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Literature DB >> 18352439

Tightening of knots in proteins.

Joanna I Sułkowska¹, Piotr Sułkowski, P Szymczak, Marek Cieplak.

Abstract

We perform theoretical studies of stretching of 20 proteins with knots within a coarse-grained model. The knot's ends are found to jump to well defined sequential locations that are associated with sharp turns, whereas in homopolymers they diffuse around and eventually slide off. The waiting times of the jumps are increasingly stochastic as the temperature is raised. Knots typically do not return to their native locations when a protein is released after stretching.

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Substances：
Solvents

Year: 2008 PMID： 18352439 DOI： 10.1103/PhysRevLett.100.058106

Source DB: PubMed Journal: Phys Rev Lett ISSN： 0031-9007 Impact factor: 9.161

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Cited

22 in total

1. Slipknotting upon native-like loop formation in a trefoil knot protein.

Authors: Jeffrey K Noel; Joanna I Sułkowska; José N Onuchic
Journal: Proc Natl Acad Sci U S A Date: 2010-08-11 Impact factor: 11.205

2. Stabilizing effect of knots on proteins.

Authors: Joanna I Sułkowska; Piotr Sulkowski; P Szymczak; Marek Cieplak
Journal: Proc Natl Acad Sci U S A Date: 2008-12-08 Impact factor: 11.205

3. Tightening the knot in phytochrome by single-molecule atomic force microscopy.

Authors: Thomas Bornschlögl; David M Anstrom; Elisabeth Mey; Joachim Dzubiella; Matthias Rief; Katrina T Forest
Journal: Biophys J Date: 2009-02-18 Impact factor: 4.033

4. Dodging the crisis of folding proteins with knots.

Authors: Joanna I Sułkowska; Piotr Sułkowski; José Onuchic
Journal: Proc Natl Acad Sci U S A Date: 2009-02-11 Impact factor: 11.205

5. Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations.

Authors: Yan Xu; Shixin Li; Zengshuai Yan; Zhen Luo; Hao Ren; Baosheng Ge; Fang Huang; Tongtao Yue
Journal: Biophys J Date: 2018-09-22 Impact factor: 4.033

6. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil.

Authors: David J Burban; Ellinor Haglund; Dominique T Capraro; Patricia A Jennings
Journal: J Phys Condens Matter Date: 2015-08-20 Impact factor: 2.333

Tightening of knots in proteins.

1. Slipknotting upon native-like loop formation in a trefoil knot protein.

2. Stabilizing effect of knots on proteins.

3. Tightening the knot in phytochrome by single-molecule atomic force microscopy.

4. Dodging the crisis of folding proteins with knots.

5. Stabilizing Effect of Inherent Knots on Proteins Revealed by Molecular Dynamics Simulations.

6. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil.

7. Sequence-specific size, structure, and stability of tight protein knots.

8. Hysteresis as a Marker for Complex, Overlapping Landscapes in Proteins.

9. A Stevedore's protein knot.

10. Knotted vs. unknotted proteins: evidence of knot-promoting loops.