Proteins no longer fold one way: after terminal remodeling, two or three mutations shift the conformational balance
Protein design has long targeted a single static structure, while natural metamorphic proteins occupy multiple folded states under the same conditions. Using RFdiffusion to partially remodel the termini of 93 native domains yielded 2,291 native-alternative conformation pairs; two sequence-design routes then made one sequence compatible with both backbones, and AlphaFold3 with BioEmu selected state-stabilizing mutations. The designs showed broadened and missing NMR crosspeaks, indicating microsecond-to-millisecond exchange in the metamorphic region; two or three mutations shifted the equilibrium toward either state, yielding crystal and NMR structures consistent with the design models.