The physicochemical basis of protein evolution: property-informed evolutionary models (PRIME).

Standard probabilistic models of coding sequence evolution effectively identify where and when selection acts but remain agnostic to the mechanistic realization of these forces. We introduce PRIME (PRoperty Informed Models of Evolution), a framework of codon-level maximum likelihood methods-including global (G-PRIME), episodic (E-PRIME), and site-specific (S-PRIME) implementations-that explicitly model amino acid exchangeability as a function of physicochemical properties. By parameterizing attributes such as molecular volume, hydropathy, and secondary structure propensities, PRIME aims to resolve the biophysical basis of selective constraint across both the sequence and the phylogeny. At the site level, S-PRIME leverages an explicit biophysical taxonomy to categorize residues as conserved, neutral, or changing for specific properties, resolving selective signals that are missed by traditional rate-based metrics. Our analysis of a benchmark of 24 diverse datasets and a genome-wide screen of 18,944 mammalian genes demonstrates that consideration of biophysical realism can yield substantial improvements in model fit, acting synergistically with rate variation to explain complex evolutionary patterns. We find that physicochemical constraints at individual sites can be reliably detected in datasets with sufficient information redundancy (substitutions per unique amino acid; AUC=0.91), with sensitivity exceeding 90% in data-rich alignments. E-PRIME reveals a distinct hierarchy in biophysical constraints: while core packing and beta-sheet scaffolds are rigidly conserved, alpha-helix propensity and surface electrostatics serve as the primary substrates for adaptive tuning. Furthermore, PRIME importance weights align with aspects of the primary semantic axes of deep learning representations (ESM-2) and capture key features of experimental fitness landscapes. By transforming abstract evolutionary rates into interpretable biophysical rules, PRIME provides a useful framework for characterizing the mechanistic drivers of protein diversity.