{"id":"https://openalex.org/W4390610848","doi":"https://doi.org/10.3389/fbinf.2023.1321287","title":"Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches","display_name":"Protein-lipid interactions and protein anchoring modulate the modes of association of the globular domain of the Prion protein and Doppel protein to model membrane patches","publication_year":2024,"publication_date":"2024-01-05","ids":{"openalex":"https://openalex.org/W4390610848","doi":"https://doi.org/10.3389/fbinf.2023.1321287","pmid":"https://pubmed.ncbi.nlm.nih.gov/38250434"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2023.1321287","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1321287","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1321287/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1321287/pdf?isPublishedV2=False","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011243479","display_name":"Patricia Soto","orcid":"https://orcid.org/0000-0002-3255-9226"},"institutions":[{"id":"https://openalex.org/I114493937","display_name":"Creighton University","ror":"https://ror.org/05wf30g94","country_code":"US","type":"education","lineage":["https://openalex.org/I114493937"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Patricia Soto","raw_affiliation_strings":["Department of Physics, Creighton University, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Creighton University, Omaha, NE, United States","institution_ids":["https://openalex.org/I114493937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045722111","display_name":"Davis T. Thalhuber","orcid":null},"institutions":[{"id":"https://openalex.org/I114493937","display_name":"Creighton University","ror":"https://ror.org/05wf30g94","country_code":"US","type":"education","lineage":["https://openalex.org/I114493937"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Davis T. Thalhuber","raw_affiliation_strings":["Department of Physics, Creighton University, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Creighton University, Omaha, NE, United States","institution_ids":["https://openalex.org/I114493937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038397659","display_name":"Frank Luceri","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Frank Luceri","raw_affiliation_strings":["Omaha Central High School, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Omaha Central High School, Omaha, NE, United States","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093658051","display_name":"Jamie Janos","orcid":null},"institutions":[{"id":"https://openalex.org/I114493937","display_name":"Creighton University","ror":"https://ror.org/05wf30g94","country_code":"US","type":"education","lineage":["https://openalex.org/I114493937"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jamie Janos","raw_affiliation_strings":["Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, United States","institution_ids":["https://openalex.org/I114493937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093658052","display_name":"Mason R. Borgman","orcid":null},"institutions":[{"id":"https://openalex.org/I114493937","display_name":"Creighton University","ror":"https://ror.org/05wf30g94","country_code":"US","type":"education","lineage":["https://openalex.org/I114493937"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mason R. Borgman","raw_affiliation_strings":["Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, United States","institution_ids":["https://openalex.org/I114493937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022344060","display_name":"Noah M. Greenwood","orcid":null},"institutions":[{"id":"https://openalex.org/I114493937","display_name":"Creighton University","ror":"https://ror.org/05wf30g94","country_code":"US","type":"education","lineage":["https://openalex.org/I114493937"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Noah M. Greenwood","raw_affiliation_strings":["Department of Physics, Creighton University, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Creighton University, Omaha, NE, United States","institution_ids":["https://openalex.org/I114493937"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104294955","display_name":"Sofia A. Acosta","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sofia Acosta","raw_affiliation_strings":["Omaha North High School, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Omaha North High School, Omaha, NE, United States","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5093658053","display_name":"Hunter Stoffel","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hunter Stoffel","raw_affiliation_strings":["Omaha Central High School, Omaha, NE, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Omaha Central High School, Omaha, NE, United States","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5011243479"],"corresponding_institution_ids":["https://openalex.org/I114493937"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00245141,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"3","issue":null,"first_page":"1321287","last_page":"1321287"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11335","display_name":"Prion Diseases and Protein Misfolding","score":1.0,"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"}},"topics":[{"id":"https://openalex.org/T11335","display_name":"Prion Diseases and Protein Misfolding","score":1.0,"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/T12494","display_name":"Alcoholism and Thiamine Deficiency","score":0.965499997138977,"subfield":{"id":"https://openalex.org/subfields/2728","display_name":"Neurology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T13201","display_name":"Infectious Encephalopathies and Encephalitis","score":0.9495000243186951,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.5806216597557068},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5085598230361938},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.5060505270957947},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.46100446581840515},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.44976526498794556},{"id":"https://openalex.org/keywords/plasma-protein-binding","display_name":"Plasma protein binding","score":0.4317893981933594},{"id":"https://openalex.org/keywords/protein-aggregation","display_name":"Protein aggregation","score":0.4287640154361725},{"id":"https://openalex.org/keywords/globular-protein","display_name":"Globular protein","score":0.4262691140174866},{"id":"https://openalex.org/keywords/protein-folding","display_name":"Protein folding","score":0.41263115406036377},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.41043755412101746},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.37226226925849915},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08688071370124817}],"concepts":[{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5806216597557068},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5085598230361938},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.5060505270957947},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.46100446581840515},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.44976526498794556},{"id":"https://openalex.org/C51639874","wikidata":"https://www.wikidata.org/wiki/Q167149","display_name":"Plasma protein binding","level":2,"score":0.4317893981933594},{"id":"https://openalex.org/C136238340","wikidata":"https://www.wikidata.org/wiki/Q7251455","display_name":"Protein aggregation","level":2,"score":0.4287640154361725},{"id":"https://openalex.org/C105168689","wikidata":"https://www.wikidata.org/wiki/Q901969","display_name":"Globular protein","level":2,"score":0.4262691140174866},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.41263115406036377},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.41043755412101746},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.37226226925849915},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08688071370124817}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2023.1321287","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1321287","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1321287/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38250434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38250434","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,"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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10796588","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10796588","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10796588/pdf/fbinf-03-1321287.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ecd404949b99405b86c0e805d6c1e5a4","is_oa":true,"landing_page_url":"https://doaj.org/article/ecd404949b99405b86c0e805d6c1e5a4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 3 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2023.1321287","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2023.1321287","pdf_url":"https://www.frontiersin.org/articles/10.3389/fbinf.2023.1321287/pdf?isPublishedV2=False","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4029151897","display_name":null,"funder_award_id":"P20 GM103427","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390610848.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W153576789","https://openalex.org/W566943510","https://openalex.org/W751085324","https://openalex.org/W1031578623","https://openalex.org/W1981021420","https://openalex.org/W1993986579","https://openalex.org/W2010745676","https://openalex.org/W2013679718","https://openalex.org/W2015329538","https://openalex.org/W2021520922","https://openalex.org/W2027154929","https://openalex.org/W2033933409","https://openalex.org/W2039955490","https://openalex.org/W2049286183","https://openalex.org/W2051864856","https://openalex.org/W2055334423","https://openalex.org/W2057477511","https://openalex.org/W2057933908","https://openalex.org/W2067540111","https://openalex.org/W2073765675","https://openalex.org/W2079435449","https://openalex.org/W2081693079","https://openalex.org/W2087357689","https://openalex.org/W2089681824","https://openalex.org/W2093522910","https://openalex.org/W2109424660","https://openalex.org/W2132262459","https://openalex.org/W2138390885","https://openalex.org/W2149761516","https://openalex.org/W2156182155","https://openalex.org/W2158707059","https://openalex.org/W2170711116","https://openalex.org/W2179698526","https://openalex.org/W2206954826","https://openalex.org/W2314292783","https://openalex.org/W2510475640","https://openalex.org/W2594343114","https://openalex.org/W2768939906","https://openalex.org/W2953033343","https://openalex.org/W2998545657","https://openalex.org/W3082532197","https://openalex.org/W3195777757","https://openalex.org/W4285394907","https://openalex.org/W4294917792","https://openalex.org/W4315471476","https://openalex.org/W4323653682","https://openalex.org/W6725805892"],"related_works":["https://openalex.org/W1912080976","https://openalex.org/W4386593040","https://openalex.org/W2042654184","https://openalex.org/W2082683692","https://openalex.org/W2030522958","https://openalex.org/W2008494223","https://openalex.org/W2035672439","https://openalex.org/W1548342541","https://openalex.org/W2148042988","https://openalex.org/W2055629216"],"abstract_inverted_index":{"The":[0,16,36,167],"Prion":[1,28,38,60,80,110,126],"protein":[2,29,39,61,81,111,127,161,169,250,281,292],"is":[3,118,170,207],"the":[4,8,21,27,45,49,64,69,89,100,107,140,143,159,171,174,203,239,275,285],"molecular":[5,135],"hallmark":[6],"of":[7,26,48,92,99,109,125,146,189],"incurable":[9],"prion":[10,249,258],"diseases":[11],"affecting":[12],"mammals,":[13],"including":[14],"humans.":[15],"protein-only":[17],"hypothesis":[18],"states":[19],"that":[20,79,105,138,188,214,274],"misfolding,":[22,82],"accumulation,":[23],"and":[24,52,55,74,84,95,193,218,257,264],"deposition":[25],"play":[30],"a":[31,122,195,289],"critical":[32,254],"role":[33],"in":[34,75,115,173,182,230,236,244,255,265,284],"toxicity.":[35],"cellular":[37],"(PrP":[40],"C":[41,148,179,191,200,233,246],")":[42],"anchors":[43],"to":[44,88,120,150,163,177,187,198,248,279,291],"extracellular":[46,184],"leaflet":[47],"plasma":[50,93],"membrane":[51,57,152,165,276,286],"prefers":[53],"cholesterol-":[54],"sphingomyelin-rich":[56],"domains.":[58],"Conformational":[59],"conversion":[62],"into":[63],"pathological":[65],"isoform":[66],"happens":[67],"on":[68],"cell":[70],"surface.":[71],"In":[72,154],"vitro":[73],"vivo":[76],"experiments":[77],"indicate":[78],"aggregation,":[83],"toxicity":[85],"are":[86,253],"sensitive":[87],"lipid":[90,113],"composition":[91],"membranes":[94],"vesicles.":[96],"A":[97],"picture":[98],"underlying":[101],"biophysical":[102],"driving":[103],"forces":[104],"explain":[106],"effect":[108],"-":[112],"interactions":[114,141,217],"physiological":[116],"conditions":[117],"needed":[119],"develop":[121],"structural":[123],"model":[124,151],"conformational":[128,219],"conversion.":[129],"To":[130],"this":[131],"end,":[132],"we":[133,156,242],"use":[134],"dynamics":[136],"simulations":[137,212],"mimic":[139],"between":[142],"globular":[144,231],"domain":[145],"PrP":[147,178,190,199,232,245],"anchored":[149,162],"patches.":[153,166],"addition,":[155],"also":[157,272],"simulate":[158],"Doppel":[160,168],"such":[164],"closest":[172],"phylogenetic":[175],"tree":[176],",":[180,192],"localizes":[181],"an":[183],"milieu":[185],"similar":[186,196],"exhibits":[194],"topology":[197],"even":[201],"if":[202],"amino":[204],"acid":[205],"sequence":[206],"only":[208],"25%":[209],"identical.":[210],"Our":[211],"show":[213],"specific":[215,227],"protein-lipid":[216],"constraints":[220],"imposed":[221],"by":[222],"GPI":[223],"anchoring":[224],"together":[225],"favor":[226],"binding":[228,240],"sites":[229,241],"but":[234],"not":[235],"Doppel.":[237],"Interestingly,":[238],"found":[243,273],"correspond":[247],"loops,":[251],"which":[252],"aggregation":[256],"disease":[259],"transmission":[260],"barrier":[261],"(\u03b22-\u03b12":[262],"loop)":[263],"initial":[266],"spontaneous":[267],"misfolding":[268],"(\u03b12-\u03b13":[269],"loop).":[270],"We":[271],"re-arranges":[277],"locally":[278],"accommodate":[280],"residues":[282],"inserted":[283],"surface":[287],"as":[288],"response":[290],"binding.":[293]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
