Protein A-like Peptide Design Based on Diffusion and ESM2 Models

Abstract

Proteins are the foundation of life, and designing functional proteins remains a key challenge in biotechnology. Before the development of AlphaFold2, the focus of design was primarily on structure-centric approaches such as using the well-known open-source software Rosetta3. Following the development of AlphaFold2, deep-learning techniques for protein design gained prominence. This study proposes a new method to generate functional proteins using the diffusion model and ESM2 protein language model. Diffusion models, which are widely used in image and natural language generation, are used here for protein design, facilitating the controlled generation of new sequences. The ESM2 model, trained on the basis of large-scale protein sequence data, provides a deep understanding of the context of the sequence, thus improving the model’s ability to generate biologically relevant proteins. In this study, we used the Protein A-like peptide as a model study object, combined the diffusion model and the ESM2 model to generate new peptide sequences from minimal input data, and verified their biological activities through experiments such as the BLI affinity test. In conclusion, we developed a new method for protein design that provides a novel strategy to meet the challenges of generic protein generation.

Keywords

• protein design
• diffusion model
• ESM2
• peptide screening
• biological activity