Integrating Protein Language Model and Molecular Dynamics Simulations to Discover Antibiofouling Peptides

• Published in: Langmuir Vol. 41; no. 1; pp. 811 - 821
• Main Authors: Imam, Ibrahim A., Bailey, Shea, Wang, Duolin, Zeng, Shuai, Xu, Dong, Shao, Qing
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 14.01.2025
• Subjects: adsorption; biofouling; Biofouling - prevention & control; data collection; evolution; glutamic acid; lysozyme; microbiome; molecular dynamics; Molecular Dynamics Simulation; peptides; Peptides - chemistry
• ISSN: 0743-7463; 1520-5827; 1520-5827
• DOI: 10.1021/acs.langmuir.4c04140

Antibiofouling peptide materials prevent the nonspecific adsorption of proteins on devices, enabling them to perform their designed functions as desired in complex biological environments. Due to their importance, research on antibiofouling peptide materials has been one of the central subjects of interfacial engineering. However, only a few antibiofouling peptide sequences have been developed. This narrow scope of antibiofouling peptide materials limits their capacity to adapt to the broad spectrum of application scenarios. To address this issue, we searched for antibiofouling peptides in the vast sequence pool of the microbiome library using a combination of deep learning-based high-throughput search and molecular dynamics (MD) simulations. A random forest-based model with an ensemble of ten independent classifiers was developed. Each classifier was trained by prompt-tuning the foundational protein language model Evolution Scaling Modeling version 2 (ESM2) on a distinct training data set. We constructed the databases containing the same amount of antibiofouling and biofouling peptide sequences to attenuate the bias of the existing databases. MD simulations were conducted to investigate the interfacial properties of six selected peptide candidates and their interactions with a lysozyme protein. Two known antibiofouling peptides, (glutamic acid (E)-lysine (K))15 and (EK-proline (P))10, and one known fouling peptide, (glycine)30, were used as the reference. The MD simulation results indicate that five of the six peptides present the potential to resist biofouling. Our research implies that deep learning and molecular simulations can be integrated to discover functional peptide materials for interfacial applications.