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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

A slipknot (a) is a conformation in which one of the protein termini adopts a hairpin-like conformation (highlighted in red) that threads a loop formed by the remainder of the chain. A knotting mechanism based on slipknots has been proposed for some proteins. In alternative, the knotting step may occur via the threading of one of the termini through the knotting loop. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
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f0015: A slipknot (a) is a conformation in which one of the protein termini adopts a hairpin-like conformation (highlighted in red) that threads a loop formed by the remainder of the chain. A knotting mechanism based on slipknots has been proposed for some proteins. In alternative, the knotting step may occur via the threading of one of the termini through the knotting loop. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Mentions: An interesting variation amongst knotted conformations is that of the slipknot, originally identified by Yeates and co-workers [10]. A slipknot is a structure that when examined in its complete form is unknotted, but becomes knotted by deletion of suitable terminal segments because—just like in a shoelace—it is the arrangement of the terminal segment that unties the knot as the chain folds back upon itself close to one of its ends (Fig. 3a). The most recent survey of the PDB found 1150 tangled proteins (including slipknots) amongst 144,554 analyzed protein entries [11]. Tangled topologies, and knotted proteins in particular, thus represent a small fraction of the folding space represented by the PDB. There are many proteins with the 31 knot in their native structure, some with the 41 knot and only a few with the 52 knot [12–14]. So far, the most complex knot type found in the PDB is the Stevedore's (or 61) knot, which was detected in protein α-haloacid dehalogenase (PDB ID: 3bjx) [15]. Information on knotted proteins can be retrieved from databases that have been created along the years [13,16]. KnotProt is likely the most up-to-date collection of tangled structures that cover knotted proteins as well as slipknots [11].


Knotted proteins: A tangled tale of Structural Biology.

Faísca PF - Comput Struct Biotechnol J (2015)

A slipknot (a) is a conformation in which one of the protein termini adopts a hairpin-like conformation (highlighted in red) that threads a loop formed by the remainder of the chain. A knotting mechanism based on slipknots has been proposed for some proteins. In alternative, the knotting step may occur via the threading of one of the termini through the knotting loop. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0015: A slipknot (a) is a conformation in which one of the protein termini adopts a hairpin-like conformation (highlighted in red) that threads a loop formed by the remainder of the chain. A knotting mechanism based on slipknots has been proposed for some proteins. In alternative, the knotting step may occur via the threading of one of the termini through the knotting loop. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)
Mentions: An interesting variation amongst knotted conformations is that of the slipknot, originally identified by Yeates and co-workers [10]. A slipknot is a structure that when examined in its complete form is unknotted, but becomes knotted by deletion of suitable terminal segments because—just like in a shoelace—it is the arrangement of the terminal segment that unties the knot as the chain folds back upon itself close to one of its ends (Fig. 3a). The most recent survey of the PDB found 1150 tangled proteins (including slipknots) amongst 144,554 analyzed protein entries [11]. Tangled topologies, and knotted proteins in particular, thus represent a small fraction of the folding space represented by the PDB. There are many proteins with the 31 knot in their native structure, some with the 41 knot and only a few with the 52 knot [12–14]. So far, the most complex knot type found in the PDB is the Stevedore's (or 61) knot, which was detected in protein α-haloacid dehalogenase (PDB ID: 3bjx) [15]. Information on knotted proteins can be retrieved from databases that have been created along the years [13,16]. KnotProt is likely the most up-to-date collection of tangled structures that cover knotted proteins as well as slipknots [11].

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