The backbones of proteins form linear chains. In the case of some proteins, these chains can be characterized as forming linear open knots. The knot type of the full chain reveals only limited information about the entanglement of the chain since, for example, subchains of an unknotted protein can form knots and subchains of a knotted protein can form different types of knots than the entire protein. To understand fully the entanglement within the backbone of a given protein, a complete analysis of the knotting within all of the subchains of that protein is necessary. In the present article, we review efforts to characterize the full knotting complexity within individual proteins and present a matrix that conveys information about various aspects of protein knotting. For a given protein, this matrix identifies the precise localization of knotted regions and shows the knot types formed by all subchains. The pattern in the matrix can be considered as a knotting fingerprint of that protein. We observe that knotting fingerprints of distantly related knotted proteins are strongly conserved during evolution and discuss how some characteristic motifs in the knotting fingerprints are related to the structure of the knotted regions and their possible biological role.
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April 2013
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Conference Article|
March 21 2013
Knot localization in proteins
Eric J. Rawdon;
Eric J. Rawdon
1
*Department of Mathematics, University of St. Thomas, 2115 Summit Avenue, St. Paul, MN 55105, U.S.A.
1To whom correspondence should be addressed (emailejrawdon@stthomas.edu).
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Kenneth C. Millett;
Kenneth C. Millett
†Department of Mathematics, University of California Santa Barbara, 552 University Road, Santa Barbara, CA 93106, U.S.A.
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Joanna I. Sułkowska;
Joanna I. Sułkowska
‡Center for Theoretical Biological Physics, University of California San Diego, 9500 Gilman Drive, San Diego, CA 92037, U.S.A.
§Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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Andrzej Stasiak
Andrzej Stasiak
∥Center for Integrative Genomics, University of Lausanne, CH-1015 Lausanne-Dorigny, Switzerland
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Biochem Soc Trans (2013) 41 (2): 538–541.
Article history
Received:
November 05 2012
Citation
Eric J. Rawdon, Kenneth C. Millett, Joanna I. Sułkowska, Andrzej Stasiak; Knot localization in proteins. Biochem Soc Trans 1 April 2013; 41 (2): 538–541. doi: https://doi.org/10.1042/BST20120329
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