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Related Concept Videos

Covalently Linked Protein Regulators02:04

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
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Modification of secretory and transmembrane proteins entering the rough ER begins in the ER lumen. These modifications aid in protein folding and stabilize the acquired tertiary structure. Protein modifications in the rough ER co-occur at different stages of protein folding.
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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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Proteomics01:33

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
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The organelle-specific signaling sequences direct proteins synthesized in the cytosol to their final destination like ER, mitochondria, peroxisomes, etc. Some of the proteins directed to ER are then trafficked via vesicles to other organelles within the cell or the extracellular environment through the Golgi complex. For example, the rough ER synthesizes soluble proteins for transportation to the lysosomes or secretion out of the cell. It can also synthesize transmembrane proteins that can...
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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SysPTM 2.0: an updated systematic resource for post-translational modification.

Jing Li1, Jia Jia, Hong Li

  • 1Key Laboratory of Biomedical Photonics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China, Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai 201203, P. R. China, Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430074, P. R. China, Department of Bioinformatics and Biostatistics, Shanghai Jiaotong University, Shanghai 200240, P. R. China, Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai 200031, P. R. China and Proteome Center Rostock, Department for Proteome Research, Institute of Immunology, University of Rostock, Rostock 18055, Germany.

Database : the Journal of Biological Databases and Curation
|April 8, 2014
PubMed
Summary

SysPTM 2.0 is an updated database resource for post-translational modifications (PTMs). It offers enhanced data and web tools for PTM analysis, aiding research into cellular processes and disease.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics
  • Proteomics

Background:

  • Post-translational modifications (PTMs) are crucial for cellular processes and disease.
  • Tandem mass spectrometry (MS/MS) has significantly increased PTM identification.
  • Systematic PTM data organization is vital for understanding cellular signaling.

Purpose of the Study:

  • To present an updated version of the SysPTM database, SysPTM 2.0.
  • To enhance data content and web-based analysis tools for PTM research.
  • To introduce new features for analyzing combinatorial histone PTMs and functional enrichment.

Main Methods:

  • Systematic collection and curation of post-translational modification data.
  • Development and enhancement of web-based bioinformatics tools (PTMBlast, PTMPathway, PTMPhylog, PTMCluster, PTMGO).
  • Integration of a new module (SysPTM-H) for graphical representation of histone PTMs.

Main Results:

  • SysPTM 2.0 features nearly doubled data content compared to the previous version.
  • Enhanced web tools facilitate PTM site annotation and functional investigation.
  • New tools enable graphical representation of histone PTMs and functional enrichment analysis.

Conclusions:

  • SysPTM 2.0 provides a comprehensive and updated resource for PTM research.
  • The enhanced tools empower systematic investigation of PTM functions and regulation.
  • This resource supports deeper understanding of cellular signaling pathways and disease mechanisms.