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Symmetry
Volume 13
Issue 9
10.3390/sym13091670
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Article

A Topological Selection of Folding Pathways from Native States of Knotted Proteins

by
Agnese Barbensi
1,
Naya Yerolemou
1,2,†,
Oliver Vipond
1,†,
Barbara I. Mahler
1,
Pawel Dabrowski-Tumanski
3 and
Dimos Goundaroulis
4,5,6,*
1
Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK
2
The Alan Turing Institute, London NW1 2DB, UK
3
Faculty of Mathematics and Natural Sciences, School of Exact Sciences, Cardinal Stefan Wyszynski University, Woycickiego 1/3, 01-938 Warsaw, Poland
4
The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
5
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
6
Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Academic Editors: Erica Flapan and Helen Wong
Symmetry 2021, 13(9), 1670; https://doi.org/10.3390/sym13091670
Received: 3 August 2021 / Revised: 26 August 2021 / Accepted: 7 September 2021 / Published: 10 September 2021
(This article belongs to the Special Issue Topological Methods in Chemistry and Molecular Biology)
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Abstract

Understanding how knotted proteins fold is a challenging problem in biology. Researchers have proposed several models for their folding pathways, based on theory, simulations and experiments. The geometry of proteins with the same knot type can vary substantially and recent simulations reveal different folding behaviour for deeply and shallow knotted proteins. We analyse proteins forming open-ended trefoil knots by introducing a topologically inspired statistical metric that measures their entanglement. By looking directly at the geometry and topology of their native states, we are able to probe different folding pathways for such proteins. In particular, the folding pathway of shallow knotted carbonic anhydrases involves the creation of a double-looped structure, contrary to what has been observed for other knotted trefoil proteins. We validate this with Molecular Dynamics simulations. By leveraging the geometry and local symmetries of knotted proteins’ native states, we provide the first numerical evidence of a double-loop folding mechanism in trefoil proteins. View Full-Text
Keywords: knotted proteins; protein folding; knotoids; knots; topological data analysis; bioinformatics; computational biology knotted proteins; protein folding; knotoids; knots; topological data analysis; bioinformatics; computational biology
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MDPI and ACS Style

Barbensi, A.; Yerolemou, N.; Vipond, O.; Mahler, B.I.; Dabrowski-Tumanski, P.; Goundaroulis, D. A Topological Selection of Folding Pathways from Native States of Knotted Proteins. Symmetry 2021, 13, 1670. https://doi.org/10.3390/sym13091670

AMA Style

Barbensi A, Yerolemou N, Vipond O, Mahler BI, Dabrowski-Tumanski P, Goundaroulis D. A Topological Selection of Folding Pathways from Native States of Knotted Proteins. Symmetry. 2021; 13(9):1670. https://doi.org/10.3390/sym13091670

Chicago/Turabian Style

Barbensi, Agnese, Naya Yerolemou, Oliver Vipond, Barbara I. Mahler, Pawel Dabrowski-Tumanski, and Dimos Goundaroulis. 2021. "A Topological Selection of Folding Pathways from Native States of Knotted Proteins" Symmetry 13, no. 9: 1670. https://doi.org/10.3390/sym13091670

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