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The protein folding rate and the geometry and topology of the native state

Jason Wang, Eleni Panagiotou
doi: https://doi.org/10.1101/2021.10.06.463425
Jason Wang
1Department of Physics, University of Pennsylvania, PA 19104, USA
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Eleni Panagiotou
2Department of Mathematics and SimCenter, University of Tennessee at Chattanooga, TN 37403, USA
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  • For correspondence: eleni-panagiotou@utc.edu
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ABSTRACT

Proteins fold in 3-dimensional conformations which are important for their function. Characterizing the global conformation of proteins rigorously and separating secondary structure effects from topological effects is a challenge. New developments in Applied Knot Theory allow to characterize the topological characteristics of proteins (knotted or not). By analyzing a small set of two-state and multi-state proteins with no knots or slipknots, our results show that 95.4% of the analyzed proteins have non-trivial topological characteristics, as reflected by the second Vassiliev measure, and that the logarithm of the experimental protein folding rate depends on both the local geometry and the topology of the protein’s native state.

Competing Interest Statement

The authors have declared no competing interest.

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  • https://www.rcsb.org/

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 07, 2021.
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The protein folding rate and the geometry and topology of the native state
Jason Wang, Eleni Panagiotou
bioRxiv 2021.10.06.463425; doi: https://doi.org/10.1101/2021.10.06.463425
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The protein folding rate and the geometry and topology of the native state
Jason Wang, Eleni Panagiotou
bioRxiv 2021.10.06.463425; doi: https://doi.org/10.1101/2021.10.06.463425

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