{"id":"https://openalex.org/W4390787837","doi":"https://doi.org/10.1021/acs.jcim.3c01412","title":"Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics","display_name":"Allosteric Activation of RhoA Complexed with p115-RhoGEF Deciphered by Conformational Dynamics","publication_year":2024,"publication_date":"2024-01-12","ids":{"openalex":"https://openalex.org/W4390787837","doi":"https://doi.org/10.1021/acs.jcim.3c01412","pmid":"https://pubmed.ncbi.nlm.nih.gov/38215280"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01412","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01412","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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 Chemical Information and Modeling","raw_type":"journal-article"},"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/A5053405483","display_name":"Nurit Haspel","orcid":"https://orcid.org/0000-0003-4810-379X"},"institutions":[{"id":"https://openalex.org/I33434090","display_name":"University of Massachusetts Boston","ror":"https://ror.org/04ydmy275","country_code":"US","type":"education","lineage":["https://openalex.org/I33434090"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nurit Haspel","raw_affiliation_strings":["Department of Computer Science, University of Massachusetts Boston, Boston, Massachusetts 02125, United States"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Massachusetts Boston, Boston, Massachusetts 02125, United States","institution_ids":["https://openalex.org/I33434090"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071084031","display_name":"Hyunbum Jang","orcid":"https://orcid.org/0000-0001-9402-4051"},"institutions":[{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hyunbum Jang","raw_affiliation_strings":["Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025357844","display_name":"Ruth Nussinov","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]},{"id":"https://openalex.org/I4210130649","display_name":"Frederick National Laboratory for Cancer Research","ror":"https://ror.org/03v6m3209","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"id":"https://openalex.org/I4210140884","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210140884"]}],"countries":["IL","US"],"is_corresponding":true,"raw_author_name":"Ruth Nussinov","raw_affiliation_strings":["Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States","Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel"],"affiliations":[{"raw_affiliation_string":"Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland 21702, United States","institution_ids":["https://openalex.org/I4210130649","https://openalex.org/I4210140884"]},{"raw_affiliation_string":"Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5025357844"],"corresponding_institution_ids":["https://openalex.org/I16391192","https://openalex.org/I4210130649","https://openalex.org/I4210140884"],"apc_list":null,"apc_paid":null,"fwci":1.6375,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.82131586,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"64","issue":"3","first_page":"862","last_page":"873"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10169","display_name":"Protein Kinase Regulation and GTPase Signaling","score":0.9998999834060669,"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/T10169","display_name":"Protein Kinase Regulation and GTPase Signaling","score":0.9998999834060669,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9947999715805054,"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/T11503","display_name":"Cytokine Signaling Pathways and Interactions","score":0.9936000108718872,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/rhoa","display_name":"RHOA","score":0.9877759218215942},{"id":"https://openalex.org/keywords/allosteric-regulation","display_name":"Allosteric regulation","score":0.7937014102935791},{"id":"https://openalex.org/keywords/gtp","display_name":"GTP'","score":0.7362702488899231},{"id":"https://openalex.org/keywords/guanine-nucleotide-exchange-factor","display_name":"Guanine nucleotide exchange factor","score":0.7035422921180725},{"id":"https://openalex.org/keywords/pleckstrin-homology-domain","display_name":"Pleckstrin homology domain","score":0.6667029857635498},{"id":"https://openalex.org/keywords/gtpase","display_name":"GTPase","score":0.5180228352546692},{"id":"https://openalex.org/keywords/small-gtpase","display_name":"Small GTPase","score":0.4316955506801605},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4092046618461609},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.38571038842201233},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35196858644485474},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.32086265087127686},{"id":"https://openalex.org/keywords/signal-transduction","display_name":"Signal transduction","score":0.29813265800476074},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.2884982228279114},{"id":"https://openalex.org/keywords/receptor","display_name":"Receptor","score":0.18341872096061707},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.07018202543258667}],"concepts":[{"id":"https://openalex.org/C2777093181","wikidata":"https://www.wikidata.org/wiki/Q15331450","display_name":"RHOA","level":3,"score":0.9877759218215942},{"id":"https://openalex.org/C166342909","wikidata":"https://www.wikidata.org/wiki/Q845326","display_name":"Allosteric regulation","level":3,"score":0.7937014102935791},{"id":"https://openalex.org/C118716","wikidata":"https://www.wikidata.org/wiki/Q5514725","display_name":"GTP'","level":3,"score":0.7362702488899231},{"id":"https://openalex.org/C126619667","wikidata":"https://www.wikidata.org/wiki/Q901088","display_name":"Guanine nucleotide exchange factor","level":3,"score":0.7035422921180725},{"id":"https://openalex.org/C49658373","wikidata":"https://www.wikidata.org/wiki/Q24776397","display_name":"Pleckstrin homology domain","level":3,"score":0.6667029857635498},{"id":"https://openalex.org/C207332259","wikidata":"https://www.wikidata.org/wiki/Q769143","display_name":"GTPase","level":2,"score":0.5180228352546692},{"id":"https://openalex.org/C2780298669","wikidata":"https://www.wikidata.org/wiki/Q415071","display_name":"Small GTPase","level":3,"score":0.4316955506801605},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4092046618461609},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.38571038842201233},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35196858644485474},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.32086265087127686},{"id":"https://openalex.org/C62478195","wikidata":"https://www.wikidata.org/wiki/Q828130","display_name":"Signal transduction","level":2,"score":0.29813265800476074},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.2884982228279114},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.18341872096061707},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.07018202543258667}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000494","descriptor_name":"Allosteric Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006160","descriptor_name":"Guanosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006160","descriptor_name":"Guanosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006160","descriptor_name":"Guanosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006160","descriptor_name":"Guanosine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064067","descriptor_name":"Rho Guanine Nucleotide Exchange Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064067","descriptor_name":"Rho Guanine Nucleotide Exchange Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064067","descriptor_name":"Rho Guanine Nucleotide Exchange Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064067","descriptor_name":"Rho Guanine Nucleotide Exchange Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.3c01412","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01412","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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 Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:38215280","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38215280","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Decent work and economic growth","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/8"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":73,"referenced_works":["https://openalex.org/W1208028934","https://openalex.org/W1879186301","https://openalex.org/W1910650341","https://openalex.org/W1975982215","https://openalex.org/W1984939079","https://openalex.org/W1992247495","https://openalex.org/W1998388607","https://openalex.org/W2007263897","https://openalex.org/W2012585995","https://openalex.org/W2029667189","https://openalex.org/W2041164953","https://openalex.org/W2046697062","https://openalex.org/W2068093278","https://openalex.org/W2073839370","https://openalex.org/W2085013781","https://openalex.org/W2096791952","https://openalex.org/W2102503844","https://openalex.org/W2123681603","https://openalex.org/W2132629607","https://openalex.org/W2146702714","https://openalex.org/W2150981663","https://openalex.org/W2162166182","https://openalex.org/W2162258785","https://openalex.org/W2180378334","https://openalex.org/W2187262623","https://openalex.org/W2188225742","https://openalex.org/W2260312731","https://openalex.org/W2278220345","https://openalex.org/W2282990014","https://openalex.org/W2316424881","https://openalex.org/W2328575291","https://openalex.org/W2334993556","https://openalex.org/W2464027273","https://openalex.org/W2500974730","https://openalex.org/W2520842278","https://openalex.org/W2731370178","https://openalex.org/W2743283968","https://openalex.org/W2770830320","https://openalex.org/W2780971412","https://openalex.org/W2802589812","https://openalex.org/W2807373400","https://openalex.org/W2807492413","https://openalex.org/W2883893863","https://openalex.org/W2936075892","https://openalex.org/W2972027434","https://openalex.org/W2999339913","https://openalex.org/W3006316865","https://openalex.org/W3012860965","https://openalex.org/W3014561685","https://openalex.org/W3016130545","https://openalex.org/W3092350202","https://openalex.org/W3115944789","https://openalex.org/W3125994377","https://openalex.org/W3136216847","https://openalex.org/W3162931282","https://openalex.org/W3183200082","https://openalex.org/W3200317384","https://openalex.org/W3216374661","https://openalex.org/W4206498754","https://openalex.org/W4225258118","https://openalex.org/W4281707651","https://openalex.org/W4281972407","https://openalex.org/W4291397588","https://openalex.org/W4302304614","https://openalex.org/W4309947189","https://openalex.org/W4362584538","https://openalex.org/W4379618742","https://openalex.org/W4381192933","https://openalex.org/W4382502697","https://openalex.org/W4383070555","https://openalex.org/W4383818900","https://openalex.org/W4385477092","https://openalex.org/W4385878004"],"related_works":["https://openalex.org/W2119264345","https://openalex.org/W2107411730","https://openalex.org/W2134699117","https://openalex.org/W2752164686","https://openalex.org/W2089809507","https://openalex.org/W2053960871","https://openalex.org/W2770830320","https://openalex.org/W2134092694","https://openalex.org/W2132021216","https://openalex.org/W2139849649"],"abstract_inverted_index":{"The":[0],"Ras":[1,18],"homologue":[2],"family":[3],"member":[4,9],"A":[5],"(RhoA)":[6],"is":[7,112,145,230],"a":[8,14],"of":[10,16,51,66,91,96,134,167,208,222],"the":[11,17,23,52,64,70,82,86,94,102,109,118,132,135,138,142,151,165,191,194,198,209,217,220,223,227,235],"Rho":[12,210],"family,":[13],"subgroup":[15],"superfamily.":[19,211],"RhoA":[20,67,185],"interacts":[21],"with":[22,37,101,117,226],"115":[24],"kDa":[25],"guanine":[26],"nucleotide":[27],"exchange":[28],"factor":[29],"(p115-RhoGEF),":[30],"which":[31],"assists":[32],"in":[33,114,184,216],"activation":[34,68,186,218],"and":[35,47,55,141,161,170,189,197],"binding":[36],"downstream":[38,244],"effectors.":[39,245],"Here,":[40],"we":[41,213],"use":[42],"molecular":[43],"dynamics":[44,49],"(MD)":[45],"simulations":[46,163],"essential":[48],"analysis":[50],"inactive":[53,76],"RhoA-GDP":[54,77],"active":[56,110,139,195],"RhoA-GTP,":[57],"when":[58],"bound":[59],"to":[60,62,127,146,177,187,231,243],"p115-RhoGEF":[61,92,119],"decipher":[63],"mechanism":[65],"at":[69],"structural":[71,172],"level.":[72],"We":[73,105,129],"observe":[74],"that":[75,108,131,181,215],"maintains":[78],"its":[79,97],"position":[80],"near":[81],"catalytic":[83],"site":[84],"on":[85],"Dbl":[87],"homology":[88,122],"(DH)":[89],"domain":[90,124,144,153,229,237],"through":[93],"interaction":[95,192,225],"Switch":[98],"I":[99],"region":[100],"DH":[103,152,236],"domain.":[104,200],"further":[106],"show":[107],"RhoA-GTP":[111,140,196,224,233],"engaged":[113],"more":[115],"interactions":[116,136],"membrane-bound":[120],"Pleckstrin":[121],"(PH)":[123],"as":[125],"compared":[126],"RhoA-GDP.":[128],"hypothesize":[130],"role":[133,221],"between":[137,193],"PH":[143,199,228],"help":[147],"release":[148,232],"it":[149,241],"from":[150,234],"upon":[154],"activation.":[155],"Our":[156],"results":[157],"support":[158],"this":[159,168],"premise,":[160],"our":[162],"uncover":[164],"beginning":[166],"process":[169],"provide":[171],"details.":[173],"They":[174],"also":[175,203],"point":[176],"allosteric":[178],"communication":[179],"pathways":[180],"take":[182],"part":[183],"promote":[188],"strengthen":[190],"Allosteric":[201],"regulation":[202],"occurs":[204],"among":[205],"other":[206],"members":[207],"Collectively,":[212],"suggest":[214],"process,":[219],"after":[238],"activation,":[239],"making":[240],"available":[242]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}