Mind the gap: An embedding guide to safely travel in sequence space

We present a hybrid approach combining a protein language model (pLM) with Monte Carlo (MC) sampling for generating enzyme mutants free of mutations deleterious for structural preservation. Given the amino acid sequence of the original enzyme and a set of residues for which the local environment should be conserved, i.e., the catalytic site, our approach generates mutants that differ vastly in the overall sequence while retaining the geometry of the conserved region, thereby representing promising candidates for further experimental screening. Unlike end-to-end deep-learning approaches, whose results are harder to interpret and control, the use of a well-established, classic technique such as MC sampling allows us to easily interpret the generative process as the sampling of an energy landscape determined by the pLM. In turn, such an interpretation enables us to steer this generative process and control its outcome by making use of robust statistical mechanics concepts, e.g., temperature, thereby explicitly guaranteeing certain properties of the generated mutants. We further show, through comparison to experimentally characterised chorismate mutase variants, that low embedding energy is a necessary condition for catalytic function, providing direct experimental grounding for the energy function at the core of our approach. Given the increasing relevance of generative algorithms in the design and search for novel, optimised enzymes, we believe that our results constitute an important step for the future development of this class of techniques. To facilitate experimental verification, we finally provide over 12,500 sequences in total for 13 different enzymes involved in catalytic processes ranging from biomass degradation to DNA replication.Author summary: Enzymes are nature’s catalysts: proteins that accelerate essential chemical reactions. Engineers often want to redesign them, but even a single amino acid change can destroy function by disrupting the precisely shaped active site where catalysis occurs.