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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

Cartoon representation of the native structure (top), reduced backbone representation obtained with the Taylor smoothing algorithm highlighting a open knot (middle) and corresponding topological knot (bottom) of proteins YibK (PDB ID: 1j85) (a), acetohydroxy acid isomeroreductase (PDB ID: 1yve) (b), and UCH-L3 (PDB ID: 1xd3) (c). The trefoil (or 31), figure-eight (or 41) and penta (or 52) knots exhibit three, four and five crossings on a planar projection. The subscript 1 in 31 (41) stands for first knot with three (four) crossings and subscript 2 in 52 stands for second knot with five crossings, according to standard knot tables The coordinates of the reduced representations were retrieved from http://knots.mit.edu/ and visualized with PyMol (The PyMOL Molecular Graphics System, Open-Source 1.5.x). The topological representations were produced with knotplot (http://www.knotplot.com/).
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f0010: Cartoon representation of the native structure (top), reduced backbone representation obtained with the Taylor smoothing algorithm highlighting a open knot (middle) and corresponding topological knot (bottom) of proteins YibK (PDB ID: 1j85) (a), acetohydroxy acid isomeroreductase (PDB ID: 1yve) (b), and UCH-L3 (PDB ID: 1xd3) (c). The trefoil (or 31), figure-eight (or 41) and penta (or 52) knots exhibit three, four and five crossings on a planar projection. The subscript 1 in 31 (41) stands for first knot with three (four) crossings and subscript 2 in 52 stands for second knot with five crossings, according to standard knot tables The coordinates of the reduced representations were retrieved from http://knots.mit.edu/ and visualized with PyMol (The PyMOL Molecular Graphics System, Open-Source 1.5.x). The topological representations were produced with knotplot (http://www.knotplot.com/).

Mentions: Taylor's algorithm is applied to a linear conformation and it was noticed that the final outcome may depend on the order of smoothing operations (i.e. if it starts at the N-terminus or at the C-terminus) [8]. Therefore, the initial conformation needs to be closed prior to the smoothing procedure through a closure method (reviewed in [9]). The combination of smoothing algorithms with closure methods and knot invariants provides a straightforward way to systematically scrutinize the universe of protein conformations deposited in the PDB in searching for different knots (Fig. 2).


Knotted proteins: A tangled tale of Structural Biology.

Faísca PF - Comput Struct Biotechnol J (2015)

Cartoon representation of the native structure (top), reduced backbone representation obtained with the Taylor smoothing algorithm highlighting a open knot (middle) and corresponding topological knot (bottom) of proteins YibK (PDB ID: 1j85) (a), acetohydroxy acid isomeroreductase (PDB ID: 1yve) (b), and UCH-L3 (PDB ID: 1xd3) (c). The trefoil (or 31), figure-eight (or 41) and penta (or 52) knots exhibit three, four and five crossings on a planar projection. The subscript 1 in 31 (41) stands for first knot with three (four) crossings and subscript 2 in 52 stands for second knot with five crossings, according to standard knot tables The coordinates of the reduced representations were retrieved from http://knots.mit.edu/ and visualized with PyMol (The PyMOL Molecular Graphics System, Open-Source 1.5.x). The topological representations were produced with knotplot (http://www.knotplot.com/).
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0010: Cartoon representation of the native structure (top), reduced backbone representation obtained with the Taylor smoothing algorithm highlighting a open knot (middle) and corresponding topological knot (bottom) of proteins YibK (PDB ID: 1j85) (a), acetohydroxy acid isomeroreductase (PDB ID: 1yve) (b), and UCH-L3 (PDB ID: 1xd3) (c). The trefoil (or 31), figure-eight (or 41) and penta (or 52) knots exhibit three, four and five crossings on a planar projection. The subscript 1 in 31 (41) stands for first knot with three (four) crossings and subscript 2 in 52 stands for second knot with five crossings, according to standard knot tables The coordinates of the reduced representations were retrieved from http://knots.mit.edu/ and visualized with PyMol (The PyMOL Molecular Graphics System, Open-Source 1.5.x). The topological representations were produced with knotplot (http://www.knotplot.com/).
Mentions: Taylor's algorithm is applied to a linear conformation and it was noticed that the final outcome may depend on the order of smoothing operations (i.e. if it starts at the N-terminus or at the C-terminus) [8]. Therefore, the initial conformation needs to be closed prior to the smoothing procedure through a closure method (reviewed in [9]). The combination of smoothing algorithms with closure methods and knot invariants provides a straightforward way to systematically scrutinize the universe of protein conformations deposited in the PDB in searching for different knots (Fig. 2).

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