamics study [微观作用力对肽自组装过程中结构演化的影响：分子模拟研究]

作者：Zhou P.; Yuan C.; Yan X.^*

来源：Scientia Sinica Chimica, 2023, 1-9.

DOI：10.1360/SSC-2023-0017

• microscopic interaction
• molecular dynamics simulation
• peptide
• self-assembly
• water bridge
• π-π interaction

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 selfassembly 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.

• 单位
  生化工程国家重点实验室; 中国科学院大学