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Knotted proteins: A tangled tale of Structural Biology.

Faísca PF - Comput Struct Biotechnol J (2015)

Bottom Line: Knotted proteins have their native structures arranged in the form of an open knot.Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments.Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.

View Article: PubMed Central - PubMed

Affiliation: Departament of Physics and BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal.

ABSTRACT
Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.

No MeSH data available.


Related in: MedlinePlus

Folding (a) and unfolding (b) kinetics for the lattice 52 knot and the lattice (shallow) trefoil. The folding (kf) and unfolding (ku) rates are given by the slope of the regression lines. Both knot types fold and unfold much slower than their unknotted control systems. However, the difference in folding and unfolding rates is much larger for the more complex knot type.
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f0030: Folding (a) and unfolding (b) kinetics for the lattice 52 knot and the lattice (shallow) trefoil. The folding (kf) and unfolding (ku) rates are given by the slope of the regression lines. Both knot types fold and unfold much slower than their unknotted control systems. However, the difference in folding and unfolding rates is much larger for the more complex knot type.

Mentions: By performing highly accurate measurements of the folding rate (based on ~ 2000 MC trajectories), we observed that the folding of knotted lattices is always slower than that of its unknotted counterparts [26,84], in line with an earlier experimental observation [91], and predictions from off-lattice simulations [24,85]. Furthermore, we noticed that folding becomes remarkably slower as the complexity of the knot increases [18] (Fig. 6a).


Knotted proteins: A tangled tale of Structural Biology.

Faísca PF - Comput Struct Biotechnol J (2015)

Folding (a) and unfolding (b) kinetics for the lattice 52 knot and the lattice (shallow) trefoil. The folding (kf) and unfolding (ku) rates are given by the slope of the regression lines. Both knot types fold and unfold much slower than their unknotted control systems. However, the difference in folding and unfolding rates is much larger for the more complex knot type.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556803&req=5

f0030: Folding (a) and unfolding (b) kinetics for the lattice 52 knot and the lattice (shallow) trefoil. The folding (kf) and unfolding (ku) rates are given by the slope of the regression lines. Both knot types fold and unfold much slower than their unknotted control systems. However, the difference in folding and unfolding rates is much larger for the more complex knot type.
Mentions: By performing highly accurate measurements of the folding rate (based on ~ 2000 MC trajectories), we observed that the folding of knotted lattices is always slower than that of its unknotted counterparts [26,84], in line with an earlier experimental observation [91], and predictions from off-lattice simulations [24,85]. Furthermore, we noticed that folding becomes remarkably slower as the complexity of the knot increases [18] (Fig. 6a).

Bottom Line: Knotted proteins have their native structures arranged in the form of an open knot.Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments.Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.

View Article: PubMed Central - PubMed

Affiliation: Departament of Physics and BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisboa, Portugal.

ABSTRACT
Knotted proteins have their native structures arranged in the form of an open knot. In the last ten years researchers have been making significant efforts to reveal their folding mechanism and understand which functional advantage(s) knots convey to their carriers. Molecular simulations have been playing a fundamental role in this endeavor, and early computational predictions about the knotting mechanism have just been confirmed in wet lab experiments. Here we review a collection of simulation results that allow outlining the current status of the field of knotted proteins, and discuss directions for future research.

No MeSH data available.


Related in: MedlinePlus