{"id":"https://openalex.org/W2906224645","doi":"https://doi.org/10.1021/acs.jproteome.8b00629","title":"Photo-Cross-Linking Mass Spectrometry and Integrative Modeling Enables Rapid Screening of Antigen Interactions Involving Bacterial Transferrin Receptors","display_name":"Photo-Cross-Linking Mass Spectrometry and Integrative Modeling Enables Rapid Screening of Antigen Interactions Involving Bacterial Transferrin Receptors","publication_year":2018,"publication_date":"2018-12-24","ids":{"openalex":"https://openalex.org/W2906224645","doi":"https://doi.org/10.1021/acs.jproteome.8b00629","mag":"2906224645","pmid":"https://pubmed.ncbi.nlm.nih.gov/30582701"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jproteome.8b00629","doi":"https://doi.org/10.1021/acs.jproteome.8b00629","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.8b00629","pdf_url":null,"source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Proteome Research","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041694646","display_name":"Daniel S. Ziemianowicz","orcid":"https://orcid.org/0000-0002-6164-2723","observed_orcids":["https://orcid.org/0000-0002-6164-2723"]},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Daniel S. Ziemianowicz","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology \u00a0and\u00a0 Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology \u00a0and\u00a0 Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009078919","display_name":"Dixon Ng","orcid":"https://orcid.org/0000-0002-8615-1787","observed_orcids":["https://orcid.org/0000-0002-8615-1787"]},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Dixon Ng","raw_affiliation_strings":["Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048328229","display_name":"Anthony Bernard Schryvers","orcid":"https://orcid.org/0000-0002-4029-3296","observed_orcids":["https://orcid.org/0000-0002-4029-3296"]},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Anthony B. Schryvers","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology \u00a0and\u00a0 Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology \u00a0and\u00a0 Department of Microbiology, Immunology & Infectious Diseases, University of Calgary, Calgary, Alberta T2N 4N1, Canada","institution_ids":["https://openalex.org/I168635309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066771113","display_name":"David C. Schriemer","orcid":"https://orcid.org/0000-0002-5202-1618","observed_orcids":["https://orcid.org/0000-0002-5202-1618"]},"institutions":[{"id":"https://openalex.org/I168635309","display_name":"University of Calgary","ror":"https://ror.org/03yjb2x39","country_code":"CA","type":"education","lineage":["https://openalex.org/I168635309"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"David C. Schriemer","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology,\u00a0 Robson DNA Science Centre, Arnie Charbonneau Cancer Institute \u00a0and\u00a0 Department of Chemistry, University of Calgary, Calgary, Alberta T2N 4N1, Canada"],"raw_orcid":"https://orcid.org/0000-0002-5202-1618","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology,\u00a0 Robson DNA Science Centre, Arnie Charbonneau Cancer Institute \u00a0and\u00a0 Department of Chemistry, University of Calgary, Calgary, Alberta T2N 4N1, Canada","institution_ids":["https://openalex.org/I168635309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5066771113"],"corresponding_institution_ids":["https://openalex.org/I168635309"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":1.4029,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.78409781,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":98},"biblio":{"volume":"18","issue":"3","first_page":"934","last_page":"946"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.5259000062942505,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.5259000062942505,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.1324000060558319,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.11100000143051147,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/integrative-structural-modeling","display_name":"integrative structural modeling","score":0.8730000257492065},{"id":"https://openalex.org/keywords/vaccine-immunogens","display_name":"vaccine immunogens","score":0.5879999995231628},{"id":"https://openalex.org/keywords/transferrin-binding-protein-b","display_name":"TbpB","score":0.875},{"id":"https://openalex.org/keywords/neisseria-meningitidis","display_name":"Neisseria meningitidis","score":0.875},{"id":"https://openalex.org/keywords/transferrin-receptor","display_name":"transferrin receptor","score":0.578000009059906},{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.8450000286102295},{"id":"https://openalex.org/keywords/n-hydroxysuccinimide-ester","display_name":"N-hydroxysuccinimide ester","score":0.9409999847412109},{"id":"https://openalex.org/keywords/protein-dynamics","display_name":"protein dynamics","score":0.8220000267028809}],"concepts":[{"id":"https://openalex.org/C2780443040","wikidata":"https://www.wikidata.org/wiki/Q3737863","display_name":"Bifunctional","level":3,"score":0.6568936705589294},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6520265936851501},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.6174479722976685},{"id":"https://openalex.org/C2778458888","wikidata":"https://www.wikidata.org/wiki/Q154625","display_name":"Neisseria meningitidis","level":3,"score":0.537746012210846},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.5126997232437134},{"id":"https://openalex.org/C22814914","wikidata":"https://www.wikidata.org/wiki/Q410473","display_name":"Transferrin","level":2,"score":0.48256316781044006},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3738666772842407},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.3407471477985382},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2899254560470581},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19336891174316406},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.1657627820968628},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.15583837032318115},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1227196455001831},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.10780301690101624}],"mesh":[{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001428","descriptor_name":"Bacterial Vaccines","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D003432","descriptor_name":"Cross-Linking Reagents","qualifier_ui":"Q000528","qualifier_name":"radiation effects","is_major_topic":false},{"descriptor_ui":"D003432","descriptor_name":"Cross-Linking Reagents","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009345","descriptor_name":"Neisseria meningitidis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011990","descriptor_name":"Receptors, Transferrin","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D011990","descriptor_name":"Receptors, Transferrin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D033882","descriptor_name":"Transferrin-Binding Protein B","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D033882","descriptor_name":"Transferrin-Binding Protein B","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jproteome.8b00629","doi":"https://doi.org/10.1021/acs.jproteome.8b00629","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jproteome.8b00629","pdf_url":null,"source":{"id":"https://openalex.org/S74367812","display_name":"Journal of Proteome Research","issn_l":"1535-3893","issn":["1535-3893","1535-3907"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-d","doyens","jufo-1","ki-jl-1","medline","norway-2","poland-100","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Proteome Research","raw_type":"journal-article"},{"id":"pmid:30582701","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30582701","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of proteome research","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6240000128746033}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1722112203","display_name":"Proteomics systems for integrative structural biology","funder_award_id":"rgpin-2017-04879","funder_id":"https://openalex.org/F4320334593","funder_display_name":"Natural Sciences and Engineering Research Council of Canada"}],"funders":[{"id":"https://openalex.org/F4320324887","display_name":"Shandong Academy of Sciences","ror":"https://ror.org/04y8d6y55"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W222303975","https://openalex.org/W1803102843","https://openalex.org/W1921676712","https://openalex.org/W1969699769","https://openalex.org/W1974563432","https://openalex.org/W1978496023","https://openalex.org/W1988735506","https://openalex.org/W1989299822","https://openalex.org/W1991366673","https://openalex.org/W1996420077","https://openalex.org/W2002001977","https://openalex.org/W2003427751","https://openalex.org/W2019472143","https://openalex.org/W2020138245","https://openalex.org/W2026507477","https://openalex.org/W2029667189","https://openalex.org/W2041011334","https://openalex.org/W2042683107","https://openalex.org/W2050970529","https://openalex.org/W2051893115","https://openalex.org/W2057403366","https://openalex.org/W2059054942","https://openalex.org/W2060822374","https://openalex.org/W2061519290","https://openalex.org/W2063853836","https://openalex.org/W2068711133","https://openalex.org/W2082401784","https://openalex.org/W2085040401","https://openalex.org/W2092000181","https://openalex.org/W2092579934","https://openalex.org/W2121501020","https://openalex.org/W2123681603","https://openalex.org/W2129138058","https://openalex.org/W2132629607","https://openalex.org/W2142654956","https://openalex.org/W2155864303","https://openalex.org/W2163756713","https://openalex.org/W2169350127","https://openalex.org/W2183276865","https://openalex.org/W2213025627","https://openalex.org/W2217471163","https://openalex.org/W2232234141","https://openalex.org/W2252898419","https://openalex.org/W2311712008","https://openalex.org/W2339073492","https://openalex.org/W2438836581","https://openalex.org/W2462419944","https://openalex.org/W2489702296","https://openalex.org/W2605951889","https://openalex.org/W2742678873","https://openalex.org/W2760627581","https://openalex.org/W2765310212","https://openalex.org/W2767994714","https://openalex.org/W2768290498","https://openalex.org/W2772111793","https://openalex.org/W2772169007","https://openalex.org/W2785169804","https://openalex.org/W2786105853","https://openalex.org/W2790014471","https://openalex.org/W2790485917","https://openalex.org/W2791212680","https://openalex.org/W2807501208"],"related_works":["https://openalex.org/W4392477269","https://openalex.org/W2099175138","https://openalex.org/W7117362476","https://openalex.org/W4240744635","https://openalex.org/W4378805310","https://openalex.org/W3008586858","https://openalex.org/W2462419944","https://openalex.org/W4391932887","https://openalex.org/W3130489482","https://openalex.org/W3004808617"],"abstract_inverted_index":{"Structure-based":[0],"approaches":[1],"to":[2,17,123,125,142,189],"the":[3,49,58,89,100,109,113,117,121,126,146,176,179],"delineation":[4],"of":[5,24,40,51,99,116,128,133,148,181,184],"immunogens":[6],"for":[7,32],"vaccine":[8,60],"development":[9],"have":[10],"a":[11,30,139],"throughput":[12],"requirement":[13],"that":[14,96,106,138,164],"is":[15,46],"difficult":[16],"meet":[18],"in":[19,38,169,175],"practice":[20],"with":[21,120,156],"conventional":[22,157,165],"methods":[23],"structure":[25,36],"determination.":[26],"Here":[27],"we":[28,94,162],"present":[29],"strategy":[31],"rapid":[33],"and":[34,57,88,112,161],"accurate":[35,143],"generation":[37],"support":[39],"antigen":[41],"engineering":[42],"programs.":[43],"The":[44],"approach":[45,76],"developed":[47],"around":[48],"modeling":[50,144],"interactions":[52,102,129],"between":[53],"host":[54],"transferrin":[55,62],"(Tf)":[56],"bacterial":[59],"target":[61],"binding":[63,110],"protein":[64,192],"B":[65],"(TbpB)":[66],"from":[67,130],"Gram-negative":[68],"pathogens":[69],"such":[70],"as":[71],"Neisseria":[72],"meningitidis.":[73],"Using":[74],"an":[75,187],"based":[77],"solely":[78],"on":[79],"cross-linking":[80,170],"mass":[81],"spectrometry":[82],"(XL-MS)":[83],"data,":[84],"monomeric":[85,118],"structural":[86,196],"models,":[87],"Integrative":[90],"Modeling":[91],"Platform":[92],"(IMP),":[93],"demonstrate":[95,163],"converged":[97],"representations":[98],"Tf:TbpB":[101],"can":[103],"be":[104],"returned":[105],"accurately":[107],"reflect":[108],"interface":[111],"relative":[114],"orientation":[115],"units,":[119],"capacity":[122],"scale":[124],"analysis":[127],"any":[131],"number":[132],"additional":[134],"strains.":[135],"We":[136],"show":[137],"key":[140],"element":[141],"involves":[145],"application":[147,180],"hetero-bifunctional":[149],"cross-linkers":[150],"incorporating":[151],"fast-acting":[152],"photoactivatable":[153],"diazirines":[154],"coupled":[155],"amine-targeting":[158],"N-hydroxysuccinimide":[159],"esters,":[160],"homo-bifunctional":[166],"reagents":[167],"used":[168],"kinetically":[171],"trap":[172],"dynamic":[173],"states":[174],"ensemble.":[177],"Therefore,":[178],"both":[182],"classes":[183],"cross-linker":[185],"provides":[186],"opportunity":[188],"empirically":[190],"detect":[191],"dynamics":[193],"during":[194],"integrative":[195],"modeling.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":3}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2019-01-01T00:00:00"}