PUMA: Discovery of Protein Units via Mutation-Aware Merging

Abstract

Proteins are the essential drivers of biological processes. At the molecular level, they are chains of amino acids that can be viewed through a linguistic lens where the twenty standard residues serve as an alphabet combining to form a complex language, referred to as the language of life. To understand this language, we must first identify its fundamental units. Analogous to words, these units are hypothesized to represent an intermediate layer between single residues and larger domains. Crucially, just as protein diversity arises from evolution, these units should inherently reflect evolutionary relationships. We introduce PUMA (Protein Units via Mutation-Aware Merging) to discover these evolutionarily meaningful units. PUMA employs an iterative merging algorithm guided by substitution matrices to identify protein units and organize them into families linked by plausible mutations. This process creates a hierarchical genealogy where parent units and their mutational variants coexist, simultaneously producing a unit vocabulary and the genealogical structure connecting them. We validate that PUMA families are biologically meaningful; mutations within a PUMA family correlate with clinically benign variants and with high-scoring mutations in high-throughput assays. Furthermore, these units align with the contextual preferences of protein language models and map to known functional annotations. PUMA's genealogical framework provides evolutionarily grounded units, offering a structured approach for understanding the language of life.