EnzymeRSI: A dual-loop recursive self-improvement system for enzyme design

원문 초록

Enzyme engineering usually optimises which candidates to assay within a fixed model and workflow; when the bottleneck is a mismatched method or a failing workflow, that route is hard to escape. We present EnzymeRSI, a dual-loop system for recursive self-improvement (RSI). The outer loop evolves harness assets without changing model weights; the inner loop develops prediction and selection algorithms under controlled conditions; a cloud laboratory system is specified for closing the physical loop with quality-controlled feedback. The outer loop raised the mean development-set Spearman correlation on ProteinGym by 0.044 across five assays, reaching 0.335 on CD19 and 0.683 on OPSD (rhodopsin); of the two first places, only CD19 was produced by the outer loop itself. In ThermoMPNN self-improvement the inner loop reached a PCC of 0.849, and on TadA-Bench a Spearman correlation of 0.307 in 1.13 h. We examined the system's experimental decision-making in three enzyme systems. For the luciferase RLuc, 10 of the 32 nominated substitutions not pre-specified reached at least twice wild-type activity in a single round. For the cytidine deaminase A3A, a variant selected by a rule that caps loss of unmodified C raised 5mC conversion in the weaker CT context from 11.4% to 46.5% and reversed the substrate preference in both contexts. For the DNA polymerase KOD-E, 189 single-substitution variants defined a landscape on which different objective functions selected divergent next steps from the same parent; one assayed combination reached 31.1 times the parent on a modified substrate. By treating the organisation of research and the development of algorithms as separately scored objects of evolution, and linking a frozen decision record to a physical measurement, this work offers an evolutionary paradigm for moving beyond the blind spots of a fixed method and for autonomous enzyme engineering.