{"id":"https://openalex.org/W2162844546","doi":"https://doi.org/10.1021/ci3001327","title":"Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2","display_name":"Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2","publication_year":2012,"publication_date":"2012-04-19","ids":{"openalex":"https://openalex.org/W2162844546","doi":"https://doi.org/10.1021/ci3001327","mag":"2162844546","pmid":"https://pubmed.ncbi.nlm.nih.gov/22512810","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3362124"},"language":"en","primary_location":{"id":"doi:10.1021/ci3001327","doi":"https://doi.org/10.1021/ci3001327","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci3001327","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3362124","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5015171885","display_name":"\u00d6zlem Demir","orcid":"https://orcid.org/0000-0002-3317-4731","observed_orcids":["https://orcid.org/0000-0002-3317-4731"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"\u00d6zlem Demir","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall,\r9500 Gilman Drive, MC-0340 La Jolla, California 92093-0332, United\rStates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall,\r9500 Gilman Drive, MC-0340 La Jolla, California 92093-0332, United\rStates","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081468273","display_name":"Rommie E. Amaro","orcid":"https://orcid.org/0000-0002-9275-9553","observed_orcids":["https://orcid.org/0000-0002-9275-9553"]},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rommie E. Amaro","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall,\r9500 Gilman Drive, MC-0340 La Jolla, California 92093-0332, United\rStates"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of California, San Diego, 3234 Urey Hall,\r9500 Gilman Drive, MC-0340 La Jolla, California 92093-0332, United\rStates","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5081468273"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.8717,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.74101801,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"52","issue":"5","first_page":"1308","last_page":"1318"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10890","display_name":"Trypanosoma species research and implications","score":0.9682999849319458,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10890","display_name":"Trypanosoma species research and implications","score":0.9682999849319458,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12610","display_name":"RNA regulation and disease","score":0.010499999858438969,"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":0.008500000461935997,"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/trypanosoma-brucei","display_name":"Trypanosoma brucei","score":0.9010000228881836},{"id":"https://openalex.org/keywords/mitochondrial-rna-editing","display_name":"mitochondrial RNA editing","score":0.9549999833106995},{"id":"https://openalex.org/keywords/editosome","display_name":"editosome","score":0.7210000157356262},{"id":"https://openalex.org/keywords/nucleotide-specificity","display_name":"nucleotide specificity","score":0.8259999752044678},{"id":"https://openalex.org/keywords/water-mediated-hydrogen-bonds","display_name":"water-mediated hydrogen bonding","score":0.8009999990463257},{"id":"https://openalex.org/keywords/inhibitor-design","display_name":"inhibitor design","score":0.6010000109672546},{"id":"https://openalex.org/keywords/molecular-dynamics-simulation","display_name":"molecular dynamics simulation","score":0.4650000035762787}],"concepts":[{"id":"https://openalex.org/C2779502636","wikidata":"https://www.wikidata.org/wiki/Q33244","display_name":"Trypanosoma brucei","level":3,"score":0.7208384871482849},{"id":"https://openalex.org/C21786251","wikidata":"https://www.wikidata.org/wiki/Q14886350","display_name":"RNA editing","level":4,"score":0.7040782570838928},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.6505006551742554},{"id":"https://openalex.org/C2776352584","wikidata":"https://www.wikidata.org/wiki/Q418533","display_name":"Nucleoside triphosphate","level":4,"score":0.6379896998405457},{"id":"https://openalex.org/C512185932","wikidata":"https://www.wikidata.org/wiki/Q28745","display_name":"Nucleotide","level":3,"score":0.5859096050262451},{"id":"https://openalex.org/C97702854","wikidata":"https://www.wikidata.org/wiki/Q4039747","display_name":"Guide RNA","level":5,"score":0.583345890045166},{"id":"https://openalex.org/C2776376580","wikidata":"https://www.wikidata.org/wiki/Q407355","display_name":"Transferase","level":3,"score":0.5600583553314209},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.5293987989425659},{"id":"https://openalex.org/C2781259782","wikidata":"https://www.wikidata.org/wiki/Q422573","display_name":"Uridine","level":4,"score":0.5078538060188293},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.45286011695861816},{"id":"https://openalex.org/C2776543447","wikidata":"https://www.wikidata.org/wiki/Q28734","display_name":"Nucleoside","level":2,"score":0.4516840875148773},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4497586786746979},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.4316113293170929},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.4262394905090332},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.40707626938819885},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.34285467863082886},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0969868004322052},{"id":"https://openalex.org/C132455925","wikidata":"https://www.wikidata.org/wiki/Q16965677","display_name":"Cas9","level":4,"score":0.0926831066608429},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D009711","descriptor_name":"Nucleotides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012316","descriptor_name":"RNA Nucleotidyltransferases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012316","descriptor_name":"RNA Nucleotidyltransferases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014346","descriptor_name":"Trypanosoma brucei brucei","qualifier_ui":"Q000201","qualifier_name":"enzymology","is_major_topic":true},{"descriptor_ui":"D014544","descriptor_name":"Uridine Triphosphate","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014544","descriptor_name":"Uridine Triphosphate","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014867","descriptor_name":"Water","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D017393","descriptor_name":"RNA Editing","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1021/ci3001327","doi":"https://doi.org/10.1021/ci3001327","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ci3001327","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,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-1","ki-jl-1","medline","norway-2","poland-100","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":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:22512810","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22512810","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":"Journal of chemical information and modeling","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2658091","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3362124","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3362124","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3362124","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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:europepmc.org:2658091","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3362124","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G4921659555","display_name":"A Structural Systems Biology Approach to Drug Discovery","funder_award_id":"DP2OD007237","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7460688074","display_name":"Towards a Structural Systems Biology Approach for Anti-Trypanosomal Therapeutics","funder_award_id":"K22AI081901","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":57,"referenced_works":["https://openalex.org/W92887003","https://openalex.org/W122057298","https://openalex.org/W179532453","https://openalex.org/W1586999333","https://openalex.org/W1841435798","https://openalex.org/W1966078827","https://openalex.org/W1969836007","https://openalex.org/W1972758026","https://openalex.org/W1976499671","https://openalex.org/W1977456409","https://openalex.org/W1982163838","https://openalex.org/W1987671305","https://openalex.org/W1990025144","https://openalex.org/W1998026805","https://openalex.org/W2015688756","https://openalex.org/W2020288705","https://openalex.org/W2021444164","https://openalex.org/W2025157967","https://openalex.org/W2029666489","https://openalex.org/W2029667189","https://openalex.org/W2031500190","https://openalex.org/W2038758364","https://openalex.org/W2057664120","https://openalex.org/W2067174909","https://openalex.org/W2069101165","https://openalex.org/W2080348578","https://openalex.org/W2081089780","https://openalex.org/W2103945336","https://openalex.org/W2104158537","https://openalex.org/W2105103540","https://openalex.org/W2106140689","https://openalex.org/W2110277124","https://openalex.org/W2110562802","https://openalex.org/W2112878090","https://openalex.org/W2113354295","https://openalex.org/W2115276551","https://openalex.org/W2116211618","https://openalex.org/W2117135374","https://openalex.org/W2124789466","https://openalex.org/W2127001229","https://openalex.org/W2131174104","https://openalex.org/W2138072853","https://openalex.org/W2144288821","https://openalex.org/W2147993766","https://openalex.org/W2148131811","https://openalex.org/W2150981663","https://openalex.org/W2151799620","https://openalex.org/W2154714625","https://openalex.org/W2161134038","https://openalex.org/W2164270482","https://openalex.org/W2169125466","https://openalex.org/W2769990393","https://openalex.org/W3037896947","https://openalex.org/W4211164760","https://openalex.org/W4298284232","https://openalex.org/W4301971420","https://openalex.org/W4302056729"],"related_works":["https://openalex.org/W137721644","https://openalex.org/W2115276551","https://openalex.org/W2021444164","https://openalex.org/W2531471005","https://openalex.org/W2080348578","https://openalex.org/W7095207004","https://openalex.org/W2050774080","https://openalex.org/W2121721627","https://openalex.org/W2055747482","https://openalex.org/W2116481264"],"abstract_inverted_index":{"The":[0],"causative":[1],"agent":[2],"of":[3,29,37,52,59,79,90,106,127,188],"African":[4],"sleeping":[5],"sickness,":[6],"Trypanosoma":[7],"brucei":[8,31],",":[9],"undergoes":[10],"an":[11,34,142,154],"unusual":[12],"mitochondrial":[13],"RNA":[14,23,87,158,178],"editing":[15,24],"process":[16],"that":[17,41,135],"is":[18,33,46,92],"essential":[19],"for":[20,83,157,216],"its":[21,64],"survival.":[22],"terminal":[25],"uridylyl":[26],"transferase":[27],"2":[28],"T.":[30],"(TbRET2)":[32],"indispensable":[35],"component":[36],"the":[38,50,54,60,76,86,104,117,138,192,206],"editosome":[39],"machinery":[40],"performs":[42],"this":[43,172],"editing.":[44],"TbRET2":[45,91,110,189,200],"required":[47],"to":[48,153],"maintain":[49],"vitality":[51],"both":[53],"insect":[55],"and":[56,62,112,149,166,174,196,208],"bloodstream":[57],"forms":[58],"parasite,":[61],"with":[63],"high-resolution":[65],"crystal":[66],"structure,":[67],"it":[68],"poses":[69],"as":[70,114,116],"a":[71],"promising":[72],"pharmaceutical":[73],"target.":[74],"Neither":[75],"exclusive":[77,121],"requirement":[78],"uridine":[80],"5'-triphosphate":[81,164,168],"(UTP)":[82],"catalysis,":[84],"nor":[85],"primer":[88,159,179],"preference":[89],"well-understood.":[93],"Using":[94],"all-atom":[95],"explicitly":[96],"solvated":[97],"molecular":[98],"dynamics":[99],"(MD)":[100],"simulations,":[101,211],"we":[102,133,182],"investigated":[103],"effect":[105],"UTP":[107,122,136],"binding":[108,139,203],"on":[109,191],"structure":[111],"dynamics,":[113],"well":[115],"determinants":[118],"governing":[119],"TbRET2's":[120],"preference.":[123],"Through":[124],"our":[125],"investigations":[126],"various":[128],"nucleoside":[129],"triphosphate":[130],"substrates":[131],"(NTPs),":[132],"show":[134],"preorganizes":[137],"site":[140],"through":[141],"extensive":[143],"water-mediated":[144],"H-bonding":[145],"network,":[146],"bringing":[147],"Glu424":[148],"Arg144":[150],"side":[151],"chains":[152],"optimum":[155],"position":[156],"binding.":[160,180],"In":[161],"contrast,":[162],"cytosine":[163],"(CTP)":[165],"adenosine":[167],"(ATP)":[169],"cannot":[170],"achieve":[171],"preorganization":[173],"thus":[175],"preclude":[176],"productive":[177],"Additionally,":[181],"have":[183],"located":[184],"ligand-binding":[185],"\"hot":[186],"spots\"":[187],"based":[190],"MD":[193,210],"conformational":[194],"ensembles":[195],"computational":[197],"fragment":[198],"mapping.":[199],"reveals":[201],"different":[202],"pockets":[204],"in":[205],"apo":[207],"UTP-bound":[209],"which":[212],"could":[213],"be":[214],"targeted":[215],"inhibitor":[217],"design.":[218]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}
