Effective Design of Multifunctional Peptides by Combining Compatible Functions

Author Summary Most proteins and peptides in nature display multiple activities either by fusing different domains (with different activities) or by evolving multiple activities in a single domain. Understanding which activities may be combined to render multifunctional proteins remains an open question relevant to understanding the organization of living organisms and to improve the design of pharmacological peptides. To address this problem, we introduce the concept of compatible activities, that is, activities that may combine without losing any of these in a single polypeptide chain. To identify compatible activities in peptide sequences, we used a machine-learning approach and discovered that a penetrating activity should be compatible with DNA-binding and antimicrobial activities. To test if these activities may combine without any functional loss, we designed peptide sequences that harbor two independent activities (nuclear localization and pheromone) and experimentally showed that all our designed peptides display penetrability, pheromone, antimicrobial and DNA-binding activities, supporting the idea that multifunctionality may be achieved combining compatible activities.