Computational Screening Service for Phase-Separated Proteins

In cells, proteins or nucleic acids form separated phases through intra- or intermolecular interactions, resulting in phase-separated compartments, also known as membraneless organelles or biomolecular condensates. Phase separation is a complex biophysical process, and any change in the nature of the system may affect the phase separation process. Proteins that can undergo phase separation in cells have certain typical sequence characteristics, such as intrinsically disordered regions (IDRs) and multiple modular structural domains. There are many sequence-based analysis tools for screening phase separation proteins. However, most of the current phase separation predictors are designed for proteins containing IDRs and therefore inevitably ignore phase separated proteins with relatively low IDR content.

Fig. 1. An interpretable machine-learning algorithm to predict disordered protein phase separation based on biophysical interactions. (Cai H, et al., 2022)

Customized Services

Phase separation is fundamental to many biological processes, and certain sequence features of proteins are associated with phase separation behavior. As an ideal partner for liquid-liquid phase separation services of proteins, CD BioSciences offers sequence-based prediction tools to screen phase-separated proteins and integrate available phase separation protein data to evaluate their performance.

• Analysis of IDR Content
  IDR-containing proteins make up a large percentage of phase-separated proteins. We have a wealth of IDR predictors that have been tested over time and can provide our customers with bioinformatics for IDR content analysis to screen potential phase-separated proteins.
• Screen of Phase-Separated Proteins
  We can analyze the sequences of a variety of phase-separated proteins, such as FUS, DEAD box protein 4 (DDX4), TATA binding protein associated factor 15 (TAF15), Ewing sarcoma protein (EWS), TAR DNA binding protein 43 (TDP43) and heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1). In close collaboration with bioinformaticians, we developed prediction tools to screen phase separation proteins explicitly based on phase-separation specific sequence features.
• Performance Evaluation of Phase-Separated Predictors
  Each of our algorithms predicts different kinds of interactions and sequence features, so these predictors cover very different classes of proteins. We integrate the available data to compare the prediction performance of the available phase separation predictors.
• Predicting Additional Features of Phase-Separated Proteins
  We also work to develop features beyond the sequence composition of the predicted phase separated proteins to provide valuable information for identifying possible phase-separated proteins, including protein-protein interaction (PPI) networks, post-translational modifications (PTM), and immunofluorescence (IF) images.

CD BioSciences has several sequence-based computational tools. These computational methods facilitate the study of phase separation phenomena by providing predictions of phase separation candidates and proteome-scale screening. Our services provide critical information for the identification of possible phase-separated proteins. If you are interested in our services, please do not hesitate to contact us for more information.