Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Meinhardt, Sarah, Manley, Michael W., Parente, Daniel J., Swint-Kruse, Liskin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
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
_version_ 1782297350344015872
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
work_keys_str_mv AT meinhardtsarah rheostatsandtoggleswitchesformodulatingproteinfunction
AT manleymichaelw rheostatsandtoggleswitchesformodulatingproteinfunction
AT parentedanielj rheostatsandtoggleswitchesformodulatingproteinfunction
AT swintkruseliskin rheostatsandtoggleswitchesformodulatingproteinfunction