{"id":"https://openalex.org/W3000857595","doi":"https://doi.org/10.1073/pnas.1912745117","title":"Combinatorial protein\u2013protein interactions on a polymerizing scaffold","display_name":"Combinatorial protein\u2013protein interactions on a polymerizing scaffold","publication_year":2020,"publication_date":"2020-01-24","ids":{"openalex":"https://openalex.org/W3000857595","doi":"https://doi.org/10.1073/pnas.1912745117","mag":"3000857595","pmid":"https://pubmed.ncbi.nlm.nih.gov/31980533"},"language":"en","primary_location":{"id":"doi:10.1073/pnas.1912745117","doi":"https://doi.org/10.1073/pnas.1912745117","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.1912745117","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1907.11533","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065314921","display_name":"Andr\u00e9s Ortiz-Mu\u00f1oz","orcid":"https://orcid.org/0000-0003-1824-3230","observed_orcids":["https://orcid.org/0000-0003-1824-3230"]},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andr\u00e9s Ortiz-Mu\u00f1oz","raw_affiliation_strings":["Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125;","aDivision of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125"],"raw_orcid":"https://orcid.org/0000-0003-1824-3230","affiliations":[{"raw_affiliation_string":"Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125;","institution_ids":["https://openalex.org/I122411786"]},{"raw_affiliation_string":"aDivision of Biology and Bioengineering, California Institute of Technology, Pasadena, CA 91125","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064056844","display_name":"H\u00e9ctor F. Medina-Abarca","orcid":"https://orcid.org/0000-0001-5828-6492","observed_orcids":["https://orcid.org/0000-0001-5828-6492"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"H\u00e9ctor F. Medina-Abarca","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, Boston, MA 02115","bDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115"],"raw_orcid":"https://orcid.org/0000-0001-5828-6492","affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, MA 02115","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"bDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067812040","display_name":"Walter Fontana","orcid":"https://orcid.org/0000-0003-4062-9957","observed_orcids":["https://orcid.org/0000-0003-4062-9957"]},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Walter Fontana","raw_affiliation_strings":["Department of Systems Biology, Harvard Medical School, Boston, MA 02115","bDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115"],"raw_orcid":"https://orcid.org/0000-0003-4062-9957","affiliations":[{"raw_affiliation_string":"Department of Systems Biology, Harvard Medical School, Boston, MA 02115","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"bDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4222,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.52358443,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"117","issue":"6","first_page":"2930","last_page":"2937"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5077999830245972,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.5077999830245972,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.08089999854564667,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.03370000049471855,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-protein-interaction","display_name":"protein-protein interaction","score":0.722000002861023},{"id":"https://openalex.org/keywords/signalosome","display_name":"signalosome","score":0.7590000033378601},{"id":"https://openalex.org/keywords/multivalent-scaffolds","display_name":"multivalent scaffolds","score":0.7749999761581421},{"id":"https://openalex.org/keywords/ligand-binding","display_name":"ligand binding","score":0.6320000290870667},{"id":"https://openalex.org/keywords/bond-percolation","display_name":"bond percolation","score":0.7319999933242798},{"id":"https://openalex.org/keywords/finite-size-effects","display_name":"finite-size effects","score":0.6779999732971191}],"concepts":[{"id":"https://openalex.org/C89429830","wikidata":"https://www.wikidata.org/wiki/Q735710","display_name":"Scaffold","level":2,"score":0.747809886932373},{"id":"https://openalex.org/C53645450","wikidata":"https://www.wikidata.org/wiki/Q907093","display_name":"Scaffold protein","level":3,"score":0.6411705017089844},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.48143383860588074},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4263780415058136},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.4113258421421051},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29841893911361694},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2727692723274231},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.272545725107193},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10340330004692078},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.07851895689964294}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011108","descriptor_name":"Polymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011108","descriptor_name":"Polymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011108","descriptor_name":"Polymers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D058105","descriptor_name":"Polymerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058105","descriptor_name":"Polymerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058105","descriptor_name":"Polymerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1073/pnas.1912745117","doi":"https://doi.org/10.1073/pnas.1912745117","is_oa":false,"landing_page_url":"https://doi.org/10.1073/pnas.1912745117","pdf_url":null,"source":{"id":"https://openalex.org/S125754415","display_name":"Proceedings of the National Academy of Sciences","issn_l":"0027-8424","issn":["0027-8424","1091-6490"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","doyens","erih-plus","jufo-3","ki-jl-3","medline","norway-2"],"host_organization":"https://openalex.org/P4310320052","host_organization_name":"National Academy of Sciences","host_organization_lineage":["https://openalex.org/P4310320052"],"host_organization_lineage_names":["National Academy of Sciences"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the National Academy of Sciences","raw_type":"journal-article"},{"id":"pmid:31980533","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31980533","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":"Proceedings of the National Academy of Sciences of the United States of America","raw_type":"Journal Article"},{"id":"pmh:oai:arXiv.org:1907.11533","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1907.11533","pdf_url":"https://arxiv.org/pdf/1907.11533","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7022191","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7022191","pdf_url":null,"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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Proc Natl Acad Sci U S A","raw_type":"Text"},{"id":"pmh:oai:authors.library.caltech.edu:100899","doi":null,"is_oa":false,"landing_page_url":"http://resolver.caltech.edu/CaltechAUTHORS:20200124-130052745","pdf_url":null,"source":{"id":"https://openalex.org/S4306402161","display_name":"CaltechAUTHORS (California Institute of Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I122411786","host_organization_name":"California Institute of Technology","host_organization_lineage":["https://openalex.org/I122411786"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"doi:10.48550/arxiv.1907.11533","doi":"https://doi.org/10.48550/arxiv.1907.11533","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1907.11533","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1907.11533","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/1907.11533","pdf_url":"https://arxiv.org/pdf/1907.11533","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W186403072","https://openalex.org/W1544046482","https://openalex.org/W1973300115","https://openalex.org/W1984723872","https://openalex.org/W2005524843","https://openalex.org/W2006466539","https://openalex.org/W2031714747","https://openalex.org/W2031809122","https://openalex.org/W2040942754","https://openalex.org/W2054352933","https://openalex.org/W2059039605","https://openalex.org/W2085978470","https://openalex.org/W2096248361","https://openalex.org/W2102424174","https://openalex.org/W2118344768","https://openalex.org/W2132475598","https://openalex.org/W2152854378","https://openalex.org/W2159629828","https://openalex.org/W2170899721","https://openalex.org/W2403526287","https://openalex.org/W2794654572","https://openalex.org/W2807744179","https://openalex.org/W4251381517"],"related_works":["https://openalex.org/W2002269843","https://openalex.org/W2264903906","https://openalex.org/W2017334119","https://openalex.org/W4283702325","https://openalex.org/W2081717811","https://openalex.org/W1973300115","https://openalex.org/W2558479656","https://openalex.org/W3023294154","https://openalex.org/W2883694650","https://openalex.org/W141012896"],"abstract_inverted_index":{"Scaffold":[0],"proteins":[1],"organize":[2],"cellular":[3],"processes":[4],"by":[5,12,131,144],"bringing":[6],"signaling":[7],"molecules":[8],"into":[9],"interaction,":[10],"sometimes":[11],"forming":[13],"large":[14],"signalosomes.":[15],"Several":[16],"of":[17,43,65,70,75,122,154,189,194,225],"these":[18],"scaffolds":[19,61],"are":[20,91],"known":[21,92],"to":[22,93,102,135,199,211,231],"polymerize.":[23],"Their":[24],"assemblies":[25],"should":[26],"therefore":[27],"not":[28],"be":[29,212,218],"understood":[30],"as":[31,35,106],"stoichiometric":[32],"aggregates,":[33],"but":[34,214],"combinatorial":[36,41],"ensembles.":[37],"We":[38,183],"analyze":[39],"the":[40,73,120,145,161,173,191,195,215],"interaction":[42,77,99],"ligands":[44,107],"loaded":[45],"on":[46,110,124,237],"polymeric":[47],"scaffolds,":[48],"in":[49,118,167,175,187,201,234],"both":[50],"a":[51,82,132,136,141,226,238],"continuum":[52],"and":[53,56,100,204],"discrete":[54,207],"setting,":[55],"compare":[57],"it":[58],"with":[59,62,171],"multivalent":[60,156,181],"fixed":[63],"number":[64],"binding":[66],"sites.":[67],"The":[68,113,206],"quantity":[69],"interest":[71],"is":[72,164],"abundance":[74],"ligand":[76,98],"possibilities-the":[78],"catalytic":[79],"potential":[80],"Q-in":[81],"configurational":[83],"mixture.":[84],"Upon":[85],"increasing":[86],"scaffold":[87,157],"abundance,":[88],"scaffolding":[89],"systems":[90],"first":[94,133],"increase":[95],"opportunities":[96],"for":[97,179],"then":[101],"shut":[103],"them":[104],"down":[105],"become":[108],"isolated":[109],"distinct":[111],"scaffolds.":[112],"polymerizing":[114],"system":[115],"stands":[116],"out":[117,210],"that":[119,153,168],"dependency":[121],"Q":[123,151,169],"protomer":[125,176,202,222],"concentration":[126,177,192,203],"switches":[127],"from":[128],"being":[129],"dominated":[130],"order":[134,138],"second":[137],"term":[139],"within":[140],"range":[142],"determined":[143],"polymerization":[146],"affinity.":[147,205],"This":[148],"behavior":[149,186,216],"boosts":[150],"beyond":[152],"any":[155,180],"system.":[158],"In":[159],"addition,":[160],"subsequent":[162],"drop-off":[163],"considerably":[165],"mitigated":[166],"decreases":[170],"half":[172],"power":[174],"than":[178],"scaffold.":[182],"explain":[184],"this":[185],"terms":[188],"how":[190],"profile":[193],"polymer-length":[196],"distribution":[197],"adjusts":[198],"changes":[200],"case":[208],"turns":[209],"similar,":[213],"can":[217],"exaggerated":[219],"at":[220],"small":[221],"numbers":[223],"because":[224],"maximal":[227],"polymer":[228],"size,":[229],"analogous":[230],"finite-size":[232],"effects":[233],"bond":[235],"percolation":[236],"lattice.":[239]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-10-01T08:54:57.152042","created_date":"2025-10-10T00:00:00"}