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Comprehensive analysis of NMR data using advanced line shape fitting

NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these par...

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Autores principales: Niklasson, Markus, Otten, Renee, Ahlner, Alexandra, Andresen, Cecilia, Schlagnitweit, Judith, Petzold, Katja, Lundström, Patrik
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer Netherlands 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662661/
https://www.ncbi.nlm.nih.gov/pubmed/29043470
http://dx.doi.org/10.1007/s10858-017-0141-6
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author Niklasson, Markus
Otten, Renee
Ahlner, Alexandra
Andresen, Cecilia
Schlagnitweit, Judith
Petzold, Katja
Lundström, Patrik
author_facet Niklasson, Markus
Otten, Renee
Ahlner, Alexandra
Andresen, Cecilia
Schlagnitweit, Judith
Petzold, Katja
Lundström, Patrik
author_sort Niklasson, Markus
collection PubMed
description NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application. The software is a completely redesigned version of PINT (https://pint-nmr.github.io/PINT/). It features a graphical user interface and includes functionality for peak picking, editing of peak lists and line shape fitting. In addition, the obtained peak intensities can be used directly to extract, for instance, relaxation rates, heteronuclear NOE values and exchange parameters. In contrast to most available software the entire process from spectral visualization to preparation of publication-ready figures is done solely using PINT and often within minutes, thereby, increasing productivity for users of all experience levels. Unique to the software are also the outstanding tools for evaluating the quality of the fitting results and extensive, but easy-to-use, customization of the fitting protocol and graphical output. In this communication, we describe the features of the new version of PINT and benchmark its performance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10858-017-0141-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-56626612017-11-15 Comprehensive analysis of NMR data using advanced line shape fitting Niklasson, Markus Otten, Renee Ahlner, Alexandra Andresen, Cecilia Schlagnitweit, Judith Petzold, Katja Lundström, Patrik J Biomol NMR Article NMR spectroscopy is uniquely suited for atomic resolution studies of biomolecules such as proteins, nucleic acids and metabolites, since detailed information on structure and dynamics are encoded in positions and line shapes of peaks in NMR spectra. Unfortunately, accurate determination of these parameters is often complicated and time consuming, in part due to the need for different software at the various analysis steps and for validating the results. Here, we present an integrated, cross-platform and open-source software that is significantly more versatile than the typical line shape fitting application. The software is a completely redesigned version of PINT (https://pint-nmr.github.io/PINT/). It features a graphical user interface and includes functionality for peak picking, editing of peak lists and line shape fitting. In addition, the obtained peak intensities can be used directly to extract, for instance, relaxation rates, heteronuclear NOE values and exchange parameters. In contrast to most available software the entire process from spectral visualization to preparation of publication-ready figures is done solely using PINT and often within minutes, thereby, increasing productivity for users of all experience levels. Unique to the software are also the outstanding tools for evaluating the quality of the fitting results and extensive, but easy-to-use, customization of the fitting protocol and graphical output. In this communication, we describe the features of the new version of PINT and benchmark its performance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10858-017-0141-6) contains supplementary material, which is available to authorized users. Springer Netherlands 2017-10-17 2017 /pmc/articles/PMC5662661/ /pubmed/29043470 http://dx.doi.org/10.1007/s10858-017-0141-6 Text en © The Author(s) 2017 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
Niklasson, Markus
Otten, Renee
Ahlner, Alexandra
Andresen, Cecilia
Schlagnitweit, Judith
Petzold, Katja
Lundström, Patrik
Comprehensive analysis of NMR data using advanced line shape fitting
title Comprehensive analysis of NMR data using advanced line shape fitting
title_full Comprehensive analysis of NMR data using advanced line shape fitting
title_fullStr Comprehensive analysis of NMR data using advanced line shape fitting
title_full_unstemmed Comprehensive analysis of NMR data using advanced line shape fitting
title_short Comprehensive analysis of NMR data using advanced line shape fitting
title_sort comprehensive analysis of nmr data using advanced line shape fitting
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5662661/
https://www.ncbi.nlm.nih.gov/pubmed/29043470
http://dx.doi.org/10.1007/s10858-017-0141-6
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