Generative steering to adapt proteins beyond native biological contexts

Abstract

Proteins evolved for native biological contexts often fail when deployed in new cellular environments or therapeutic settings. We present ProVADA, a test-time framework that steers a pretrained protein generator toward externally defined properties while preserving functional constraints. Its Mixture-Adaptation Directed Annealing sampler combines coordinated mutations, population selection, and annealing to navigate rugged objective landscapes. Experimentally, ProVADA converted secreted human renin into an active, drug-inhibitable cytosolic protease and extensively deimmunized two murine single-chain antibody fragments to reduce HLA visibility while retaining antigen recognition. ESCAPE-seq measurements confirmed substantial depletion of HLA-I binder peptides across alleles. Deimmunized FMC63 variants retained CAR-T-cell killing and showed fewer binders than a tested humanized comparator. Together, these results demonstrate that broad sequence redesign can adapt functional proteins to non-native biological contexts.