The simplicity of protein sequence-function relationships

Yeonwoo Park, Brian P. H. Metzger and Joseph W. Thornton ()
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Yeonwoo Park: University of Chicago
Brian P. H. Metzger: University of Chicago
Joseph W. Thornton: University of Chicago

Nature Communications, 2024, vol. 15, issue 1, 1-14

Abstract: Abstract How complex are the rules by which a protein’s sequence determines its function? High-order epistatic interactions among residues are thought to be pervasive, suggesting an idiosyncratic and unpredictable sequence-function relationship. But many prior studies may have overestimated epistasis, because they analyzed sequence-function relationships relative to a single reference sequence—which causes measurement noise and local idiosyncrasies to snowball into high-order epistasis—or they did not fully account for global nonlinearities. Here we present a reference-free method that jointly infers specific epistatic interactions and global nonlinearity using a bird’s-eye view of sequence space. This technique yields the simplest explanation of sequence-function relationships and is more robust than existing methods to measurement noise, missing data, and model misspecification. We reanalyze 20 experimental datasets and find that context-independent amino acid effects and pairwise interactions, along with a simple nonlinearity to account for limited dynamic range, explain a median of 96% of phenotypic variance and over 92% in every case. Only a tiny fraction of genotypes are strongly affected by higher-order epistasis. Sequence-function relationships are also sparse: a miniscule fraction of amino acids and interactions account for 90% of phenotypic variance. Sequence-function causality across these datasets is therefore simple, opening the way for tractable approaches to characterize proteins’ genetic architecture.

Date: 2024
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DOI: 10.1038/s41467-024-51895-5

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