KnotProt 2.0: a database of proteins with knots and other entangled structures
Pawel Dabrowski-Tumanski1,2, Pawel Rubach2,3, Dimos Goundaroulis4
1Faculty of Chemistry, University of Warsaw, Pasteura 1, Warsaw, Poland.
Nucleic Acids Research
|December 4, 2018
Summary
The KnotProt 2.0 database now tracks protein knots and entangled structures, including new features for analyzing disulfide bonds, ion interactions, and knotoids. This updated resource aids in understanding protein entanglement complexity.
Area of Science:
- Biochemistry
- Structural Biology
- Bioinformatics
Background:
- Proteins can form complex knots and entangled structures, influencing their function.
- Previous databases lacked comprehensive analysis of various entanglement types.
Purpose of the Study:
- To update and expand the KnotProt database with new features for analyzing protein entanglement.
- To provide a comprehensive resource for studying knotted and entangled protein structures.
Main Methods:
- Characterization of probabilistic and deterministic entanglements (disulfide bonds, ion interactions).
- Refined entanglement analysis using knotoids.
- Identification of cysteine knots.
- Analysis of all or non-redundant protein sets.
- Regular updates from the Protein Data Bank (PDB).
Main Results:
- KnotProt 2.0 classifies over 2000 entangled protein structures.
- Introduced knotting fingerprints for complexity representation.
- Provides biological and geometrical statistics for entangled proteins.
Conclusions:
- KnotProt 2.0 is a valuable, updated resource for studying protein entanglement.
- The database facilitates deeper insights into the structure and function of knotted proteins.
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