Pi-Pi contacts are an overlooked protein feature relevant to phase separation

• Main Authors: Robert McCoy Vernon, Paul Andrew Chong, Brian Tsang, Tae Hun Kim, Alaji Bah, Patrick Farber, Hong Lin, Julie Deborah Forman-Kay
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2018-02-01
• Series: eLife
• Subjects: protein phase separation; protein interactions; pi interactions; protein structure; prediction; bioinformatics
• Online Access: https://elifesciences.org/articles/31486

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing.