Topology in soft and biological matter

Tubiana, Luca; Alexander, Gareth P.; Barbensi, Agnese; Buck, Dorothy; Cartwright, Julyan H.E.; Chwastyk, Mateusz; Cieplak, Marek; Coluzza, Ivan; Čopar, Simon; Craik, David J.; Di Stefano, Marco; Everaers, Ralf; Faísca, Patrícia F.N.; Ferrari, Franco; Giacometti, Achille; Goundaroulis, Dimos; Haglund, Ellinor; Hou, Ya-Ming; Ilieva, Nevena; Jackson, Sophie E.; Japaridze, Aleksandre; Kaplan, Noam; Klotz, Alexander R.; Li, Hongbin; Likos, Christos N.; Locatelli, Emanuele; López-León, Teresa; Machon, Thomas; Micheletti, Cristian; Michieletto, Davide; Niemi, Antti; Niemyska, Wanda; Niewieczerzal, Szymon; Nitti, Francesco; Orlandini, Enzo; Pasquali, Samuela; Perlinska, Agata P.; Podgornik, Rudolf; Potestio, Raffaello; Pugno, Nicola M.; Ravnik, Miha; Ricca, Renzo; Rohwer, Christian M.; Rosa, Angelo; Smrek, Jan; Souslov, Anton; Stasiak, Andrzej; Steer, Danièle; Sułkowska, Joanna; Sułkowski, Piotr; Sumners, De Witt L.; Svaneborg, Carsten; Szymczak, Piotr; Tarenzi, Thomas; Travasso, Rui; Virnau, Peter; Vlassopoulos, Dimitris; Ziherl, Primož; Žumer, Slobodan

doi:10.1016/j.physrep.2024.04.002

Cited by 12 publications

(1 citation statement)

References 774 publications

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“…A deeply knotted protein should have at least one large knot tail since its knotted core is located far from the corresponding terminus. When the deletion of 20 or more residues from one of the termini is required to untie the chain, the knot classifies as deep; otherwise, it is considered shallow. , Research on knotted proteins has been directed to solve two fundamental problems: 1) understanding their folding and knotting mechanisms (reviewed in , ), and 2) identifying the knot’s functional role (reviewed in , ).…”

Section: Introductionmentioning

confidence: 99%

Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Ferreira,

Sriramoju,

Hsu

et al. 2024

J. Chem. Inf. Model.

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Knotted proteins are present in nature, but there is still an open issue regarding the existence of a universal role for these remarkable structures. To address this question, we used classical molecular dynamics (MD) simulations combined with in vitro experiments to investigate the role of the Gordian knot in the catalytic activity of UCH-L1. To create an unknotted form of UCH-L1, we modified its amino acid sequence by truncating several residues from its N-terminus. Remarkably, we find that deleting the first two N-terminal residues leads to a partial loss of enzyme activity with conservation of secondary structural content and knotted topological state. This happens because the integrity of the N-terminus is critical to ensure the correct alignment of the catalytic triad. However, the removal of five residues from the Nterminus, which significantly disrupts the native structure and the topological state, leads to a complete loss of enzymatic activity. Overall, our findings indicate that UCH-L1's catalytic activity depends critically on the integrity of the N-terminus and the secondary structure content, with the latter being strongly coupled with the knotted topological state.

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Section: Introductionmentioning

confidence: 99%

Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Ferreira,

Sriramoju,

Hsu

et al. 2024

J. Chem. Inf. Model.

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Rheology of Ring Copolymers in Dilute Solutions

Kumar,

Biswas

2024

J. Phys. Chem. B

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Topological comparison of flexible and semiflexible chains in polymer melts with θ-chains

Schmitt,

Wettermann,

Daoulas

et al. 2024

The Journal of Chemical Physics

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A central paradigm of polymer physics states that chains in melts behave like random walks as intra- and interchain interactions effectively cancel each other out. Likewise, θ-chains, i.e., chains at the transition from a swollen coil to a globular phase, are also thought to behave like ideal chains, as attractive forces are counterbalanced by repulsive entropic contributions. While the simple mapping to an equivalent Kuhn chain works rather well in most scenarios with corrections to scaling, random walks do not accurately capture the topology and knots, particularly for flexible chains. In this paper, we demonstrate with Monte Carlo and molecular dynamics simulations that chains in polymer melts and θ-chains not only agree on a structural level for a range of stiffnesses but also topologically. They exhibit similar knotting probabilities and knot sizes, both of which are not captured by ideal chain representations. This discrepancy comes from the suppression of small knots in real chains, which is strongest for very flexible chains because excluded volume effects are still active locally and become weaker with increasing semiflexibility. Our findings suggest that corrections to ideal behavior are indeed similar for the two scenarios of real chains and that the structure and topology of a chain in a melt can be approximately reproduced by a corresponding θ-chain.

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Topology in soft and biological matter

Cited by 12 publications

References 774 publications

Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Is There a Functional Role for the Knotted Topology in Protein UCH-L1?

Rheology of Ring Copolymers in Dilute Solutions

Topological comparison of flexible and semiflexible chains in polymer melts with θ-chains

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