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KnotProt: a database of proteins with knots and slipknots.

Jamroz M, Niemyska W, Rawdon EJ, Stasiak A, Millett KC, Sułkowski P, Sulkowska JI - Nucleic Acids Res. (2014)

Bottom Line: The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot.In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting.As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.

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An example of data presentation for a knotted protein (PDB code 1yrl) in the KnotProt database. In this example the analyzed polypeptide chain of Escherichia coli ketol-acid reductoisomerase reveals that the entire polypeptide chain forms a 41 knot, and has a subchain forming a 31 knot. Diagram in top left: knotting fingerprint revealing the positions of subchains forming 41 and 31 knots. Top right: graphical representation of protein structure in JSmol. Table in the middle: detailed data about knots and slipknots formed by backbone subchains. Bottom: sequence representation with the knot core and knot tails highlighted in appropriate colors.
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Figure 1: An example of data presentation for a knotted protein (PDB code 1yrl) in the KnotProt database. In this example the analyzed polypeptide chain of Escherichia coli ketol-acid reductoisomerase reveals that the entire polypeptide chain forms a 41 knot, and has a subchain forming a 31 knot. Diagram in top left: knotting fingerprint revealing the positions of subchains forming 41 and 31 knots. Top right: graphical representation of protein structure in JSmol. Table in the middle: detailed data about knots and slipknots formed by backbone subchains. Bottom: sequence representation with the knot core and knot tails highlighted in appropriate colors.

Mentions: The KnotProt database contains detailed information about the entanglement in proteins and presents it in the form of a ‘knotting fingerprint.’ The knotting fingerprint encodes information about the knot type of each subchain of a protein backbone and represents it in the form of a matrix diagram, see Figure 1 and the detailed description in the ‘MATERIALS AND METHODS’ section. The KnotProt database also presents extensive statistics about proteins with knots and slipknots based on their biological function, molecular tags, family association, type of fold, as well as geometric data: knotting patterns, knot and slipknot lengths and depths, etc. Interestingly, the KnotProt analysis reveals that proteins with knots and slipknots can be classified into a few distinct motifs, represented by particular patterns within the matrix diagrams. These data can be used, for example, to find proteins with knots or slipknots with a given homological sequence, a similar structure, or performing a particular biological function. As an additional feature, a user can analyze structures and generate knotting fingerprints of uploaded proteins. It is also possible to upload and analyze a whole set of structures (e.g. analyze the evolution of a knot along a folding or unfolding trajectory). The KnotProt database is automatically updated every week, immediately after new structures are deposited in the PDB.


KnotProt: a database of proteins with knots and slipknots.

Jamroz M, Niemyska W, Rawdon EJ, Stasiak A, Millett KC, Sułkowski P, Sulkowska JI - Nucleic Acids Res. (2014)

An example of data presentation for a knotted protein (PDB code 1yrl) in the KnotProt database. In this example the analyzed polypeptide chain of Escherichia coli ketol-acid reductoisomerase reveals that the entire polypeptide chain forms a 41 knot, and has a subchain forming a 31 knot. Diagram in top left: knotting fingerprint revealing the positions of subchains forming 41 and 31 knots. Top right: graphical representation of protein structure in JSmol. Table in the middle: detailed data about knots and slipknots formed by backbone subchains. Bottom: sequence representation with the knot core and knot tails highlighted in appropriate colors.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383900&req=5

Figure 1: An example of data presentation for a knotted protein (PDB code 1yrl) in the KnotProt database. In this example the analyzed polypeptide chain of Escherichia coli ketol-acid reductoisomerase reveals that the entire polypeptide chain forms a 41 knot, and has a subchain forming a 31 knot. Diagram in top left: knotting fingerprint revealing the positions of subchains forming 41 and 31 knots. Top right: graphical representation of protein structure in JSmol. Table in the middle: detailed data about knots and slipknots formed by backbone subchains. Bottom: sequence representation with the knot core and knot tails highlighted in appropriate colors.
Mentions: The KnotProt database contains detailed information about the entanglement in proteins and presents it in the form of a ‘knotting fingerprint.’ The knotting fingerprint encodes information about the knot type of each subchain of a protein backbone and represents it in the form of a matrix diagram, see Figure 1 and the detailed description in the ‘MATERIALS AND METHODS’ section. The KnotProt database also presents extensive statistics about proteins with knots and slipknots based on their biological function, molecular tags, family association, type of fold, as well as geometric data: knotting patterns, knot and slipknot lengths and depths, etc. Interestingly, the KnotProt analysis reveals that proteins with knots and slipknots can be classified into a few distinct motifs, represented by particular patterns within the matrix diagrams. These data can be used, for example, to find proteins with knots or slipknots with a given homological sequence, a similar structure, or performing a particular biological function. As an additional feature, a user can analyze structures and generate knotting fingerprints of uploaded proteins. It is also possible to upload and analyze a whole set of structures (e.g. analyze the evolution of a knot along a folding or unfolding trajectory). The KnotProt database is automatically updated every week, immediately after new structures are deposited in the PDB.

Bottom Line: The pattern visible in the matrix gives the knotting fingerprint of a given protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end of the cataloged protein structure before converting it from a knot to a different type of knot.In addition, the database presents extensive information about the biological functions, families and fold types of proteins with non-trivial knotting.As an additional feature, the KnotProt database enables users to submit protein or polymer chains and generate their knotting fingerprints.

View Article: PubMed Central - PubMed

Affiliation: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.

Show MeSH
Related in: MedlinePlus