Aggregation Rules of Short Peptides

Jiaqi Wang, Zihan Liu, Shuang Zhao, Yu Zhang, Tengyan Xu*, Stan Z. Li*, Wenbin Li*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

The elucidation of aggregation rules for short peptides (e.g., tetrapeptides and pentapeptides) is crucial for the precise manipulation of aggregation. In this study, we derive comprehensive aggregation rules for tetrapeptides and pentapeptides across the entire sequence space based on the aggregation propensity values predicted by a transformer-based deep learning model. Our analysis focuses on three quantitative aspects. First, we investigate the type and positional effects of amino acids on aggregation, considering both the first- and second-order contributions. By identifying specific amino acids and amino acid pairs that promote or attenuate aggregation, we gain insights into the underlying aggregation mechanisms. Second, we explore the transferability of aggregation propensities between tetrapeptides and pentapeptides, aiming to explore the possibility of enhancing or mitigating aggregation by concatenating or removing specific amino acids at the termini. Finally, we evaluate the aggregation morphologies of over 20,000 tetrapeptides, regarding the morphology distribution and type and positional contributions of each amino acid. This work extends the existing aggregation rules from tripeptide sequences to millions of tetrapeptide and pentapeptide sequences, offering experimentalists an explicit roadmap for fine-tuning the aggregation behavior of short peptides for diverse applications, including hydrogels, emulsions, or pharmaceuticals.

Original languageEnglish
JournalJACS Au
DOIs
Publication statusPublished - 3 Sept 2024

Keywords

  • aggregating morphologies
  • aggregation rules
  • complete sequence space
  • deep learning
  • molecular dynamics
  • short peptides
  • transferability relation

Fingerprint

Dive into the research topics of 'Aggregation Rules of Short Peptides'. Together they form a unique fingerprint.

Cite this