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Possible pathways for protein knot folding

Banff International Research Station for Mathematical Innovation and Discovery

How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. In this talk, we introduce a new theory of knot folding that could describe a pathway for the formation of all currently known protein knot types and predict knot types that might be identified in the future. We analyze fingerprint data from crystal structures of protein knots as evidence that particular protein knots may fold according to specific configurations from our theory. In particular, our approach confirms Taylor's twisted hairpin theory of knot folding for the \(3_1\)-knotted proteins and the $4_1$-knotted KARI's as special cases, and presents an alternative folding mechanism for the $4_1$-knotted phytochromes and the $5_2$- and $6_1$-knotted proteins.

Mathematics; Biology and other natural sciences; Manifolds and cell complexes; Mathematical biology

video/mp4

Author affiliation: Pomona College

2020-09-04

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/75856

Unreviewed

http://creativecommons.org/licenses/by-nc-nd/4.0/