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Nuclear Localization Signals and Import

Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
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Disentangling Glycan-Protein Interactions: Nuclear Magnetic Resonance (NMR) to the Rescue
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Knot localization in proteins.

Eric J Rawdon1, Kenneth C Millett, Joanna I Sułkowska

  • 1Department of Mathematics, University of St. Thomas, 2115 Summit Avenue, St. Paul, MN 55105, U.S.A. ejrawdon@stthomas.edu

Biochemical Society Transactions
|March 22, 2013
PubMed
Summary

Protein knotting complexity requires analyzing all subchains, not just the entire chain. A new matrix reveals conserved "knotting fingerprints" linked to protein structure and function.

Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Biology

Background:

  • Protein backbones form linear chains, which can exhibit knotting.
  • Analyzing only the entire protein chain's knot type is insufficient for understanding entanglement.
  • Subchains within proteins can form knots independently of the overall chain's knot type.

Purpose of the Study:

  • To review methods for characterizing the full knotting complexity within individual proteins.
  • To introduce a novel matrix for visualizing protein knotting.
  • To investigate the evolutionary conservation and functional implications of protein knotting patterns.

Main Methods:

  • Development of a matrix to map knot types and locations within all protein subchains.
  • Analysis of knotting patterns across diverse protein families.

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  • Comparison of knotting fingerprints between related and unrelated proteins.

    • Main Results:

    • The proposed matrix provides a comprehensive view of protein entanglement, identifying specific knotted regions and their types.
    • Knotting fingerprints are highly conserved across distantly related proteins during evolution.
    • Specific motifs within knotting fingerprints correlate with the structure and potential biological roles of knotted regions.

    Conclusions:

    • A complete analysis of subchain knotting is essential for understanding protein entanglement.
    • The 'knotting fingerprint' matrix offers a powerful tool for protein knot analysis.
    • Conserved knotting patterns suggest functional or structural importance in protein evolution.