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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9695063/ https://www.ncbi.nlm.nih.gov/pubmed/36430350 http://dx.doi.org/10.3390/ijms232213871 |
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author | Especial, João N. C. Rey, Antonio Faísca, Patrícia F. N. |
author_facet | Especial, João N. C. Rey, Antonio Faísca, Patrícia F. N. |
author_sort | Especial, João N. C. |
collection | PubMed |
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. |
format | Online Article Text |
id | pubmed-9695063 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-96950632022-11-26 A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins Especial, João N. C. Rey, Antonio Faísca, Patrícia F. N. Int J Mol Sci Article 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. MDPI 2022-11-10 /pmc/articles/PMC9695063/ /pubmed/36430350 http://dx.doi.org/10.3390/ijms232213871 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Especial, João N. C. Rey, Antonio Faísca, Patrícia F. N. A Note on the Effects of Linear Topology Preservation in Monte Carlo Simulations of Knotted Proteins |
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 | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9695063/ https://www.ncbi.nlm.nih.gov/pubmed/36430350 http://dx.doi.org/10.3390/ijms232213871 |
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