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Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle
Our current view on how protein complexes assemble and disassemble at promoter sites is based on experimental data. For instance this data is provided by biochemical methods (e.g. ChIP-on-chip assays) or GFP-based assays. These two approaches suggest very different characteristics for protein recrui...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562237/ https://www.ncbi.nlm.nih.gov/pubmed/23383305 http://dx.doi.org/10.1371/journal.pone.0055046 |
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author | Schölling, Manuel Thurner, Stefan Hanel, Rudolf |
author_facet | Schölling, Manuel Thurner, Stefan Hanel, Rudolf |
author_sort | Schölling, Manuel |
collection | PubMed |
description | Our current view on how protein complexes assemble and disassemble at promoter sites is based on experimental data. For instance this data is provided by biochemical methods (e.g. ChIP-on-chip assays) or GFP-based assays. These two approaches suggest very different characteristics for protein recruitment processes that regulate and initiate gene transcription. Biochemical methods suggest a strictly ordered and consecutive protein recruitment while GFP-based assays draw a picture much closer to chaotic or stochastic recruitment. To understand the reason for these conflicting results, we design a generalized recruitment model (GRM) that allows to simulate all possible scenarios between strictly sequential recruitment and completely probabilistic recruitment. With this model we show that probabilistic, transient binding events that are visible in GFP experiments can not be detected by ChIP experiments. We demonstrate that sequential recruitment processes and probabilistic recruitment processes that contain “shortcuts” exhibit periodic dynamics and are hard to distinguish with standard ChIP measurements. Therefore we propose a simple experimental method that can be used to discriminate sequential from probabilistic recruitment processes. We discuss the limitations of this method. |
format | Online Article Text |
id | pubmed-3562237 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-35622372013-02-04 Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle Schölling, Manuel Thurner, Stefan Hanel, Rudolf PLoS One Research Article Our current view on how protein complexes assemble and disassemble at promoter sites is based on experimental data. For instance this data is provided by biochemical methods (e.g. ChIP-on-chip assays) or GFP-based assays. These two approaches suggest very different characteristics for protein recruitment processes that regulate and initiate gene transcription. Biochemical methods suggest a strictly ordered and consecutive protein recruitment while GFP-based assays draw a picture much closer to chaotic or stochastic recruitment. To understand the reason for these conflicting results, we design a generalized recruitment model (GRM) that allows to simulate all possible scenarios between strictly sequential recruitment and completely probabilistic recruitment. With this model we show that probabilistic, transient binding events that are visible in GFP experiments can not be detected by ChIP experiments. We demonstrate that sequential recruitment processes and probabilistic recruitment processes that contain “shortcuts” exhibit periodic dynamics and are hard to distinguish with standard ChIP measurements. Therefore we propose a simple experimental method that can be used to discriminate sequential from probabilistic recruitment processes. We discuss the limitations of this method. Public Library of Science 2013-02-01 /pmc/articles/PMC3562237/ /pubmed/23383305 http://dx.doi.org/10.1371/journal.pone.0055046 Text en © 2013 Schölling et al 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 Schölling, Manuel Thurner, Stefan Hanel, Rudolf Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle |
title | Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle |
title_full | Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle |
title_fullStr | Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle |
title_full_unstemmed | Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle |
title_short | Protein Complex Formation: Computational Clarification of the Sequential versus Probabilistic Recruitment Puzzle |
title_sort | protein complex formation: computational clarification of the sequential versus probabilistic recruitment puzzle |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562237/ https://www.ncbi.nlm.nih.gov/pubmed/23383305 http://dx.doi.org/10.1371/journal.pone.0055046 |
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