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Dissecting the structural heterogeneity of proteins by native mass spectrometry

A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct p...

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Autores principales: Reid, Deseree J., Thibert, Stephanie, Zhou, Mowei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley & Sons, Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10031758/
https://www.ncbi.nlm.nih.gov/pubmed/36851867
http://dx.doi.org/10.1002/pro.4612
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author Reid, Deseree J.
Thibert, Stephanie
Zhou, Mowei
author_facet Reid, Deseree J.
Thibert, Stephanie
Zhou, Mowei
author_sort Reid, Deseree J.
collection PubMed
description A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins.
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spelling pubmed-100317582023-04-01 Dissecting the structural heterogeneity of proteins by native mass spectrometry Reid, Deseree J. Thibert, Stephanie Zhou, Mowei Protein Sci Reviews A single gene yields many forms of proteins via combinations of posttranscriptional/posttranslational modifications. Proteins also fold into higher‐order structures and interact with other molecules. The combined molecular diversity leads to the heterogeneity of proteins that manifests as distinct phenotypes. Structural biology has generated vast amounts of data, effectively enabling accurate structural prediction by computational methods. However, structures are often obtained heterologously under homogeneous states in vitro. The lack of native heterogeneity under cellular context creates challenges in precisely connecting the structural data to phenotypes. Mass spectrometry (MS) based proteomics methods can profile proteome composition of complex biological samples. Most MS methods follow the “bottom‐up” approach, which denatures and digests proteins into short peptide fragments for ease of detection. Coupled with chemical biology approaches, higher‐order structures can be probed via incorporation of covalent labels on native proteins that are maintained at the peptide level. Alternatively, native MS follows the “top‐down” approach and directly analyzes intact proteins under nondenaturing conditions. Various tandem MS activation methods can dissect the intact proteins for in‐depth structural elucidation. Herein, we review recent native MS applications for characterizing heterogeneous samples, including proteins binding to mixtures of ligands, homo/hetero‐complexes with varying stoichiometry, intrinsically disordered proteins with dynamic conformations, glycoprotein complexes with mixed modification states, and active membrane protein complexes in near‐native membrane environments. We summarize the benefits, challenges, and ongoing developments in native MS, with the hope to demonstrate an emerging technology that complements other tools by filling the knowledge gaps in understanding the molecular heterogeneity of proteins. John Wiley & Sons, Inc. 2023-04-01 /pmc/articles/PMC10031758/ /pubmed/36851867 http://dx.doi.org/10.1002/pro.4612 Text en © 2023 Battelle Memorial Institute. Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Reviews
Reid, Deseree J.
Thibert, Stephanie
Zhou, Mowei
Dissecting the structural heterogeneity of proteins by native mass spectrometry
title Dissecting the structural heterogeneity of proteins by native mass spectrometry
title_full Dissecting the structural heterogeneity of proteins by native mass spectrometry
title_fullStr Dissecting the structural heterogeneity of proteins by native mass spectrometry
title_full_unstemmed Dissecting the structural heterogeneity of proteins by native mass spectrometry
title_short Dissecting the structural heterogeneity of proteins by native mass spectrometry
title_sort dissecting the structural heterogeneity of proteins by native mass spectrometry
topic Reviews
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10031758/
https://www.ncbi.nlm.nih.gov/pubmed/36851867
http://dx.doi.org/10.1002/pro.4612
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