{"id":"https://openalex.org/W2321756963","doi":"https://doi.org/10.1021/jz3001882","title":"Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits","display_name":"Nucleotide Dynamics at the A-Site Cleft in the Peptidyltransferase Center of H. marismortui 50S Ribosomal Subunits","publication_year":2012,"publication_date":"2012-03-27","ids":{"openalex":"https://openalex.org/W2321756963","doi":"https://doi.org/10.1021/jz3001882","mag":"2321756963","pmid":"https://pubmed.ncbi.nlm.nih.gov/26286564"},"language":"en","primary_location":{"id":"doi:10.1021/jz3001882","doi":"https://doi.org/10.1021/jz3001882","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jz3001882","pdf_url":null,"source":{"id":"https://openalex.org/S123480357","display_name":"The Journal of Physical Chemistry Letters","issn_l":"1948-7185","issn":["1948-7185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-1","medline","norway-1","poland-200","russia-white-list-1","vabb-shw"],"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":"The Journal of Physical Chemistry Letters","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/A5100449579","display_name":"Yuhang Wang","orcid":"https://orcid.org/0000-0003-3715-8349","observed_orcids":["https://orcid.org/0000-0003-3715-8349","https://orcid.org/0000-0002-5185-1556"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuhang Wang","raw_affiliation_strings":["Department\rof Chemistry and Biochemistry, \u2021School of Chemical, Biological, and Materials\rEngineering, and \u03beDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry and Biochemistry, \u2021School of Chemical, Biological, and Materials\rEngineering, and \u03beDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103575399","display_name":"Jana K. Shen","orcid":"https://orcid.org/0000-0002-3234-0769","observed_orcids":["https://orcid.org/0000-0002-3234-0769"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jana K. Shen","raw_affiliation_strings":["Department\rof Chemistry and Biochemistry, \u2021School of Chemical, Biological, and Materials\rEngineering, and \u03beDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry and Biochemistry, \u2021School of Chemical, Biological, and Materials\rEngineering, and \u03beDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States","institution_ids":["https://openalex.org/I8692664"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039675671","display_name":"Susan J. Schroeder","orcid":"https://orcid.org/0000-0003-4755-2294","observed_orcids":["https://orcid.org/0000-0003-4755-2294"]},"institutions":[{"id":"https://openalex.org/I8692664","display_name":"University of Oklahoma","ror":"https://ror.org/02aqsxs83","country_code":"US","type":"education","lineage":["https://openalex.org/I8692664"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Susan J. Schroeder","raw_affiliation_strings":["Department\rof Chemistry and Biochemistry, \u2021School of Chemical, Biological, and Materials\rEngineering, and \u03beDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department\rof Chemistry and Biochemistry, \u2021School of Chemical, Biological, and Materials\rEngineering, and \u03beDepartment of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma, United States","institution_ids":["https://openalex.org/I8692664"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5039675671","https://openalex.org/A5103575399"],"corresponding_institution_ids":["https://openalex.org/I8692664"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.2573,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.5588924,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"3","issue":"8","first_page":"1007","last_page":"1010"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9994999766349792,"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":0.9994999766349792,"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":0.00039999998989515007,"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/T10432","display_name":"DNA and Nucleic Acid Chemistry","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"}}],"keywords":[{"id":"https://openalex.org/keywords/peptidyl-transferase-center","display_name":"peptidyl transferase center","score":0.8930000066757202},{"id":"https://openalex.org/keywords/50s-ribosomal-subunit","display_name":"50S ribosomal subunit","score":0.9079999923706055},{"id":"https://openalex.org/keywords/haloarcula-marismortui","display_name":"Haloarcula marismortui","score":0.9449999928474426},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"antibiotic resistance","score":0.7940000295639038},{"id":"https://openalex.org/keywords/rrna-mutations","display_name":"rRNA mutations","score":0.5839999914169312},{"id":"https://openalex.org/keywords/potassium-ion-coordination","display_name":"potassium ion coordination","score":0.746999979019165},{"id":"https://openalex.org/keywords/hydrogen-bond-network","display_name":"hydrogen bond network","score":0.7519999742507935},{"id":"https://openalex.org/keywords/conformational-dynamics","display_name":"conformational dynamics","score":0.9259999990463257},{"id":"https://openalex.org/keywords/rational-drug-design","display_name":"rational drug design","score":0.6050000190734863},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.546999990940094}],"concepts":[{"id":"https://openalex.org/C69080955","wikidata":"https://www.wikidata.org/wiki/Q1088533","display_name":"50S","level":5,"score":0.8714820146560669},{"id":"https://openalex.org/C2778321597","wikidata":"https://www.wikidata.org/wiki/Q424702","display_name":"Peptidyl transferase","level":5,"score":0.8298141360282898},{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.6935244202613831},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5727531313896179},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5321254730224609},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4957509934902191},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.4822124242782593},{"id":"https://openalex.org/C112887158","wikidata":"https://www.wikidata.org/wiki/Q169324","display_name":"Hydrogen bond","level":3,"score":0.4447345733642578},{"id":"https://openalex.org/C41183919","wikidata":"https://www.wikidata.org/wiki/Q423026","display_name":"Active site","level":3,"score":0.4367717206478119},{"id":"https://openalex.org/C38062823","wikidata":"https://www.wikidata.org/wiki/Q3408228","display_name":"Ribosomal protein","level":5,"score":0.4242652356624603},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.418867290019989},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3651409447193146},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.33775004744529724},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27120083570480347},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27022117376327515},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.26028165221214294},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.166153222322464},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.10853162407875061},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.07392868399620056},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1021/jz3001882","doi":"https://doi.org/10.1021/jz3001882","is_oa":false,"landing_page_url":"https://doi.org/10.1021/jz3001882","pdf_url":null,"source":{"id":"https://openalex.org/S123480357","display_name":"The Journal of Physical Chemistry Letters","issn_l":"1948-7185","issn":["1948-7185"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-1","medline","norway-1","poland-200","russia-white-list-1","vabb-shw"],"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":"The Journal of Physical Chemistry Letters","raw_type":"journal-article"},{"id":"pmid:26286564","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26286564","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 physical chemistry letters","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"id":"https://metadata.un.org/sdg/14","score":0.5799999833106995,"display_name":"Life below water"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3238736380","display_name":"Electrostatic modulation of protein dynamics and interactions","funder_award_id":"R01GM098818","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":24,"referenced_works":["https://openalex.org/W124036635","https://openalex.org/W1964500513","https://openalex.org/W1966078827","https://openalex.org/W1967986998","https://openalex.org/W1975510301","https://openalex.org/W1983534198","https://openalex.org/W1983948144","https://openalex.org/W1984878181","https://openalex.org/W1999756176","https://openalex.org/W2021385540","https://openalex.org/W2044910218","https://openalex.org/W2046002103","https://openalex.org/W2068051461","https://openalex.org/W2068143879","https://openalex.org/W2080190754","https://openalex.org/W2097654784","https://openalex.org/W2106886734","https://openalex.org/W2110803333","https://openalex.org/W2113745092","https://openalex.org/W2131288855","https://openalex.org/W2153839483","https://openalex.org/W2154319440","https://openalex.org/W2156400868","https://openalex.org/W2166117980"],"related_works":["https://openalex.org/W2057748647","https://openalex.org/W3108261562","https://openalex.org/W2979332793","https://openalex.org/W2027528391","https://openalex.org/W2012443293","https://openalex.org/W3109810495","https://openalex.org/W1988555400","https://openalex.org/W6927941294","https://openalex.org/W4402389273","https://openalex.org/W3176778853"],"abstract_inverted_index":{"Resistance":[0],"mutations":[1,119],"to":[2,41,52],"antibiotics":[3],"targeting":[4],"rRNA":[5],"can":[6,120],"be":[7],"far":[8],"from":[9],"the":[10,17,36,42,57,68,71,78,82,88,94,99,106,115,122,126,131,140],"drug-binding":[11,58],"site.":[12,59],"Crystallography":[13],"studies":[14],"revealed":[15],"that":[16,87,117],"antibiotic":[18,95,135],"resistance":[19],"mutation":[20,73,89],"G2482A":[21,72],"(G2447A":[22],"in":[23,27,125,146],"E.":[24],"coli":[25],")":[26],"Haloarcula":[28],"marismortui":[29],"50S":[30,83,107],"ribosomes":[31],"does":[32],"not":[33],"directly":[34],"contact":[35],"drug":[37,148],"or":[38],"introduce":[39],"changes":[40],"ribosomal":[43,127],"structure":[44],"except":[45],"for":[46],"losing":[47],"a":[48,53],"potassium":[49],"ion":[50,75],"coordinated":[51],"base":[54],"triple":[55],"at":[56,93,105],"Using":[60],"molecular":[61],"dynamics":[62,80,145],"simulations,":[63],"we":[64],"tested":[65],"hypotheses":[66],"regarding":[67],"effects":[69],"of":[70,81,134,142],"and":[74,102],"coordination":[76],"on":[77],"conformational":[79,91,144],"ribosome.":[84],"Simulations":[85],"show":[86],"enhances":[90],"fluctuation":[92],"binding":[96],"site,":[97],"weakens":[98],"hydrogen-bonding":[100],"network,":[101],"increases":[103],"flexibility":[104],"peptidyl":[108],"transferase":[109],"center":[110],"(PTC).":[111],"Our":[112],"data":[113],"supports":[114],"view":[116],"distant":[118],"perturb":[121],"dynamic":[123],"network":[124],"PTC,":[128],"thereby":[129],"raising":[130],"entropic":[132],"cost":[133],"binding.":[136],"These":[137],"results":[138],"underscore":[139],"importance":[141],"considering":[143],"rational":[147],"design.":[149]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2016-06-24T00:00:00"}