BIAPSS - BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences

Abstract

AbstractLiquid-liquid phase separation (LLPS) has recently emerged as a cornerstone mechanism underlying the biogenesis of membraneless organelles (MLOs). However, a quantitative molecular grammar of protein sequences that controls the LLPS remains poorly understood. The progress in this field is hampered by the insufficiency of comprehensive databases and associated computational infrastructure for targeting biophysical and statistical analysis of phase separating biopolymers. Therefore, we have created a novel open-source web platform named BIAPSS (BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences) which contains interactive data analytic tools in combination with a comprehensive repository of bioinformatic data for on-the-fly exploration of sequence-dependent properties of proteins with known LLPS behavior. BIAPSS includes a residue-resolution biophysical analyzer for interrogating individual protein sequences (SingleSEQ tab). The latter allows users to correlate regions prone to phase separation with a large array of physicochemical attributes and various short linear motifs. BIAPSS also includes global statistics derived over the universe of most of the known LLPS-driver protein sequences (MultiSEQ tab) for revealing the regularities and sequence-specific signals driving phase separation. Finally, BIAPSS incorporates an extensive cross-reference section that links all entries to primary LLPS databases and other external resources thereby serving as a central navigation hub for the phase separation community. All of the data used by BIAPSS is freely available for download as well-formatted pre-processed data with detailed descriptions, facilitating rapid implementation in user-defined computational protocols.Abstract FigureTOC - graphical abstractAuthor summaryProteins, especially those with low complexity and intrinsically disordered regions, have recently come into the limelight because of mounting evidence showing that these regions can drive the formation of membraneless organelles (MLOs) in cells. The underlying physical mechanism for forming MLOs is liquid-liquid phase separation (LLPS); a thermodynamically driven process whereby a cellular milieu with a relatively well-mixed distribution of biomolecules gets decomposed into liquid droplets where the concentration of selected biomolecules is higher. Deciphering molecular sequence grammar of phase separation has turned out to be challenging because of the complexity of this process in cells and the vastness of sequence space of LLPS-driver proteins. While the field is still in its infancy the growth of experimental data has already spurred the creation of several major databases which collect and annotate bimolecular systems with confirmed LLPS behavior. What is currently missing is a framework that would leverage the existing databases by integrating them with deep biophysical and bioinformatic analysis for identifying statistically significant features of protein sequences implicated in LLPS. In this work, we have addressed this challenge by creating an open-source web platform named BIAPSS (BioInformatic Analysis of liquid-liquid Phase-Separating protein Sequences) which integrates a comprehensive repository of pre-processed bioinformatic data for LLPS-driver protein sequences with interactive analytic applications for on-the-fly analysis of biophysical features relevant for LLPS behavior. BIAPSS empowers users with novel and effective tools for exploring LLPS-related sequence signals for individual proteins (SingleSEQ tab) and globally by integrating common regularities across subgroups or the entire LLPS sequence superset (MultiSEQ). The long-term plan for BIAPSS is to serve as a unifying hub for the experimental and computational community with a comprehensive set of analytic tools, biophysically featured data, and standardized protocols facilitating the identification of sequence hot spots driving the LLPS, which all can support applications for designing new sequences of biomedical interest.