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Rheostats and Toggle Switches for Modulating Protein Function
The millions of protein sequences generated by genomics are expected to transform protein engineering and personalized medicine. To achieve these goals, tools for predicting outcomes of amino acid changes must be improved. Currently, advances are hampered by insufficient experimental data about nonc...
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/PMC3875437/ https://www.ncbi.nlm.nih.gov/pubmed/24386217 http://dx.doi.org/10.1371/journal.pone.0083502 |
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author | Meinhardt, Sarah Manley, Michael W. Parente, Daniel J. Swint-Kruse, Liskin |
author_facet | Meinhardt, Sarah Manley, Michael W. Parente, Daniel J. Swint-Kruse, Liskin |
author_sort | Meinhardt, Sarah |
collection | PubMed |
description | The millions of protein sequences generated by genomics are expected to transform protein engineering and personalized medicine. To achieve these goals, tools for predicting outcomes of amino acid changes must be improved. Currently, advances are hampered by insufficient experimental data about nonconserved amino acid positions. Since the property “nonconserved” is identified using a sequence alignment, we designed experiments to recapitulate that context: Mutagenesis and functional characterization was carried out in 15 LacI/GalR homologs (rows) at 12 nonconserved positions (columns). Multiple substitutions were made at each position, to reveal how various amino acids of a nonconserved column were tolerated in each protein row. Results showed that amino acid preferences of nonconserved positions were highly context-dependent, had few correlations with physico-chemical similarities, and were not predictable from their occurrence in natural LacI/GalR sequences. Further, unlike the “toggle switch” behaviors of conserved positions, substitutions at nonconserved positions could be rank-ordered to show a “rheostatic”, progressive effect on function that spanned several orders of magnitude. Comparisons to various sequence analyses suggested that conserved and strongly co-evolving positions act as functional toggles, whereas other important, nonconserved positions serve as rheostats for modifying protein function. Both the presence of rheostat positions and the sequence analysis strategy appear to be generalizable to other protein families and should be considered when engineering protein modifications or predicting the impact of protein polymorphisms. |
format | Online Article Text |
id | pubmed-3875437 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-38754372014-01-02 Rheostats and Toggle Switches for Modulating Protein Function Meinhardt, Sarah Manley, Michael W. Parente, Daniel J. Swint-Kruse, Liskin PLoS One Research Article The millions of protein sequences generated by genomics are expected to transform protein engineering and personalized medicine. To achieve these goals, tools for predicting outcomes of amino acid changes must be improved. Currently, advances are hampered by insufficient experimental data about nonconserved amino acid positions. Since the property “nonconserved” is identified using a sequence alignment, we designed experiments to recapitulate that context: Mutagenesis and functional characterization was carried out in 15 LacI/GalR homologs (rows) at 12 nonconserved positions (columns). Multiple substitutions were made at each position, to reveal how various amino acids of a nonconserved column were tolerated in each protein row. Results showed that amino acid preferences of nonconserved positions were highly context-dependent, had few correlations with physico-chemical similarities, and were not predictable from their occurrence in natural LacI/GalR sequences. Further, unlike the “toggle switch” behaviors of conserved positions, substitutions at nonconserved positions could be rank-ordered to show a “rheostatic”, progressive effect on function that spanned several orders of magnitude. Comparisons to various sequence analyses suggested that conserved and strongly co-evolving positions act as functional toggles, whereas other important, nonconserved positions serve as rheostats for modifying protein function. Both the presence of rheostat positions and the sequence analysis strategy appear to be generalizable to other protein families and should be considered when engineering protein modifications or predicting the impact of protein polymorphisms. Public Library of Science 2013-12-30 /pmc/articles/PMC3875437/ /pubmed/24386217 http://dx.doi.org/10.1371/journal.pone.0083502 Text en © 2013 Meinhardt 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 Meinhardt, Sarah Manley, Michael W. Parente, Daniel J. Swint-Kruse, Liskin Rheostats and Toggle Switches for Modulating Protein Function |
title | Rheostats and Toggle Switches for Modulating Protein Function |
title_full | Rheostats and Toggle Switches for Modulating Protein Function |
title_fullStr | Rheostats and Toggle Switches for Modulating Protein Function |
title_full_unstemmed | Rheostats and Toggle Switches for Modulating Protein Function |
title_short | Rheostats and Toggle Switches for Modulating Protein Function |
title_sort | rheostats and toggle switches for modulating protein function |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3875437/ https://www.ncbi.nlm.nih.gov/pubmed/24386217 http://dx.doi.org/10.1371/journal.pone.0083502 |
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