A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins
Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium...
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MDPI AG
2022-11-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/23/22/13871 |
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| author | João N. C. Especial Antonio Rey Patrícia F. N. Faísca |
| author_facet | João N. C. Especial Antonio Rey Patrícia F. N. Faísca |
| author_sort | João N. C. Especial |
| collection | DOAJ |
| description | Monte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models, that there is no difference in equilibrium properties calculated with a move set that preserves linear topology and one that does not. However, for complex structures, such as those of deeply knotted proteins, the preservation of linear topology provides correct equilibrium results but only after long relaxation. In any case, to analyze folding pathways, knotting mechanisms and folding kinetics, the preservation of linear topology may be an unavoidable requirement. |
| first_indexed | 2024-03-09T18:17:50Z |
| format | Article |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T18:17:50Z |
| publishDate | 2022-11-01 |
| publisher | MDPI AG |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-9439ac1f070843b8bb95de2aae74e6cb2023-11-24T08:34:47ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672022-11-0123221387110.3390/ijms232213871A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted ProteinsJoão N. C. Especial0Antonio Rey1Patrícia F. N. Faísca2Departamento de Física, BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, PortugalDepartamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense, 28040 Madrid, SpainDepartamento de Física, BioISI-Biosystems and Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, PortugalMonte Carlo simulations are a powerful technique and are widely used in different fields. When applied to complex molecular systems with long chains, such as those in synthetic polymers and proteins, they have the advantage of providing a fast and computationally efficient way to sample equilibrium ensembles and calculate thermodynamic and structural properties under desired conditions. Conformational Monte Carlo techniques employ a move set to perform the transitions in the simulation Markov chain. While accepted conformations must preserve the sequential bonding of the protein chain model and excluded volume among its units, the moves themselves may take the chain across itself. We call this a break in linear topology preservation. In this manuscript, we show, using simple protein models, that there is no difference in equilibrium properties calculated with a move set that preserves linear topology and one that does not. However, for complex structures, such as those of deeply knotted proteins, the preservation of linear topology provides correct equilibrium results but only after long relaxation. In any case, to analyze folding pathways, knotting mechanisms and folding kinetics, the preservation of linear topology may be an unavoidable requirement.https://www.mdpi.com/1422-0067/23/22/13871knotted proteinsprotein foldingoff-lattice modelMonte Carlo simulations |
| spellingShingle | João N. C. Especial Antonio Rey Patrícia F. N. Faísca A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins International Journal of Molecular Sciences knotted proteins protein folding off-lattice model Monte Carlo simulations |
| title | A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins |
| title_full | A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins |
| title_fullStr | A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins |
| title_full_unstemmed | A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins |
| title_short | A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins |
| title_sort | note on the effects of linear topology preservation in monte carlo simulations of knotted proteins |
| topic | knotted proteins protein folding off-lattice model Monte Carlo simulations |
| url | https://www.mdpi.com/1422-0067/23/22/13871 |
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