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Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy

Intrinsically disordered proteins lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. They are abundant in nature and responsible for a large variety of cellular functions. While numerous bioinf...

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Autores principales: Micsonai, András, Moussong, Éva, Murvai, Nikoletta, Tantos, Ágnes, Tőke, Orsolya, Réfrégiers, Matthieu, Wien, Frank, Kardos, József
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110821/
https://www.ncbi.nlm.nih.gov/pubmed/35591946
http://dx.doi.org/10.3389/fmolb.2022.863141
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author Micsonai, András
Moussong, Éva
Murvai, Nikoletta
Tantos, Ágnes
Tőke, Orsolya
Réfrégiers, Matthieu
Wien, Frank
Kardos, József
author_facet Micsonai, András
Moussong, Éva
Murvai, Nikoletta
Tantos, Ágnes
Tőke, Orsolya
Réfrégiers, Matthieu
Wien, Frank
Kardos, József
author_sort Micsonai, András
collection PubMed
description Intrinsically disordered proteins lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. They are abundant in nature and responsible for a large variety of cellular functions. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. It is usable in a wide concentration range under various buffer conditions. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we propose an automatized binary disorder–order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. Moreover, the method can be used even for strong absorbing samples, such as the case of crowded environmental conditions, if the spectrum can be recorded down to the wavelength of 212 nm. We believe the classification method will be useful in identifying disorder and will also facilitate the growth of experimental data in IDP databases. The method is implemented on a webserver and freely available for academic users.
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spelling pubmed-91108212022-05-18 Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy Micsonai, András Moussong, Éva Murvai, Nikoletta Tantos, Ágnes Tőke, Orsolya Réfrégiers, Matthieu Wien, Frank Kardos, József Front Mol Biosci Molecular Biosciences Intrinsically disordered proteins lack a stable tertiary structure and form dynamic conformational ensembles due to their characteristic physicochemical properties and amino acid composition. They are abundant in nature and responsible for a large variety of cellular functions. While numerous bioinformatics tools have been developed for in silico disorder prediction in the last decades, there is a need for experimental methods to verify the disordered state. CD spectroscopy is widely used for protein secondary structure analysis. It is usable in a wide concentration range under various buffer conditions. Even without providing high-resolution information, it is especially useful when NMR, X-ray, or other techniques are problematic or one simply needs a fast technique to verify the structure of proteins. Here, we propose an automatized binary disorder–order classification method by analyzing far-UV CD spectroscopy data. The method needs CD data at only three wavelength points, making high-throughput data collection possible. The mathematical analysis applies the k-nearest neighbor algorithm with cosine distance function, which is independent of the spectral amplitude and thus free of concentration determination errors. Moreover, the method can be used even for strong absorbing samples, such as the case of crowded environmental conditions, if the spectrum can be recorded down to the wavelength of 212 nm. We believe the classification method will be useful in identifying disorder and will also facilitate the growth of experimental data in IDP databases. The method is implemented on a webserver and freely available for academic users. Frontiers Media S.A. 2022-05-03 /pmc/articles/PMC9110821/ /pubmed/35591946 http://dx.doi.org/10.3389/fmolb.2022.863141 Text en Copyright © 2022 Micsonai, Moussong, Murvai, Tantos, Tőke, Réfrégiers, Wien and Kardos. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Micsonai, András
Moussong, Éva
Murvai, Nikoletta
Tantos, Ágnes
Tőke, Orsolya
Réfrégiers, Matthieu
Wien, Frank
Kardos, József
Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy
title Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy
title_full Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy
title_fullStr Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy
title_full_unstemmed Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy
title_short Disordered–Ordered Protein Binary Classification by Circular Dichroism Spectroscopy
title_sort disordered–ordered protein binary classification by circular dichroism spectroscopy
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110821/
https://www.ncbi.nlm.nih.gov/pubmed/35591946
http://dx.doi.org/10.3389/fmolb.2022.863141
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