Environment-conditioned design of alpha-helical peptides

Abstract

Designing peptide sequences that remain stable and selective across heterogeneous environments remains a central challenge in biomolecular modeling. Here we introduce an interpretable, physics-based Hamiltonian for environment-conditioned design of -helical peptide sequences. The model integrates helix propensities, pairwise interactions, electrostatics, anisotropic solvent exposure, and interfacial geometry into a unified energy function. To enable comparison across sequence lengths and environments, all contributions are rescaled and expressed as Z-scores relative to random sequence ensembles, yielding a normalized design landscape with balanced physical terms. This formulation defines a structured optimization problem that can be explored using exact, heuristic, and hybrid quantum- classical approaches without modification of the underlying model. The Hamiltonian recovers polar and apolar limits, discriminates experimentally characterized water-soluble and transmembrane -helical peptide sequences, and captures the preferential stabilization of membrane-active sequences at anionic interfaces over non-functional controls. It further enables multi-objective and selective design, generating candidate sequences with tunable environmental specificity.