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Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins
Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Netherlands
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824835/ https://www.ncbi.nlm.nih.gov/pubmed/26891900 http://dx.doi.org/10.1007/s10858-016-0024-2 |
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author | Piai, Alessandro Gonnelli, Leonardo Felli, Isabella C. Pierattelli, Roberta Kazimierczuk, Krzysztof Grudziąż, Katarzyna Koźmiński, Wiktor Zawadzka-Kazimierczuk, Anna |
author_facet | Piai, Alessandro Gonnelli, Leonardo Felli, Isabella C. Pierattelli, Roberta Kazimierczuk, Krzysztof Grudziąż, Katarzyna Koźmiński, Wiktor Zawadzka-Kazimierczuk, Anna |
author_sort | Piai, Alessandro |
collection | PubMed |
description | Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10858-016-0024-2) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4824835 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Springer Netherlands |
record_format | MEDLINE/PubMed |
spelling | pubmed-48248352016-04-20 Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins Piai, Alessandro Gonnelli, Leonardo Felli, Isabella C. Pierattelli, Roberta Kazimierczuk, Krzysztof Grudziąż, Katarzyna Koźmiński, Wiktor Zawadzka-Kazimierczuk, Anna J Biomol NMR Article Resonance assignment is a prerequisite for almost any NMR-based study of proteins. It can be very challenging in some cases, however, due to the nature of the protein under investigation. This is the case with intrinsically disordered proteins, for example, whose NMR spectra suffer from low chemical shifts dispersion and generally low resolution. For these systems, sequence specific assignment is highly time-consuming, so the prospect of using automatic strategies for their assignment is very attractive. In this article we present a new version of the automatic assignment program TSAR dedicated to intrinsically disordered proteins. In particular, we demonstrate how the automatic procedure can be improved by incorporating methods for amino acid recognition and information on chemical shifts in selected amino acids. The approach was tested in silico on 16 disordered proteins and experimentally on α-synuclein, with remarkably good results. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10858-016-0024-2) contains supplementary material, which is available to authorized users. Springer Netherlands 2016-02-18 2016 /pmc/articles/PMC4824835/ /pubmed/26891900 http://dx.doi.org/10.1007/s10858-016-0024-2 Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. |
spellingShingle | Article Piai, Alessandro Gonnelli, Leonardo Felli, Isabella C. Pierattelli, Roberta Kazimierczuk, Krzysztof Grudziąż, Katarzyna Koźmiński, Wiktor Zawadzka-Kazimierczuk, Anna Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
title | Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
title_full | Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
title_fullStr | Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
title_full_unstemmed | Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
title_short | Amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
title_sort | amino acid recognition for automatic resonance assignment of intrinsically disordered proteins |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824835/ https://www.ncbi.nlm.nih.gov/pubmed/26891900 http://dx.doi.org/10.1007/s10858-016-0024-2 |
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