{"id":"https://openalex.org/W4410061479","doi":"https://doi.org/10.1101/2025.05.02.651724","title":"Characterization of a potential antibiotic target site on the ribosome","display_name":"Characterization of a potential antibiotic target site on the ribosome","publication_year":2025,"publication_date":"2025-05-02","ids":{"openalex":"https://openalex.org/W4410061479","doi":"https://doi.org/10.1101/2025.05.02.651724","pmid":"https://pubmed.ncbi.nlm.nih.gov/40654926","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12247951"},"language":"en","primary_location":{"id":"doi:10.1101/2025.05.02.651724","doi":"https://doi.org/10.1101/2025.05.02.651724","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.05.02.651724","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/02/2025.05.02.651724.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/02/2025.05.02.651724.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5117424539","display_name":"Michael Golstein","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Golstein","raw_affiliation_strings":["Boston College;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston College;","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100322464","display_name":"Yang Wang","orcid":"https://orcid.org/0000-0001-5890-7287","observed_orcids":["https://orcid.org/0000-0001-5890-7287"]},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Wang","raw_affiliation_strings":["Boston College;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston College;","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050733346","display_name":"Sandra Byju","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandra Byju","raw_affiliation_strings":["Northeastern University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northeastern University","institution_ids":["https://openalex.org/I12912129"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045188605","display_name":"Udayan Mohanty","orcid":"https://orcid.org/0000-0002-8778-974X","observed_orcids":["https://orcid.org/0000-0002-8778-974X"]},"institutions":[{"id":"https://openalex.org/I103531236","display_name":"Boston College","ror":"https://ror.org/02n2fzt79","country_code":"US","type":"education","lineage":["https://openalex.org/I103531236"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Udayan Mohanty","raw_affiliation_strings":["Boston College;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston College;","institution_ids":["https://openalex.org/I103531236"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5049076496","display_name":"Paul C. Whitford","orcid":"https://orcid.org/0000-0001-7104-2265","observed_orcids":["https://orcid.org/0000-0001-7104-2265"]},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Paul Charles Whitford","raw_affiliation_strings":["Northeastern University"],"raw_orcid":"https://orcid.org/0000-0001-7104-2265","affiliations":[{"raw_affiliation_string":"Northeastern University","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5049076496"],"corresponding_institution_ids":["https://openalex.org/I12912129"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T11482","display_name":"RNA modifications and cancer","score":0.0,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/ribosome","display_name":"ribosome","score":0.777999997138977},{"id":"https://openalex.org/keywords/antibiotic-targets","display_name":"antibiotic targets","score":0.7229999899864197},{"id":"https://openalex.org/keywords/small-molecule-binding-sites","display_name":"small molecule binding sites","score":0.7149999737739563},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.6380000114440918},{"id":"https://openalex.org/keywords/computational-screening","display_name":"computational screening","score":0.6679999828338623},{"id":"https://openalex.org/keywords/broad-spectrum-antibiotics","display_name":"broad-spectrum antibiotics","score":0.8849999904632568},{"id":"https://openalex.org/keywords/antimicrobial-drug-design","display_name":"antimicrobial drug design","score":0.7620000243186951},{"id":"https://openalex.org/keywords/mitochondrial-ribosome","display_name":"mitochondrial ribosome","score":0.828000009059906}],"concepts":[{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.7273253202438354},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6623013615608215},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.519649863243103},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46560150384902954},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.46540147066116333},{"id":"https://openalex.org/C161624437","wikidata":"https://www.wikidata.org/wiki/Q1988322","display_name":"Small molecule","level":2,"score":0.4507938027381897},{"id":"https://openalex.org/C77430603","wikidata":"https://www.wikidata.org/wiki/Q166992","display_name":"Internal ribosome entry site","level":5,"score":0.41764581203460693},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24068033695220947},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.16763758659362793},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.08541002869606018},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1101/2025.05.02.651724","doi":"https://doi.org/10.1101/2025.05.02.651724","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.05.02.651724","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/02/2025.05.02.651724.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:40654926","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40654926","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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12247951","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12247951","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":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1101/2025.05.02.651724","doi":"https://doi.org/10.1101/2025.05.02.651724","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2025.05.02.651724","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2025/05/02/2025.05.02.651724.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1660942031","display_name":"Quantifying the effects of ions and collective rearrangements during ribosome function","funder_award_id":"1915843","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6001776492","display_name":"Center for Theoretical Biological Physics","funder_award_id":"2019745","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6356480378","display_name":"Elucidating the mechanisms that enable translation in bacterial and eukaryotic ribosomes","funder_award_id":"1r35gm153502-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410061479.pdf","grobid_xml":"https://content.openalex.org/works/W4410061479.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3215899105","https://openalex.org/W2096307300","https://openalex.org/W2152341456","https://openalex.org/W2324009933","https://openalex.org/W2040579080","https://openalex.org/W1484216450","https://openalex.org/W2523243310","https://openalex.org/W4404845984","https://openalex.org/W2125777370","https://openalex.org/W2008931123"],"abstract_inverted_index":{"The":[0],"ribosome":[1,146],"is":[2,91,139],"a":[3,49,56,73,88,106,149,163,191],"known":[4],"antibiotic":[5,168],"target,":[6],"where":[7],"various":[8],"classes":[9],"of":[10,16,22,33,51,131,184,194],"small":[11,61,78],"molecules":[12,62,79,133],"impact":[13],"different":[14],"stages":[15],"translation.":[17],"There":[18],"are":[19],"multiple":[20],"modes":[21],"function,":[23],"such":[24],"as":[25,162],"interfering":[26],"with":[27],"the":[28,34,40,44,67,83,99,111,129,135,143,153,181],"decoding":[29],"process,":[30],"impeding":[31],"movement":[32],"nascent":[35],"protein":[36,85],"chain":[37],"and":[38,147,169],"occluding":[39],"catalytic":[41],"center.":[42],"In":[43,97],"present":[45,141],"study,":[46],"we":[47,71,120],"used":[48],"range":[50],"computational":[52,74],"methods":[53],"to":[54,76,104,124,179,189],"demonstrate":[55],"new":[57,192],"mechanism":[58],"by":[59],"which":[60],"may":[63,160],"impede":[64],"translation":[65],"in":[66,87,94,142,152,187],"bacterial":[68,95],"ribosome.":[69,136],"Specifically,":[70],"use":[72],"screen":[75],"identify":[77],"that":[80,90,109],"can":[81,126],"bind":[82],"ribosomal":[84],"L33":[86,125,138],"region":[89],"generally":[92],"conserved":[93],"species.":[96],"addition,":[98],"binding":[100,123,158],"position":[101],"allows":[102],"it":[103],"introduce":[105],"steric":[107],"obstacle":[108],"impedes":[110],"P/E":[112],"hybrid-state":[113],"formation":[114],"steps.":[115],"Using":[116],"molecular":[117],"dynamics":[118],"simulations,":[119],"show":[121],"how":[122,178],"slow":[127],"down":[128],"kinetics":[130],"tRNA":[132],"on":[134],"Since":[137],"not":[140],"cytosolic":[144],"human":[145,154],"has":[148],"distinct":[150],"sequence":[151],"mitochondrial":[155],"ribosome,":[156],"this":[157],"site":[159],"serve":[161],"novel":[164],"target":[165],"for":[166],"future":[167],"antimicrobial":[170],"design":[171],"efforts.":[172],"This":[173],"analysis":[174],"provides":[175],"insights":[176],"into":[177],"optimize":[180],"inhibitory":[182],"effects":[183],"L33-targeting":[185],"molecules,":[186],"order":[188],"develop":[190],"class":[193],"broad-spectrum":[195],"antibiotics/antimicrobials.":[196]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2025-05-04T00:00:00"}
