{"id":"https://openalex.org/W2000219572","doi":"https://doi.org/10.1063/1.3516589","title":"Macromolecular crowding effects on protein\u2013protein binding affinity and specificity","display_name":"Macromolecular crowding effects on protein\u2013protein binding affinity and specificity","publication_year":2010,"publication_date":"2010-11-22","ids":{"openalex":"https://openalex.org/W2000219572","doi":"https://doi.org/10.1063/1.3516589","mag":"2000219572","pmid":"https://pubmed.ncbi.nlm.nih.gov/21133453"},"language":"en","primary_location":{"id":"doi:10.1063/1.3516589","doi":"https://doi.org/10.1063/1.3516589","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.3516589","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","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/A5030859062","display_name":"Young C. Kim","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1288214837","display_name":"United States Naval Research Laboratory","ror":"https://ror.org/04d23a975","country_code":"US","type":"facility","lineage":["https://openalex.org/I1288214837","https://openalex.org/I1330347796","https://openalex.org/I175003984","https://openalex.org/I3130687028"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Young C. Kim","raw_affiliation_strings":["Naval Research Laboratory 1 Center for Computational Materials Science, , Washington, DC 20375, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Naval Research Laboratory 1 Center for Computational Materials Science, , Washington, DC 20375, USA","institution_ids":["https://openalex.org/I1288214837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059620610","display_name":"Robert B. Best","orcid":"https://orcid.org/0000-0002-7893-3543","observed_orcids":["https://orcid.org/0000-0002-7893-3543"]},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Robert B. Best","raw_affiliation_strings":["University of Cambridge 2 Department of Chemistry, , Cambridge, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Cambridge 2 Department of Chemistry, , Cambridge, United Kingdom","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088540108","display_name":"Jeetain Mittal","orcid":"https://orcid.org/0000-0002-9725-6402","observed_orcids":["https://orcid.org/0000-0002-9725-6402"]},"institutions":[{"id":"https://openalex.org/I186143895","display_name":"Lehigh University","ror":"https://ror.org/012afjb06","country_code":"US","type":"education","lineage":["https://openalex.org/I186143895"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeetain Mittal","raw_affiliation_strings":["Lehigh University 3 Department of Chemical Engineering, , Bethlehem, Pennsylvania 18015, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lehigh University 3 Department of Chemical Engineering, , Bethlehem, Pennsylvania 18015, USA","institution_ids":["https://openalex.org/I186143895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":2.7917,"has_fulltext":false,"cited_by_count":95,"citation_normalized_percentile":{"value":0.91026556,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"133","issue":"20","first_page":"205101","last_page":"205101"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9937000274658203,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9937000274658203,"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/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0017999999690800905,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.00139999995008111,"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/macromolecular-crowding","display_name":"macromolecular crowding","score":1.0},{"id":"https://openalex.org/keywords/protein-protein-binding","display_name":"protein-protein binding","score":0.9020000100135803},{"id":"https://openalex.org/keywords/binding-affinity","display_name":"binding affinity","score":0.7760000228881836},{"id":"https://openalex.org/keywords/binding-specificity","display_name":"binding specificity","score":0.9909999966621399},{"id":"https://openalex.org/keywords/protein-complex-assembly","display_name":"protein complex formation","score":0.7860000133514404},{"id":"https://openalex.org/keywords/scaled-particle-theory","display_name":"scaled particle theory","score":0.8550000190734863},{"id":"https://openalex.org/keywords/excluded-volume","display_name":"excluded volume","score":0.7160000205039978},{"id":"https://openalex.org/keywords/coarse-grained-models","display_name":"coarse-grained models","score":0.6800000071525574},{"id":"https://openalex.org/keywords/binding-free-energy","display_name":"binding free energy","score":0.7789999842643738}],"concepts":[{"id":"https://openalex.org/C181990884","wikidata":"https://www.wikidata.org/wiki/Q11396092","display_name":"Macromolecular crowding","level":3,"score":0.9429832696914673},{"id":"https://openalex.org/C149333683","wikidata":"https://www.wikidata.org/wiki/Q5189188","display_name":"Crowding","level":2,"score":0.7649558782577515},{"id":"https://openalex.org/C204389451","wikidata":"https://www.wikidata.org/wiki/Q178593","display_name":"Macromolecule","level":2,"score":0.7593652009963989},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.660986602306366},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.4566236734390259},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3853502869606018},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.32976827025413513},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.20354127883911133},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11793068051338196},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"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":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025801","descriptor_name":"Ubiquitin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1063/1.3516589","doi":"https://doi.org/10.1063/1.3516589","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.3516589","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},{"id":"pmid:21133453","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21133453","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":"The Journal of chemical physics","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W188424936","https://openalex.org/W194476900","https://openalex.org/W1572679597","https://openalex.org/W1618858311","https://openalex.org/W1967130569","https://openalex.org/W1970948529","https://openalex.org/W1975645148","https://openalex.org/W1985701335","https://openalex.org/W1988377264","https://openalex.org/W1990728218","https://openalex.org/W1990758568","https://openalex.org/W1994877064","https://openalex.org/W2012080863","https://openalex.org/W2018783142","https://openalex.org/W2024863504","https://openalex.org/W2027913596","https://openalex.org/W2032129760","https://openalex.org/W2035723991","https://openalex.org/W2037161130","https://openalex.org/W2038823703","https://openalex.org/W2049747350","https://openalex.org/W2058523300","https://openalex.org/W2060267025","https://openalex.org/W2065290987","https://openalex.org/W2066671675","https://openalex.org/W2070018773","https://openalex.org/W2078016208","https://openalex.org/W2084572582","https://openalex.org/W2085519055","https://openalex.org/W2089102241","https://openalex.org/W2089625041","https://openalex.org/W2091967731","https://openalex.org/W2095783535","https://openalex.org/W2102059060","https://openalex.org/W2107957687","https://openalex.org/W2131820445","https://openalex.org/W2150766477","https://openalex.org/W2165360511","https://openalex.org/W2171546617","https://openalex.org/W2492595718"],"related_works":["https://openalex.org/W2048126441","https://openalex.org/W2149110160","https://openalex.org/W2054686015","https://openalex.org/W2465287763","https://openalex.org/W2025763556","https://openalex.org/W2081712963","https://openalex.org/W2911705503","https://openalex.org/W2322792831","https://openalex.org/W1988097837","https://openalex.org/W4225646941"],"abstract_inverted_index":{"Macromolecular":[0],"crowding":[1,26,63,116,163,209,243],"in":[2,39,156,189,224],"cells":[3],"is":[4,30],"recognized":[5],"to":[6,57,162,231],"have":[7,245],"a":[8,53,77,121,181,190,225],"significant":[9],"impact":[10],"on":[11,27,64],"biological":[12],"function,":[13,81],"yet":[14],"quantitative":[15,122],"models":[16],"for":[17,100],"its":[18],"effects":[19,60,179,248],"are":[20,74,91,141],"relatively":[21],"undeveloped.":[22],"The":[23,178],"influence":[24],"of":[25,31,45,61,67,84,115,124,180,183,213,219,236,253],"protein-protein":[28,68],"interactions":[29,83],"particular":[32],"interest,":[33],"since":[34],"these":[35],"mediate":[36],"many":[37],"processes":[38],"the":[40,43,59,65,72,88,96,113,125,130,144,154,157,169,195,205,211,217,232,237,250],"cell,":[41],"including":[42],"self-assembly":[44],"larger":[46],"complexes,":[47,103,239],"recognition,":[48],"and":[49,82,105,134,255],"signaling.":[50],"We":[51,93,202],"use":[52],"residue-level":[54],"coarse-grained":[55],"model":[56,173,197],"investigate":[58],"macromolecular":[62,242],"assembly":[66],"complexes.":[69,257],"Interactions":[70],"between":[71],"proteins":[73,133],"treated":[75],"using":[76],"fully":[78],"transferable":[79],"energy":[80,99,160],"protein":[85,102,135,146],"residues":[86],"with":[87,198],"spherical":[89],"crowders":[90],"repulsive.":[92],"show":[94],"that":[95,153,208,241],"binding":[97,158],"free":[98,159],"two":[101],"ubiquitin/UIM1":[104],"cytochrome":[106],"c/cytochrome":[107],"c":[108],"peroxidase,":[109],"decreases":[110],"modestly":[111],"as":[112],"concentration":[114],"agents":[117],"increases.":[118],"To":[119],"obtain":[120,204],"description":[123],"stabilizing":[126],"effect,":[127],"we":[128,151],"map":[129],"aspherical":[131],"individual":[132],"complexes":[136,215,223],"onto":[137],"spheres":[138],"whose":[139],"radii":[140],"calculated":[142],"from":[143],"crowder-excluded":[145],"volumes.":[147],"With":[148],"this":[149],"correspondence,":[150],"find":[152],"change":[155],"due":[161,230],"can":[164,244],"be":[165,187],"quantitatively":[166],"described":[167],"by":[168,194],"scaled":[170],"particle":[171],"theory":[172],"without":[174],"any":[175],"fitting":[176],"parameters.":[177],"mixture":[182],"different-size":[184],"crowders-as":[185],"would":[186],"found":[188],"real":[191],"cell-are":[192],"predicted":[193],"same":[196],"an":[199],"additivity":[200],"ansatz.":[201],"also":[203],"remarkable":[206],"result":[207],"increases":[210],"fraction":[212],"specific":[214],"at":[216],"expense":[218],"nonspecific":[220,238],"transient":[221],"encounter":[222],"crowded":[226],"environment.":[227],"This":[228],"result,":[229],"greater":[233],"excluded":[234],"volume":[235],"demonstrates":[240],"subtle":[246],"functional":[247],"beyond":[249],"relative":[251],"stability":[252],"bound":[254],"unbound":[256]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":10},{"year":2012,"cited_by_count":7}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2016-06-24T00:00:00"}