In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria

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 pop...

Celý popis

Uloženo v:
Podrobná bibliografie
Vydáno v:Journal of proteome research Ročník 19; číslo 1; s. 327
Hlavní autoři: 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
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 03.01.2020
Témata:
Chromatography, Gel
Cross-Linking Reagents - chemistry
Humans
K562 Cells
Mass Spectrometry - methods
Mitochondria - chemistry
Mitochondrial Proteins - analysis
Mitochondrial Proteins - chemistry
Protein Conformation
Protein Interaction Maps
Succinimides - chemistry
Workflow
noncleavable DSS cross-linker
in situ large-scale structural biology
comparative modeling
human mitochondria
cross-linking mass spectrometry
ISSN:1535-3907, 1535-3907
On-line přístup:Zjistit podrobnosti o přístupu
Tagy: Přidat tag
Žádné tagy, Buďte první, kdo vytvoří štítek k tomuto záznamu!
Abstract 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.
AbstractList 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.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.
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.
Author Ryl, Petra S J
Bohlke-Schneider, Michael
Sinn, Ludwig
Mendes, Marta M L
Rappsilber, Juri
Budzinski, Lisa
Stuiver, Marchel
Lenz, Swantje
Fischer, Lutz
O'Reilly, Francis J
Author_xml – sequence: 1
  givenname: Petra S J
  orcidid: 0000-0003-3016-3874
  surname: Ryl
  fullname: Ryl, Petra S J
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 2
  givenname: Michael
  surname: Bohlke-Schneider
  fullname: Bohlke-Schneider, Michael
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 3
  givenname: Swantje
  orcidid: 0000-0002-8839-5371
  surname: Lenz
  fullname: Lenz, Swantje
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 4
  givenname: Lutz
  surname: Fischer
  fullname: Fischer, Lutz
  organization: Wellcome Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , Edinburgh EH9 3BF , Scotland , United Kingdom
– sequence: 5
  givenname: Lisa
  surname: Budzinski
  fullname: Budzinski, Lisa
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 6
  givenname: Marchel
  surname: Stuiver
  fullname: Stuiver, Marchel
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 7
  givenname: Marta M L
  surname: Mendes
  fullname: Mendes, Marta M L
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 8
  givenname: Ludwig
  surname: Sinn
  fullname: Sinn, Ludwig
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 9
  givenname: Francis J
  surname: O'Reilly
  fullname: O'Reilly, Francis J
  organization: Bioanalytics, Institute of Biotechnology , Technische Universität Berlin , 13355 Berlin , Germany
– sequence: 10
  givenname: Juri
  orcidid: 0000-0001-5999-1310
  surname: Rappsilber
  fullname: Rappsilber, Juri
  organization: Wellcome Centre for Cell Biology, School of Biological Sciences , University of Edinburgh , Edinburgh EH9 3BF , Scotland , United Kingdom
BackLink https://www.ncbi.nlm.nih.gov/pubmed/31746214$$D View this record in MEDLINE/PubMed
BookMark eNpNkE1LAzEYhINU7If-BCVHL1vzudk9SlFbaBGsgrclm31XU7tJTbKH_nsXrOBpBuZhGGaKRs47QOiakjkljN5pE-e7Q_AJfAfzsiZECnqGJlRymfGSqNE_P0bTGHeEUKkIv0BjTpXIGRUT9L5yeGtTj7cp9Cb1Qe_xC8QUtHUp4jb4Di-CjzFbW_dl3Qfe6Bjx9gAmDRmkcMTW4WXfaYc3Nnnz6V0TrL5E563eR7g66Qy9PT68LpbZ-vlptbhfZ1pInrLaqBwKwoiRoCXwvNFECVYrTptCNrnWtGjrVkCZ12ULkqiaFEDBkFw0JSNshm5_e4cvvvthedXZaGC_1w58HyvGaS44YaoY0JsT2tcdNNUh2E6HY_X3BvsB50NneA
CitedBy_id crossref_primary_10_1038_s41556_025_01620_1
crossref_primary_10_1038_s41467_024_52558_1
crossref_primary_10_1089_omi_2022_0137
crossref_primary_10_1098_rsob_220363
crossref_primary_10_1042_EBC20220168
crossref_primary_10_1002_mas_21908
crossref_primary_10_1016_j_mcpro_2025_101065
crossref_primary_10_1038_s41467_024_52844_y
crossref_primary_10_6023_A22010055
crossref_primary_10_1016_j_jmb_2024_168656
crossref_primary_10_1002_advs_202408462
crossref_primary_10_1186_s12859_023_05473_z
crossref_primary_10_1038_s41467_021_23441_0
crossref_primary_10_1016_j_aca_2021_338838
crossref_primary_10_1016_j_str_2021_11_007
crossref_primary_10_1038_s41592_022_01454_x
crossref_primary_10_1038_s41467_021_23666_z
crossref_primary_10_15252_embj_2020106174
crossref_primary_10_3389_fchem_2022_994572
crossref_primary_10_1038_s41467_023_39485_3
crossref_primary_10_1002_mas_21717
crossref_primary_10_3389_fcell_2021_796128
crossref_primary_10_1016_j_cbpa_2020_07_008
crossref_primary_10_1016_j_isci_2024_110140
crossref_primary_10_1016_j_mcpro_2025_101057
crossref_primary_10_1002_pmic_202100145
crossref_primary_10_1073_pnas_2103554118
crossref_primary_10_1016_j_bbapap_2021_140655
crossref_primary_10_1073_pnas_2106950118
crossref_primary_10_1002_ijch_202300084
crossref_primary_10_12688_wellcomeopenres_17160_1
crossref_primary_10_1007_s40242_022_2037_6
crossref_primary_10_1016_j_sbi_2020_06_012
crossref_primary_10_12688_wellcomeopenres_17160_2
ContentType Journal Article
DBID CGR
CUY
CVF
ECM
EIF
NPM
7X8
DOI 10.1021/acs.jproteome.9b00541
DatabaseName Medline
MEDLINE
MEDLINE (Ovid)
MEDLINE
MEDLINE
PubMed
MEDLINE - Academic
DatabaseTitle MEDLINE
Medline Complete
MEDLINE with Full Text
PubMed
MEDLINE (Ovid)
MEDLINE - Academic
DatabaseTitleList MEDLINE - Academic
MEDLINE
Database_xml – sequence: 1
  dbid: NPM
  name: PubMed
  url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 2
  dbid: 7X8
  name: MEDLINE - Academic
  url: https://search.proquest.com/medline
  sourceTypes: Aggregation Database
DeliveryMethod no_fulltext_linktorsrc
Discipline Chemistry
EISSN 1535-3907
ExternalDocumentID 31746214
Genre Research Support, Non-U.S. Gov't
Journal Article
GrantInformation_xml – fundername: Wellcome Trust
  grantid: 203149
– fundername: Wellcome Trust
  grantid: 103139/Z/13/Z
GroupedDBID ---
4.4
53G
55A
5GY
5VS
7~N
AABXI
AAHBH
ABJNI
ABMVS
ABQRX
ABUCX
ACGFS
ACS
ADHLV
AEESW
AENEX
AFEFF
AHGAQ
ALMA_UNASSIGNED_HOLDINGS
AQSVZ
BAANH
CGR
CS3
CUPRZ
CUY
CVF
DU5
EBS
ECM
ED~
EIF
F5P
GGK
GNL
IH9
IHE
JG~
NPM
P2P
RNS
ROL
UI2
VF5
VG9
W1F
7X8
ABBLG
ABLBI
ID FETCH-LOGICAL-a453t-bc76e8020c5ea5e36da0742b731d85d6aa18fbf4e96b9fe507b08e1ec064d9202
IEDL.DBID 7X8
ISICitedReferencesCount 52
ISICitedReferencesURI http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=000506722100030&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
ISSN 1535-3907
IngestDate Fri Jul 11 16:55:02 EDT 2025
Thu Jan 02 22:55:35 EST 2025
IsDoiOpenAccess false
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 1
Keywords noncleavable DSS cross-linker
in situ large-scale structural biology
comparative modeling
human mitochondria
cross-linking mass spectrometry
Language English
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-a453t-bc76e8020c5ea5e36da0742b731d85d6aa18fbf4e96b9fe507b08e1ec064d9202
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 23
ORCID 0000-0003-3016-3874
0000-0001-5999-1310
0000-0002-8839-5371
OpenAccessLink https://pubmed.ncbi.nlm.nih.gov/PMC7010328
PMID 31746214
PQID 2316430278
PQPubID 23479
ParticipantIDs proquest_miscellaneous_2316430278
pubmed_primary_31746214
PublicationCentury 2000
PublicationDate 2020-01-03
PublicationDateYYYYMMDD 2020-01-03
PublicationDate_xml – month: 01
  year: 2020
  text: 2020-01-03
  day: 03
PublicationDecade 2020
PublicationPlace United States
PublicationPlace_xml – name: United States
PublicationTitle Journal of proteome research
PublicationTitleAlternate J Proteome Res
PublicationYear 2020
SSID ssj0015703
Score 2.5043745
Snippet The field of structural biology is increasingly focusing on studying proteins in situ, i.e., in their greater biological context. Cross-linking mass...
SourceID proquest
pubmed
SourceType Aggregation Database
Index Database
StartPage 327
SubjectTerms Chromatography, Gel
Cross-Linking Reagents - chemistry
Humans
K562 Cells
Mass Spectrometry - methods
Mitochondria - chemistry
Mitochondrial Proteins - analysis
Mitochondrial Proteins - chemistry
Protein Conformation
Protein Interaction Maps
Succinimides - chemistry
Workflow
Title In Situ Structural Restraints from Cross-Linking Mass Spectrometry in Human Mitochondria
URI https://www.ncbi.nlm.nih.gov/pubmed/31746214
https://www.proquest.com/docview/2316430278
Volume 19
WOSCitedRecordID wos000506722100030&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D
hasFullText
inHoldings 1
isFullTextHit
isPrint
link http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwpV1LS8QwEA7qCnrx_VhfRPCatWnTpj2JLC4K7rK4Cr2VNA9YwXa1XX-_k7RlT4LgpdBDSztMZr7JTL4PoRsuBTdGMKJU7hEGOYMIDbdh4knDTUx5YJzYBJ9M4jRNpu2GW9WOVXYx0QVqVUq7R34LOASSp-2T3S0-iVWNst3VVkJjHfUCgDJ2pIunqy6CZZdq-FJDArU9707w-PRWyGrw7qgQyg89cMSAjP6OMl22Ge3-9zv30E6LM_F94xj7aE0XB2hr2Mm7HaL0qcCzeb3EM8cga9k38IuunGREXWF77AQPbQolz428Ah4DzsZWr762FAfwEjwvsGsC4DHEBYijhQJ3PkJvo4fX4SNpZRaIYGFQk1zySMcAG2WoRaiDSAlbMOc8oCoOVSQEjU1umE6iPDEaAGTuxZpqCWhGJb7nH6ONoiz0KcKGSq48ZhSsdJZY2mGmpMkjP0-YiGXUR9ed0TL4XdubEIUul1W2MlsfnTSWzxYN30YGEIdFPmVnf3j6HG37tiJ2g2IXqGdgEetLtCm_63n1deX8A66T6fgHPtPHrg
linkProvider ProQuest
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=In+Situ+Structural+Restraints+from+Cross-Linking+Mass+Spectrometry+in+Human+Mitochondria&rft.jtitle=Journal+of+proteome+research&rft.au=Ryl%2C+Petra+S+J&rft.au=Bohlke-Schneider%2C+Michael&rft.au=Lenz%2C+Swantje&rft.au=Fischer%2C+Lutz&rft.date=2020-01-03&rft.issn=1535-3907&rft.eissn=1535-3907&rft.volume=19&rft.issue=1&rft.spage=327&rft_id=info:doi/10.1021%2Facs.jproteome.9b00541&rft.externalDBID=NO_FULL_TEXT
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1535-3907&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1535-3907&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1535-3907&client=summon