{"id":"https://openalex.org/W3201698754","doi":"https://doi.org/10.1021/acs.jcim.1c01022","title":"Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch <i>ykkC</i>-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands","display_name":"Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch <i>ykkC</i>-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands","publication_year":2021,"publication_date":"2021-10-05","ids":{"openalex":"https://openalex.org/W3201698754","doi":"https://doi.org/10.1021/acs.jcim.1c01022","mag":"3201698754","pmid":"https://pubmed.ncbi.nlm.nih.gov/34609872"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.1c01022","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01022","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/A5032975949","display_name":"Indu Negi","orcid":"https://orcid.org/0000-0003-2839-1886"},"institutions":[{"id":"https://openalex.org/I51452335","display_name":"Panjab University","ror":"https://ror.org/04p2sbk06","country_code":"IN","type":"education","lineage":["https://openalex.org/I51452335"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Indu Negi","raw_affiliation_strings":["Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India","institution_ids":["https://openalex.org/I51452335"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060976190","display_name":"Amanpreet Singh Mahmi","orcid":null},"institutions":[{"id":"https://openalex.org/I51452335","display_name":"Panjab University","ror":"https://ror.org/04p2sbk06","country_code":"IN","type":"education","lineage":["https://openalex.org/I51452335"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Amanpreet Singh Mahmi","raw_affiliation_strings":["Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India","institution_ids":["https://openalex.org/I51452335"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090527330","display_name":"Preethi Seelam Prabhakar","orcid":"https://orcid.org/0000-0002-8749-4685"},"institutions":[{"id":"https://openalex.org/I65181880","display_name":"Indian Institute of Technology Hyderabad","ror":"https://ror.org/01j4v3x97","country_code":"IN","type":"education","lineage":["https://openalex.org/I65181880"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Preethi Seelam Prabhakar","raw_affiliation_strings":["Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT\u2212H), Gachibowli, Hyderabad, Telangana 500032, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT\u2212H), Gachibowli, Hyderabad, Telangana 500032, India","institution_ids":["https://openalex.org/I65181880"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046203598","display_name":"Purshotam Sharma","orcid":"https://orcid.org/0000-0002-5164-9833"},"institutions":[{"id":"https://openalex.org/I51452335","display_name":"Panjab University","ror":"https://ror.org/04p2sbk06","country_code":"IN","type":"education","lineage":["https://openalex.org/I51452335"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Purshotam Sharma","raw_affiliation_strings":["Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India"],"raw_orcid":"https://orcid.org/0000-0002-5164-9833","affiliations":[{"raw_affiliation_string":"Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India","institution_ids":["https://openalex.org/I51452335"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5046203598"],"corresponding_institution_ids":["https://openalex.org/I51452335"],"apc_list":null,"apc_paid":null,"fwci":0.57,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.64975033,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"61","issue":"10","first_page":"5243","last_page":"5255"},"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":0.9965999722480774,"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":0.9907000064849854,"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/aptamer","display_name":"Aptamer","score":0.8611006736755371},{"id":"https://openalex.org/keywords/riboswitch","display_name":"Riboswitch","score":0.8130124807357788},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.7482384443283081},{"id":"https://openalex.org/keywords/ligand","display_name":"Ligand (biochemistry)","score":0.5928592681884766},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.5067513585090637},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.47756463289260864},{"id":"https://openalex.org/keywords/biophysics","display_name":"Biophysics","score":0.43595147132873535},{"id":"https://openalex.org/keywords/binding-selectivity","display_name":"Binding selectivity","score":0.41896387934684753},{"id":"https://openalex.org/keywords/stereochemistry","display_name":"Stereochemistry","score":0.37448886036872864},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3092711865901947},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.24733728170394897},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.14716371893882751},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12369704246520996},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11926090717315674},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08063280582427979},{"id":"https://openalex.org/keywords/non-coding-rna","display_name":"Non-coding RNA","score":0.0738171637058258}],"concepts":[{"id":"https://openalex.org/C128972844","wikidata":"https://www.wikidata.org/wiki/Q418722","display_name":"Aptamer","level":2,"score":0.8611006736755371},{"id":"https://openalex.org/C148625055","wikidata":"https://www.wikidata.org/wiki/Q418840","display_name":"Riboswitch","level":5,"score":0.8130124807357788},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7482384443283081},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.5928592681884766},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5067513585090637},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.47756463289260864},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.43595147132873535},{"id":"https://openalex.org/C96739231","wikidata":"https://www.wikidata.org/wiki/Q4914025","display_name":"Binding selectivity","level":2,"score":0.41896387934684753},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.37448886036872864},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3092711865901947},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.24733728170394897},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.14716371893882751},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12369704246520996},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11926090717315674},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08063280582427979},{"id":"https://openalex.org/C194993378","wikidata":"https://www.wikidata.org/wiki/Q427087","display_name":"Non-coding RNA","level":4,"score":0.0738171637058258},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009690","descriptor_name":"Nucleic Acid Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019791","descriptor_name":"Guanidine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019791","descriptor_name":"Guanidine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019791","descriptor_name":"Guanidine","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},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058928","descriptor_name":"Riboswitch","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.1c01022","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.1c01022","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:34609872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34609872","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":[{"score":0.5600000023841858,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"},{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions"}],"awards":[{"id":"https://openalex.org/G1067967194","display_name":null,"funder_award_id":"F.4-5(176-FRP/2015(BSR))","funder_id":"https://openalex.org/F4320320767","funder_display_name":"University Grants Commission"}],"funders":[{"id":"https://openalex.org/F4320320767","display_name":"University Grants Commission","ror":"https://ror.org/04p800546"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":85,"referenced_works":["https://openalex.org/W255996521","https://openalex.org/W1963675638","https://openalex.org/W1970389871","https://openalex.org/W1976499671","https://openalex.org/W1977148902","https://openalex.org/W1977482735","https://openalex.org/W1978643307","https://openalex.org/W1981225934","https://openalex.org/W1984614201","https://openalex.org/W1986173091","https://openalex.org/W1994028292","https://openalex.org/W2006198724","https://openalex.org/W2008697605","https://openalex.org/W2014118668","https://openalex.org/W2023167098","https://openalex.org/W2023246179","https://openalex.org/W2029667189","https://openalex.org/W2035266068","https://openalex.org/W2035687084","https://openalex.org/W2048706341","https://openalex.org/W2051632928","https://openalex.org/W2052111270","https://openalex.org/W2053208573","https://openalex.org/W2061029954","https://openalex.org/W2067258168","https://openalex.org/W2083268880","https://openalex.org/W2088196774","https://openalex.org/W2088440641","https://openalex.org/W2089468765","https://openalex.org/W2096959765","https://openalex.org/W2098769462","https://openalex.org/W2104482488","https://openalex.org/W2106478835","https://openalex.org/W2114998496","https://openalex.org/W2120200447","https://openalex.org/W2122199548","https://openalex.org/W2122282339","https://openalex.org/W2122914162","https://openalex.org/W2123412671","https://openalex.org/W2125794794","https://openalex.org/W2125952821","https://openalex.org/W2127613646","https://openalex.org/W2128728535","https://openalex.org/W2131841865","https://openalex.org/W2132920850","https://openalex.org/W2141152740","https://openalex.org/W2147447439","https://openalex.org/W2152054441","https://openalex.org/W2157052506","https://openalex.org/W2180478938","https://openalex.org/W2311078281","https://openalex.org/W2313946562","https://openalex.org/W2404280981","https://openalex.org/W2413259996","https://openalex.org/W2563066745","https://openalex.org/W2564414785","https://openalex.org/W2578167366","https://openalex.org/W2605443933","https://openalex.org/W2606133359","https://openalex.org/W2615615267","https://openalex.org/W2624146956","https://openalex.org/W2764099114","https://openalex.org/W2769114003","https://openalex.org/W2801289443","https://openalex.org/W2883990554","https://openalex.org/W2914640169","https://openalex.org/W2938480481","https://openalex.org/W2961068473","https://openalex.org/W3015083259","https://openalex.org/W3029946173","https://openalex.org/W3044495674","https://openalex.org/W3047613627","https://openalex.org/W3088465705","https://openalex.org/W3089496483","https://openalex.org/W3092282472","https://openalex.org/W3099560547","https://openalex.org/W3124452157","https://openalex.org/W3127550073","https://openalex.org/W3161109941","https://openalex.org/W3169873395","https://openalex.org/W3178880074","https://openalex.org/W3179033580","https://openalex.org/W3187433942","https://openalex.org/W4234269719","https://openalex.org/W4237490993"],"related_works":["https://openalex.org/W3151547568","https://openalex.org/W2918944057","https://openalex.org/W2968280723","https://openalex.org/W2754583082","https://openalex.org/W2695995371","https://openalex.org/W4392936003","https://openalex.org/W4398775841","https://openalex.org/W2025242074","https://openalex.org/W1972092865","https://openalex.org/W2810077789"],"abstract_inverted_index":{"Guanidinium":[0],"ion":[1,31],"is":[2,222],"a":[3,19,28,35,133,268,291],"toxic":[4],"cellular":[5],"metabolite.":[6],"The":[7],"ykkC-III":[8],"riboswitch,":[9],"an":[10],"mRNA":[11],"stretch,":[12],"regulates":[13],"the":[14,25,50,55,61,67,73,76,84,88,103,111,115,120,145,154,159,165,169,178,184,194,200,207,213,219,228,240,244,252,255,259,272,277,287,305],"gene":[15,121,208,306],"expression":[16,116,260,278],"by":[17,290,308],"undergoing":[18],"conformational":[20],"change":[21],"in":[22,39,43,239],"response":[23],"to":[24,114,157,190,258,302],"binding":[26,77,104,220],"of":[27,49,54,82,105,135,164,183,212,216,243,270,294],"free":[29],"guanidinium":[30,41,229],"and":[32,65,99,101,161,203,296],"thereby":[33,204],"plays":[34],"potentially":[36],"important":[37],"role":[38],"alleviating":[40],"toxicity":[42],"cells.":[44],"An":[45],"experimental":[46],"crystal":[47],"structure":[48],"guanidinium-bound":[51,166],"aptamer":[52,85,112,147,201,256,273],"domain":[53,86,113,202,257,274],"riboswitch":[56],"from":[57,91,110,254],"Thermobifida":[58],"Fusca":[59],"revealed":[60],"overall":[62],"RNA":[63],"architecture":[64],"mapped":[66],"specific":[68,292],"noncovalent":[69],"interactions":[70,192],"that":[71,188],"stabilize":[72],"ligand":[74,90,107,288],"within":[75,218],"pocket":[78,186,221],"aptamer.":[79],"However,":[80],"details":[81,163,242],"how":[83,102,271],"discriminates":[87],"cognate":[89,106],"its":[92],"closest":[93],"structurally":[94],"analogous":[95],"physiological":[96],"metabolites":[97],"(arginine":[98],"urea),":[100],"arrays":[108],"information":[109,253],"platform":[117],"for":[118],"regulating":[119],"expression,":[122],"are":[123],"not":[124],"well":[125,176,236],"understood.":[126],"To":[127],"fill":[128],"this":[129],"void,":[130],"we":[131,266],"perform":[132],"cumulative":[134],"2":[136],"\u03bcs":[137],"all-atom":[138],"explicit-solvent":[139],"molecular":[140],"dynamics":[141],"(MD)":[142],"simulations":[143],"on":[144,153,263],"full":[146],"domain,":[148],"augmented":[149],"with":[150,168,193,276],"quantum-chemical":[151],"calculations":[152],"ligand-binding":[155,185],"pocket,":[156],"compare":[158],"structural":[160],"dynamical":[162,241],"state":[167],"arginine":[170,217,249],"or":[171,225],"urea":[172,197],"bound":[173],"states,":[174],"as":[175,177,235,237],"unbound":[179],"(open)":[180],"state.":[181],"Analysis":[182],"reveals":[187],"due":[189],"unfavorable":[191],"binding-pocket":[195],"residues,":[196],"cannot":[198,205,250],"bind":[199],"alter":[206],"expression.":[209],"Although":[210],"interaction":[211],"guanidyl":[214],"moiety":[215],"either":[223],"comparable":[224],"stronger":[226],"than":[227],"ion,":[230],"additional":[231],"non-native":[232],"hydrogen-bonding":[233],"networks,":[234],"differences":[238],"arginine-bound":[245],"state,":[246],"explain":[247],"why":[248],"transmit":[251],"platform.":[261,279],"Based":[262],"our":[264,281],"simulations,":[265],"propose":[267],"mechanism":[269],"communicates":[275],"Overall,":[280],"work":[282],"provides":[283],"interesting":[284],"insights":[285],"into":[286],"recognition":[289],"class":[293],"riboswitches":[295],"may":[297],"hopefully":[298],"inspire":[299],"future":[300],"studies":[301],"further":[303],"understand":[304],"regulation":[307],"riboswitches.":[309]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2025-10-10T00:00:00"}
