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PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition
Alex K Lancaster1, Andrew Nutter-Upham2, Susan Lindquist1
1Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, Department of Pathology, Beth Israel Deaconess Medical Center, Center for Biomedical Informatics, Harvard Medical School, 10 Shattuck Street, Boston, MA 02115, USA, Department of Biology, Howard Hughes Medical Institute, MIT, 77 Massachusetts Avenue, Cambridge, MA 02139 and Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA 01655, USA.
Prion-Like Amino Acid Composition (PLAAC) identifies protein domains with prion-like characteristics. This tool aids researchers in evolutionary and biomedical science by analyzing protein sequences for prion-forming potential.
Area of Science:
- Evolutionary biology
- Biomedical science
- Proteomics
Background:
- Prions are self-templating protein aggregates that propagate distinct biological states.
- Yeast prions, the best-understood, feature prion-forming domains rich in glutamine (Q) and asparagine (N).
- Identifying prion-like domains is crucial for understanding protein aggregation and disease.
Purpose of the Study:
- To introduce PLAAC, a web application for scanning protein sequences.
- To detect domains with prion-like amino acid composition.
- To provide researchers with a tool for analyzing prion-forming potential.
Main Methods:
- PLAAC utilizes a web application interface for sequence input (file upload or direct paste).
- The tool analyzes protein sequences for regions with biased amino acid composition, particularly Q and N enrichment.
- It generates summary scores and allows for sequence-based score visualization.
Main Results:
- PLAAC ranks input sequences based on calculated summary scores.
- Visualizations display scores along protein sequences, aiding in the identification of potential prion-forming domains.
- Downloadable text files and image formats (PDF, PNG) facilitate further analysis and reporting.
Conclusions:
- PLAAC offers a valuable computational tool for researchers studying prions and protein aggregation.
- The application aids in the discovery and characterization of novel prion-like proteins.
- PLAAC supports both evolutionary and biomedical research by providing sequence analysis capabilities.
