Tightening the Knot in Phytochrome by Single-Molecule Atomic Force Microscopy

Bornschlögl, Thomas; Anstrom, David M.; Mey, Elisabeth; Dzubiella, Joachim; Rief, Matthias; Forest, Katrina T.

doi:10.1016/j.bpj.2008.11.012

Cited by 75 publications

(91 citation statements)

References 45 publications

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“…This is supported by the results where a covalent linkage between the sister GAF domains does not alter the PAS-GAF photocycle (63). The origin of the spectral change is not clear as the mutated residues reside far from the chromophore (Fig.…”

Section: Three Monomerizing Mutations Reveal Two Dimerizationsupporting

confidence: 72%

Light-induced Changes in the Dimerization Interface of Bacteriophytochromes

Takala

Björling

Linna

et al. 2015

Journal of Biological Chemistry

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Background: Bacteriophytochromes are dimeric histidine kinases, but the functional role of their dimerization interfaces is unclear. Results: The phytochrome from Deinococcus radiodurans has two dimerization interfaces, which are critical for thermal back reversion and are altered by illumination. Conclusion:The dimerization interfaces cause strain in the structure. Significance: A functional role for the dimerization interfaces is proposed.

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Section: Three Monomerizing Mutations Reveal Two Dimerizationsupporting

confidence: 72%

Light-induced Changes in the Dimerization Interface of Bacteriophytochromes

Takala

Björling

Linna

et al. 2015

Journal of Biological Chemistry

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“…These malformed topologies would include cases where the knot is missing. In type a, nonspecific knots of type ii and iii must jump along the sequence to find the correct native position, but this process might be prohibitively slow (12,24,(25)(26). Nonspecific knots of type iv must backtrack completely.…”

Section: Resultsmentioning

confidence: 99%

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

Noel

Sułkowska

Onuchic

2010

Proc. Natl. Acad. Sci. U.S.A.

111

163

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Protein knots and slipknots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Recent experimental results show that knotting, starting from a fully extended polypeptide, has not yet been observed. Understanding the nucleation process of folding knots is thus a natural challenge for both experimental and theoretical investigation. In this study, we employ energy landscape theory and molecular dynamics to elucidate the entire folding mechanism. The full free energy landscape of a knotted protein is mapped using an all-atom structure-based protein model. Results show that, due to the topological constraint, the protein folds through a three-state mechanism that contains (i) a precise nucleation site that creates a correctly twisted native loop (first barrier) and (ii) a rate-limiting free energy barrier that is traversed by two parallel knot-forming routes. The main route corresponds to a slipknot conformation, a collapsed configuration where the C-terminal helix adopts a hairpin-like configuration while threading, and the minor route to an entropically limited plug motion, where the extended terminus is threaded as through a needle. Knot formation is a late transition state process and results show that random (nonspecific) knots are a very rare and unstable set of configurations both at and below folding temperature. Our study shows that a native-biased landscape is sufficient to fold complex topologies and presents a folding mechanism generalizable to all known knotted protein topologies: knotting via threading a native-like loop in a preordered intermediate.free energy landscape | knotted protein kinetics | nontrivial protein topology | protein folding | structure-based model P rotein structures have been observed with several complex folding motifs including knots and slipknots. These include nontrivial topologies containing 3 1 , 4 1 , 5 2 , and 6 1 knots (1-5). While the mechanism by which these proteins manage to reliably fold from a disordered linear polypeptide into complicated topologies is still largely a mystery, energy landscape theory is starting to provide us the key to resolve this challenge. In a minimally frustrated, funnel-like energy landscape, one expects that native contacts are on average favorable and dominate over nonfavorable nonnative ones (6-8). Topological constraints imposed by the existence of a native knot radically alters the funneled landscape. Many routes are barred from reaching the native state due to the obstacle imposed by the knot. Forming a knot requires intricate crossings of the polypeptide; any one made incorrectly leads to an unknotted protein or a wrong chirality. Therefore at first sight the problem of folding knots appears perplexing, but there is no reason to doubt that clues will be found in the native structure itself. Here it is shown how an all-atom structure-based model, which is dominated by native attractive interactions, is sufficient to uncover the energy landscape and folding routes of the smallest kn...

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“…As to the function of the interchain entanglement, it is possible that it leads to an increased thermal stability of the system. Experiments on knotted proteins have been done for monomeric systems such as ubuiquitin hydrolases UCH-L1 (PDB:2ETL) 23 and UCH-L3 (PDB:1XD1) 24 or a bacteriophotochrome (PDB:2O9C) 9 , even though the latter protein forms dimers in a solution. (From now on, we shall refer to the proteins by their PDB structure codes for brevity.)…”

Section: Introductionmentioning

confidence: 99%

Structural entanglements in protein complexes

Zhao

Chwastyk

Cieplak

2017

The Journal of Chemical Physics

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We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface, and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction.

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Tightening the Knot in Phytochrome by Single-Molecule Atomic Force Microscopy

Cited by 75 publications

References 45 publications

Light-induced Changes in the Dimerization Interface of Bacteriophytochromes

Light-induced Changes in the Dimerization Interface of Bacteriophytochromes

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

Structural entanglements in protein complexes

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