The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations
For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivat...
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| Format: | Article |
| Language: | English |
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MDPI AG
2013-12-01
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| Series: | Biomolecules |
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| Online Access: | http://www.mdpi.com/2218-273X/4/1/1 |
| _version_ | 1818844032001900544 |
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| author | Roberto Covino Tatjana Škrbić Silvio a Beccara Pietro Faccioli Cristian Micheletti |
| author_facet | Roberto Covino Tatjana Škrbić Silvio a Beccara Pietro Faccioli Cristian Micheletti |
| author_sort | Roberto Covino |
| collection | DOAJ |
| description | For several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events. |
| first_indexed | 2024-12-19T05:07:18Z |
| format | Article |
| id | doaj.art-dd62655e8fd84035a90081a6f5d80dab |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-12-19T05:07:18Z |
| publishDate | 2013-12-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-dd62655e8fd84035a90081a6f5d80dab2022-12-21T20:34:53ZengMDPI AGBiomolecules2218-273X2013-12-014111910.3390/biom4010001biom4010001The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics SimulationsRoberto Covino0Tatjana Škrbić1Silvio a Beccara2Pietro Faccioli3Cristian Micheletti4Department of Physics, University of Trento, Via Sommarive 14, Trento 38123, ItalySISSA—Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, ItalyInterdisciplinary Laboratory for Computational Science, FBK-CMM and University of Trento,Trento 38123, ItalyDepartment of Physics, University of Trento, Via Sommarive 14, Trento 38123, ItalySISSA—Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, Trieste 34136, ItalyFor several decades, the presence of knots in naturally-occurring proteins was largely ruled out a priori for its supposed incompatibility with the efficiency and robustness of folding processes. For this very same reason, the later discovery of several unrelated families of knotted proteins motivated researchers to look into the physico-chemical mechanisms governing the concerted sequence of folding steps leading to the consistent formation of the same knot type in the same protein location. Besides experiments, computational studies are providing considerable insight into these mechanisms. Here, we revisit a number of such recent investigations within a common conceptual and methodological framework. By considering studies employing protein models with different structural resolution (coarse-grained or atomistic) and various force fields (from pure native-centric to realistic atomistic ones), we focus on the role of native and non-native interactions. For various unrelated instances of knotted proteins, non-native interactions are shown to be very important for favoring the emergence of conformations primed for successful self-knotting events.http://www.mdpi.com/2218-273X/4/1/1knotted proteinsfolding simulationsnon-native interactions |
| spellingShingle | Roberto Covino Tatjana Škrbić Silvio a Beccara Pietro Faccioli Cristian Micheletti The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations Biomolecules knotted proteins folding simulations non-native interactions |
| title | The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations |
| title_full | The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations |
| title_fullStr | The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations |
| title_full_unstemmed | The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations |
| title_short | The Role of Non-Native Interactions in the Folding of Knotted Proteins: Insights from Molecular Dynamics Simulations |
| title_sort | role of non native interactions in the folding of knotted proteins insights from molecular dynamics simulations |
| topic | knotted proteins folding simulations non-native interactions |
| url | http://www.mdpi.com/2218-273X/4/1/1 |
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