Analysis and design of disordered polypeptides with optimized sequence patterning properties

Intrinsically disordered proteins (IDPs) exhibit phase separation behavior that is closely linked to their degree of single-chain compaction, which in turn is governed by both amino acid composition and sequence patterning. Existing metrics such as sequence charge decoration (SCD) and sequence hydropathy decoration (SHD) describe these effects but are largely limited to describing differences between sequences of similar length and overall composition. In this work, we present a shuffle-based normalization scheme for SCD and SHD, enabling comparison of sequence patterning between very different IDP sequences. Leveraging this normalization scheme toward design space, we develop a Monte Carlo based sequence design algorithm that generates novel IDPs with desired patterning features. Our design framework is further strengthened by incorporating additional metrics such as sequence aromatic decoration (SAD), compositional RMSD, and a previously developed sequence based ΔG predictor. We validate our approach through coarse-grained MD simulations, showing that the designed sequences exhibit tunable phase behavior. This strategy lays the groundwork for rational design of IDPs for biomedical and biotechnology applications, as well as basic biophysical research.Author summary: Intrinsically disordered proteins behave similar to polymers in solution, having no defined structure. Their behavior is dictated by the collection of shapes the protein adopts, known as it’s “conformational ensemble” which is tuned by its amino acid sequence and the solution environment. In this work, we have developed parameters to describe the patterning of charged and hydrophobic amino acids within these protein sequences, which are predictive of their ability to phase separate and form dense liquid-like droplets in solution. Importantly, the parameters we develop are motivated by physics and can be applied across a large number of amino acid sequences rapidly. This will enable researchers to rapidly predict the behavior of large libraries of protein sequences. We have additionally developed a software to design randomized amino acid sequences with desired amino acid composition and patterning properties. Finally, we have tested our design scheme and parameters by running simulations of designed IDP sequences and quantified each of their ability to phase separate.