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Finite Size Effects in Simulations of Protein Aggregation
It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligom...
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Formato: | Texto |
Lenguaje: | English |
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Public Library of Science
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441439/ https://www.ncbi.nlm.nih.gov/pubmed/18612385 http://dx.doi.org/10.1371/journal.pone.0002641 |
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author | Pawar, Amol Favrin, Giorgio |
author_facet | Pawar, Amol Favrin, Giorgio |
author_sort | Pawar, Amol |
collection | PubMed |
description | It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligomeric species are starting to make significant contributions to our understanding of the determinants of protein aggregation. We simulate different systems at constant concentration but with a different number of peptides and we study the how the finite number of proteins affects the underlying free energy of the system and therefore the relative stability of the species involved in the process. If not taken into account, this finite size effect can undermine the validity of theoretical predictions regarding the relative stability of the species involved and the rates of conversion from one to the other. We discuss the reasons that give rise to this finite size effect form both a probabilistic and energy fluctuations point of view and also how this problem can be dealt by a finite size scaling analysis. |
format | Text |
id | pubmed-2441439 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-24414392008-07-09 Finite Size Effects in Simulations of Protein Aggregation Pawar, Amol Favrin, Giorgio PLoS One Research Article It is becoming increasingly clear that the soluble protofibrillar species that proceed amyloid fibril formation are associated with a range of neurodegenerative disorders such as Alzheimer's and Parkinson diseases. Computer simulations of the processes that lead to the formation of these oligomeric species are starting to make significant contributions to our understanding of the determinants of protein aggregation. We simulate different systems at constant concentration but with a different number of peptides and we study the how the finite number of proteins affects the underlying free energy of the system and therefore the relative stability of the species involved in the process. If not taken into account, this finite size effect can undermine the validity of theoretical predictions regarding the relative stability of the species involved and the rates of conversion from one to the other. We discuss the reasons that give rise to this finite size effect form both a probabilistic and energy fluctuations point of view and also how this problem can be dealt by a finite size scaling analysis. Public Library of Science 2008-07-09 /pmc/articles/PMC2441439/ /pubmed/18612385 http://dx.doi.org/10.1371/journal.pone.0002641 Text en Pawar, Favrin. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Pawar, Amol Favrin, Giorgio Finite Size Effects in Simulations of Protein Aggregation |
title | Finite Size Effects in Simulations of Protein Aggregation |
title_full | Finite Size Effects in Simulations of Protein Aggregation |
title_fullStr | Finite Size Effects in Simulations of Protein Aggregation |
title_full_unstemmed | Finite Size Effects in Simulations of Protein Aggregation |
title_short | Finite Size Effects in Simulations of Protein Aggregation |
title_sort | finite size effects in simulations of protein aggregation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441439/ https://www.ncbi.nlm.nih.gov/pubmed/18612385 http://dx.doi.org/10.1371/journal.pone.0002641 |
work_keys_str_mv | AT pawaramol finitesizeeffectsinsimulationsofproteinaggregation AT favringiorgio finitesizeeffectsinsimulationsofproteinaggregation |