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In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria
[Image: see text] The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2019
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010328/ https://www.ncbi.nlm.nih.gov/pubmed/31746214 http://dx.doi.org/10.1021/acs.jproteome.9b00541 |
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author | Ryl, Petra S. J. Bohlke-Schneider, Michael Lenz, Swantje Fischer, Lutz Budzinski, Lisa Stuiver, Marchel Mendes, Marta M. L. Sinn, Ludwig O’Reilly, Francis J. Rappsilber, Juri |
author_facet | Ryl, Petra S. J. Bohlke-Schneider, Michael Lenz, Swantje Fischer, Lutz Budzinski, Lisa Stuiver, Marchel Mendes, Marta M. L. Sinn, Ludwig O’Reilly, Francis J. Rappsilber, Juri |
author_sort | Ryl, Petra S. J. |
collection | PubMed |
description | [Image: see text] The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here, we apply the popular noncleavable cross-linker disuccinimidyl suberate (DSS) to human mitochondria and identify 5518 distance restraints between protein residues. Each distance restraint on proteins or their interactions provides structural information within mitochondria. Comparing these restraints to protein data bank (PDB)-deposited structures and comparative models reveals novel protein conformations. Our data suggest, among others, substrates and protein flexibility of mitochondrial heat shock proteins. Through this study, we bring forward two central points for the progression of CLMS towards large-scale in situ structural biology: First, clustered conflicts of cross-link data reveal in situ protein conformation states in contrast to error-rich individual conflicts. Second, noncleavable cross-linkers are compatible with proteome-wide studies. |
format | Online Article Text |
id | pubmed-7010328 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-70103282020-02-11 In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria Ryl, Petra S. J. Bohlke-Schneider, Michael Lenz, Swantje Fischer, Lutz Budzinski, Lisa Stuiver, Marchel Mendes, Marta M. L. Sinn, Ludwig O’Reilly, Francis J. Rappsilber, Juri J Proteome Res [Image: see text] The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass spectrometry (CLMS) is contributing to this effort, typically through the use of mass spectrometry (MS)-cleavable cross-linkers. Here, we apply the popular noncleavable cross-linker disuccinimidyl suberate (DSS) to human mitochondria and identify 5518 distance restraints between protein residues. Each distance restraint on proteins or their interactions provides structural information within mitochondria. Comparing these restraints to protein data bank (PDB)-deposited structures and comparative models reveals novel protein conformations. Our data suggest, among others, substrates and protein flexibility of mitochondrial heat shock proteins. Through this study, we bring forward two central points for the progression of CLMS towards large-scale in situ structural biology: First, clustered conflicts of cross-link data reveal in situ protein conformation states in contrast to error-rich individual conflicts. Second, noncleavable cross-linkers are compatible with proteome-wide studies. American Chemical Society 2019-11-20 2020-01-03 /pmc/articles/PMC7010328/ /pubmed/31746214 http://dx.doi.org/10.1021/acs.jproteome.9b00541 Text en Copyright © 2019 American Chemical Society This is an open access article published under a Creative Commons Attribution (CC-BY) License (http://pubs.acs.org/page/policy/authorchoice_ccby_termsofuse.html) , which permits unrestricted use, distribution and reproduction in any medium, provided the author and source are cited. |
spellingShingle | Ryl, Petra S. J. Bohlke-Schneider, Michael Lenz, Swantje Fischer, Lutz Budzinski, Lisa Stuiver, Marchel Mendes, Marta M. L. Sinn, Ludwig O’Reilly, Francis J. Rappsilber, Juri In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria |
title | In Situ Structural
Restraints from Cross-Linking Mass
Spectrometry in Human Mitochondria |
title_full | In Situ Structural
Restraints from Cross-Linking Mass
Spectrometry in Human Mitochondria |
title_fullStr | In Situ Structural
Restraints from Cross-Linking Mass
Spectrometry in Human Mitochondria |
title_full_unstemmed | In Situ Structural
Restraints from Cross-Linking Mass
Spectrometry in Human Mitochondria |
title_short | In Situ Structural
Restraints from Cross-Linking Mass
Spectrometry in Human Mitochondria |
title_sort | in situ structural
restraints from cross-linking mass
spectrometry in human mitochondria |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010328/ https://www.ncbi.nlm.nih.gov/pubmed/31746214 http://dx.doi.org/10.1021/acs.jproteome.9b00541 |
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