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OutCyte: a novel tool for predicting unconventional protein secretion
Linlin Zhao1,2, Gereon Poschmann1, Daniel Waldera-Lupa1
1Institute of Molecular Medicine, Medical Faculty, Heinrich-Heine-University, Düsseldorf, Germany.
Scientific Reports
|December 21, 2019
Summary
Predicting unconventional protein secretion (UPS) is crucial for understanding protein function. OutCyte is a new tool that accurately identifies UPS proteins, aiding in the annotation of extracellular proteins.
Area of Science:
- Proteomics
- Bioinformatics
- Molecular Biology
Background:
- Accurate prediction of protein localization is vital for functional inference.
- While the endoplasmic reticulum-Golgi pathway is known for protein secretion, many proteins utilize unconventional secretory pathways (UPS).
- Reliable prediction of UPS remains a significant challenge in bioinformatics.
Purpose of the Study:
- To develop a fast and accurate computational tool for predicting unconventional protein secretion (UPS).
- To provide a novel method for classifying proteins as UPS or intracellular based on sequence features.
- To facilitate the annotation of extracellular proteins by accounting for UPS mechanisms.
Main Methods:
- Developed OutCyte, a two-step prediction tool for UPS.
- Step 1: Accurately filters proteins with known N-terminal signal peptides.
- Step 2: Classifies signal peptide-absent proteins as UPS or intracellular using sequence-derived physicochemical features.
Main Results:
- OutCyte is the first tool built using experimentally validated UPS proteins.
- Achieved high accuracy in predicting UPS proteins.
- Provides a reliable method for distinguishing UPS from intracellular proteins.
Conclusions:
- OutCyte offers a significant advancement in predicting unconventional protein secretion.
- The tool will aid in the functional annotation of proteins, particularly those localized to the extracellular space via UPS.
- OutCyte contributes to a more comprehensive understanding of protein trafficking and extracellular proteomes.
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