{"id":"https://openalex.org/W2746979629","doi":"https://doi.org/10.1021/acs.jcim.7b00340","title":"Structure-Based Energetics of Stop Codon Recognition by Eukaryotic Release Factor","display_name":"Structure-Based Energetics of Stop Codon Recognition by Eukaryotic Release Factor","publication_year":2017,"publication_date":"2017-08-21","ids":{"openalex":"https://openalex.org/W2746979629","doi":"https://doi.org/10.1021/acs.jcim.7b00340","mag":"2746979629","pmid":"https://pubmed.ncbi.nlm.nih.gov/28825483"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.7b00340","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00340","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/A5003972338","display_name":"Amit Kumar","orcid":"https://orcid.org/0000-0003-2099-0008"},"institutions":[{"id":"https://openalex.org/I1317621060","display_name":"Indian Institute of Technology Guwahati","ror":"https://ror.org/0022nd079","country_code":"IN","type":"education","lineage":["https://openalex.org/I1317621060"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Amit Kumar","raw_affiliation_strings":["Department of Biosciences\rand Bioengineering, Indian Institute of Technology, Guwahati, Guwahati 781039, Assam, India"],"affiliations":[{"raw_affiliation_string":"Department of Biosciences\rand Bioengineering, Indian Institute of Technology, Guwahati, Guwahati 781039, Assam, India","institution_ids":["https://openalex.org/I1317621060"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081721780","display_name":"Debadrita Basu","orcid":"https://orcid.org/0000-0003-4137-7472"},"institutions":[{"id":"https://openalex.org/I1317621060","display_name":"Indian Institute of Technology Guwahati","ror":"https://ror.org/0022nd079","country_code":"IN","type":"education","lineage":["https://openalex.org/I1317621060"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Debadrita Basu","raw_affiliation_strings":["Department of Biosciences\rand Bioengineering, Indian Institute of Technology, Guwahati, Guwahati 781039, Assam, India"],"affiliations":[{"raw_affiliation_string":"Department of Biosciences\rand Bioengineering, Indian Institute of Technology, Guwahati, Guwahati 781039, Assam, India","institution_ids":["https://openalex.org/I1317621060"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032959524","display_name":"Priyadarshi Satpati","orcid":"https://orcid.org/0000-0002-0391-3580"},"institutions":[{"id":"https://openalex.org/I1317621060","display_name":"Indian Institute of Technology Guwahati","ror":"https://ror.org/0022nd079","country_code":"IN","type":"education","lineage":["https://openalex.org/I1317621060"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Priyadarshi Satpati","raw_affiliation_strings":["Department of Biosciences\rand Bioengineering, Indian Institute of Technology, Guwahati, Guwahati 781039, Assam, India"],"affiliations":[{"raw_affiliation_string":"Department of Biosciences\rand Bioengineering, Indian Institute of Technology, Guwahati, Guwahati 781039, Assam, India","institution_ids":["https://openalex.org/I1317621060"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003972338"],"corresponding_institution_ids":["https://openalex.org/I1317621060"],"apc_list":null,"apc_paid":null,"fwci":0.319,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.58124453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"57","issue":"9","first_page":"2321","last_page":"2328"},"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":0.9994999766349792,"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/T10604","display_name":"RNA Research and Splicing","score":0.9983999729156494,"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/release-factor","display_name":"Release factor","score":0.9316067099571228},{"id":"https://openalex.org/keywords/stop-codon","display_name":"Stop codon","score":0.7332149744033813},{"id":"https://openalex.org/keywords/transfer-rna","display_name":"Transfer RNA","score":0.6252432465553284},{"id":"https://openalex.org/keywords/p-site","display_name":"P-site","score":0.5654515027999878},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.5519541501998901},{"id":"https://openalex.org/keywords/ribosome","display_name":"Ribosome","score":0.4879557490348816},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.48499152064323425},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.48491865396499634},{"id":"https://openalex.org/keywords/translational-frameshift","display_name":"Translational frameshift","score":0.4840085208415985},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4824305474758148},{"id":"https://openalex.org/keywords/a-site","display_name":"A-site","score":0.4784812331199646},{"id":"https://openalex.org/keywords/ribosomal-rna","display_name":"Ribosomal RNA","score":0.43875208497047424},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3427008390426636},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.27306920289993286},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2543920874595642},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.2408863604068756}],"concepts":[{"id":"https://openalex.org/C2779498050","wikidata":"https://www.wikidata.org/wiki/Q1994527","display_name":"Release factor","level":5,"score":0.9316067099571228},{"id":"https://openalex.org/C20580545","wikidata":"https://www.wikidata.org/wiki/Q28354","display_name":"Stop codon","level":3,"score":0.7332149744033813},{"id":"https://openalex.org/C153957851","wikidata":"https://www.wikidata.org/wiki/Q201448","display_name":"Transfer RNA","level":4,"score":0.6252432465553284},{"id":"https://openalex.org/C106774688","wikidata":"https://www.wikidata.org/wiki/Q6588997","display_name":"P-site","level":5,"score":0.5654515027999878},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5519541501998901},{"id":"https://openalex.org/C88478588","wikidata":"https://www.wikidata.org/wiki/Q42244","display_name":"Ribosome","level":4,"score":0.4879557490348816},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.48499152064323425},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.48491865396499634},{"id":"https://openalex.org/C95811502","wikidata":"https://www.wikidata.org/wiki/Q7322407","display_name":"Translational frameshift","level":5,"score":0.4840085208415985},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4824305474758148},{"id":"https://openalex.org/C96267730","wikidata":"https://www.wikidata.org/wiki/Q4647010","display_name":"A-site","level":3,"score":0.4784812331199646},{"id":"https://openalex.org/C67905577","wikidata":"https://www.wikidata.org/wiki/Q215980","display_name":"Ribosomal RNA","level":3,"score":0.43875208497047424},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3427008390426636},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.27306920289993286},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2543920874595642},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.2408863604068756}],"mesh":[{"descriptor_ui":"D010454","descriptor_name":"Peptide Termination Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010454","descriptor_name":"Peptide Termination Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010454","descriptor_name":"Peptide Termination Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D010454","descriptor_name":"Peptide Termination Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010454","descriptor_name":"Peptide Termination Factors","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010454","descriptor_name":"Peptide Termination Factors","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":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D018388","descriptor_name":"Codon, Terminator","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020029","descriptor_name":"Base Pairing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.7b00340","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.7b00340","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:28825483","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28825483","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":[{"id":"https://metadata.un.org/sdg/10","score":0.5699999928474426,"display_name":"Reduced inequalities"},{"id":"https://metadata.un.org/sdg/16","score":0.44999998807907104,"display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323155","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750"},{"id":"https://openalex.org/F4320327457","display_name":"Indian Institute of Technology Guwahati","ror":"https://ror.org/0022nd079"},{"id":"https://openalex.org/F4320334771","display_name":"Science and Engineering Research Board","ror":"https://ror.org/03ffdsr55"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1195318580","https://openalex.org/W1559355994","https://openalex.org/W1923736252","https://openalex.org/W1965347340","https://openalex.org/W1966866477","https://openalex.org/W1970745923","https://openalex.org/W1974167806","https://openalex.org/W1976499671","https://openalex.org/W1978966052","https://openalex.org/W1982680156","https://openalex.org/W1983435302","https://openalex.org/W1989067983","https://openalex.org/W1990868071","https://openalex.org/W1993969571","https://openalex.org/W2017086463","https://openalex.org/W2022203526","https://openalex.org/W2027408247","https://openalex.org/W2032279044","https://openalex.org/W2038940439","https://openalex.org/W2039584947","https://openalex.org/W2044656372","https://openalex.org/W2052196208","https://openalex.org/W2059703010","https://openalex.org/W2066841033","https://openalex.org/W2067174909","https://openalex.org/W2073504319","https://openalex.org/W2082772268","https://openalex.org/W2083101591","https://openalex.org/W2083135136","https://openalex.org/W2085063254","https://openalex.org/W2091328421","https://openalex.org/W2101404563","https://openalex.org/W2104825395","https://openalex.org/W2105326796","https://openalex.org/W2109154308","https://openalex.org/W2126330038","https://openalex.org/W2126437265","https://openalex.org/W2126780661","https://openalex.org/W2128911048","https://openalex.org/W2131623467","https://openalex.org/W2132262459","https://openalex.org/W2132650893","https://openalex.org/W2132746070","https://openalex.org/W2145473270","https://openalex.org/W2149482038","https://openalex.org/W2150981663","https://openalex.org/W2151295074","https://openalex.org/W2159131581","https://openalex.org/W2186864552","https://openalex.org/W2269683575","https://openalex.org/W2414292512"],"related_works":["https://openalex.org/W2031838169","https://openalex.org/W2129815091","https://openalex.org/W4392382550","https://openalex.org/W1536971824","https://openalex.org/W2746979629","https://openalex.org/W2148163730","https://openalex.org/W2172095534","https://openalex.org/W2121030623","https://openalex.org/W2033946310","https://openalex.org/W2408868665"],"abstract_inverted_index":{"In":[0],"translation":[1,130],"termination,":[2],"the":[3,25,39,54,85,91,103,110,151,194,199,210,214],"eukaryotic":[4,129],"release":[5,23,68],"factor":[6,69],"(eRF1)":[7],"recognizes":[8],"mRNA":[9,88,181],"stop":[10,63,118,154,190],"codons":[11,64,212,230],"(UAA,":[12],"UAG,":[13],"or":[14],"UGA)":[15],"in":[16,38,53,77,90,213],"a":[17,43,66,117,121,165,220],"ribosomal":[18,92],"A":[19,93],"site":[20,94],"and":[21,42,56,75,145,228],"triggers":[22],"of":[24,45,72,100,128,143,153,201,209],"nascent":[26],"polypeptide":[27],"chain":[28],"from":[29],"P-site":[30],"tRNA.":[31],"eRF1":[32,83,114,163,224],"is":[33,196],"highly":[34],"selective":[35],"for":[36,113,177],"U":[37],"first":[40],"position":[41],"combination":[44],"purines":[46],"(except":[47],"two":[48,73],"consecutive":[49],"guanines,":[50],"i.e.,":[51],"GG)":[52],"second":[55],"third":[57],"positions.":[58],"Eukaryotes":[59],"decode":[60],"all":[61],"three":[62],"with":[65],"single":[67],"eRF1,":[70],"instead":[71,99],"(RF1":[74],"RF2),":[76],"bacteria.":[78],"Furthermore,":[79,193],"unlike":[80],"bacterial":[81],"RF1/RF2,":[82],"stabilizes":[84],"compact":[86,180],"U-turn":[87],"configuration":[89],"by":[95,157,198,207],"accommodating":[96],"four":[97],"nucleotides":[98],"three.":[101],"Despite":[102],"available":[104],"cryo-EM":[105,126],"structures":[106,127],"(resolution":[107],"\u223c3.5-3.8":[108],"\u00c5),":[109],"energetic":[111],"principle":[112],"selectivity":[115],"toward":[116],"codon":[119,155,191],"remains":[120],"fundamentally":[122],"unsolved":[123],"problem.":[124],"Using":[125],"termination":[131],"complexes":[132,147],"as":[133],"templates,":[134],"we":[135],"carried":[136],"out":[137],"molecular":[138],"dynamics":[139],"free":[140],"energy":[141],"simulations":[142],"cognate":[144,227],"near-cognate":[146,215,229],"to":[148,173,189,222],"quantitatively":[149],"address":[150],"energetics":[152],"recognition":[156],"eRF1.":[158],"Our":[159,217],"results":[160],"suggest":[161],"that":[162,174],"has":[164],"higher":[166],"discriminatory":[167],"power":[168],"against":[169],"sense":[170],"codons,":[171],"compared":[172],"reported":[175],"earlier":[176],"RF1/RF2.":[178],"The":[179],"formed":[182],"specific":[183],"intra-mRNA":[184],"interactions,":[185],"which":[186],"itself":[187],"contributed":[188],"specificity.":[192],"specificity":[195],"enhanced":[197],"loss":[200],"protein-mRNA":[202],"interactions":[203],"and,":[204],"most":[205],"importantly,":[206],"desolvation":[208],"incorrect":[211],"complexes.":[216],"work":[218],"provides":[219],"clue":[221],"how":[223],"discriminates":[225],"between":[226],"during":[231],"protein":[232],"synthesis.":[233]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
