{"id":"https://openalex.org/W2091091663","doi":"https://doi.org/10.1021/ja901276n","title":"Response of Small-Scale, Methyl Rotors to Protein\u2212Ligand Association: A Simulation Analysis of Calmodulin\u2212Peptide Binding","display_name":"Response of Small-Scale, Methyl Rotors to Protein\u2212Ligand Association: A Simulation Analysis of Calmodulin\u2212Peptide Binding","publication_year":2009,"publication_date":"2009-07-06","ids":{"openalex":"https://openalex.org/W2091091663","doi":"https://doi.org/10.1021/ja901276n","mag":"2091091663","pmid":"https://pubmed.ncbi.nlm.nih.gov/19621963"},"language":"en","primary_location":{"id":"doi:10.1021/ja901276n","doi":"https://doi.org/10.1021/ja901276n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ja901276n","pdf_url":null,"source":{"id":"https://openalex.org/S111155417","display_name":"Journal of the American Chemical Society","issn_l":"0002-7863","issn":["0002-7863","1520-5126","1943-2984"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-3","medline","norway-2","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":"Journal of the American Chemical Society","raw_type":"journal-article"},"parent_works":[],"lineage":["https://openalex.org/W2091091663"],"child_works_count":0,"type":"article","is_traditional":true,"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/A5032090372","display_name":"Marimuthu Krishnan","orcid":"https://orcid.org/0000-0002-2549-919X","observed_orcids":["https://orcid.org/0000-0002-2549-919X"]},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Marimuthu Krishnan","raw_affiliation_strings":["UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I75027704"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018366869","display_name":"Jeremy C. Smith","orcid":"https://orcid.org/0000-0002-2978-3227","observed_orcids":["https://orcid.org/0000-0002-2978-3227"]},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]},{"id":"https://openalex.org/I75027704","display_name":"University of Tennessee at Knoxville","ror":"https://ror.org/020f3ap87","country_code":"US","type":"education","lineage":["https://openalex.org/I75027704"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeremy C. Smith","raw_affiliation_strings":["UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, and Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996","institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I75027704"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032090372"],"corresponding_institution_ids":["https://openalex.org/I1289243028","https://openalex.org/I75027704"],"apc_list":{"value":4500,"currency":"USD","value_usd":4500},"apc_paid":null,"fwci":0.5363,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.58337138,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"131","issue":"29","first_page":"10083","last_page":"10091"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9628999829292297,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9628999829292297,"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/T11809","display_name":"Advanced NMR Techniques and Applications","score":0.020600000396370888,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.00800000037997961,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/calmodulin","display_name":"calmodulin","score":0.9810000061988831},{"id":"https://openalex.org/keywords/methyl-group-rotation","display_name":"methyl group rotation","score":0.6259999871253967},{"id":"https://openalex.org/keywords/protein-ligand-binding","display_name":"protein-ligand binding","score":0.7799999713897705},{"id":"https://openalex.org/keywords/smooth-muscle-myosin-light-chain-kinase","display_name":"smooth muscle myosin light chain kinase","score":0.8429999947547913},{"id":"https://openalex.org/keywords/peptide-binding","display_name":"peptide binding","score":0.6269999742507935},{"id":"https://openalex.org/keywords/rotational-entropy","display_name":"rotational entropy","score":0.968999981880188},{"id":"https://openalex.org/keywords/nmr-order-parameters","display_name":"NMR order parameters","score":0.8360000252723694},{"id":"https://openalex.org/keywords/rotational-relaxation-time","display_name":"rotational relaxation time","score":0.6850000023841858},{"id":"https://openalex.org/keywords/binding-interface","display_name":"binding interface","score":0.4490000009536743}],"concepts":[{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.8902621269226074},{"id":"https://openalex.org/C29688787","wikidata":"https://www.wikidata.org/wiki/Q409145","display_name":"Calmodulin","level":3,"score":0.8009058833122253},{"id":"https://openalex.org/C2778565081","wikidata":"https://www.wikidata.org/wiki/Q4407","display_name":"Methyl group","level":3,"score":0.5907083749771118},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.5441060066223145},{"id":"https://openalex.org/C2778639546","wikidata":"https://www.wikidata.org/wiki/Q7370322","display_name":"Rotational correlation time","level":3,"score":0.5174837112426758},{"id":"https://openalex.org/C116569031","wikidata":"https://www.wikidata.org/wiki/Q899107","display_name":"Ligand (biochemistry)","level":3,"score":0.468483567237854},{"id":"https://openalex.org/C93282013","wikidata":"https://www.wikidata.org/wiki/Q420754","display_name":"Binding energy","level":2,"score":0.4605258107185364},{"id":"https://openalex.org/C2776029896","wikidata":"https://www.wikidata.org/wiki/Q3935810","display_name":"Relaxation (psychology)","level":2,"score":0.4383009970188141},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.4112258553504944},{"id":"https://openalex.org/C71240020","wikidata":"https://www.wikidata.org/wiki/Q186011","display_name":"Stereochemistry","level":1,"score":0.35848158597946167},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.3401390016078949},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.28771641850471497},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.27030789852142334},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.14154598116874695},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.13304153084754944},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.09649500250816345},{"id":"https://openalex.org/C2781311116","wikidata":"https://www.wikidata.org/wiki/Q83306","display_name":"Group (periodic table)","level":2,"score":0.09567898511886597},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08159339427947998},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07963487505912781},{"id":"https://openalex.org/C184779094","wikidata":"https://www.wikidata.org/wiki/Q26383","display_name":"Atomic physics","level":1,"score":0.07934287190437317},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002147","descriptor_name":"Calmodulin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008745","descriptor_name":"Methylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009218","descriptor_name":"Myosins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009218","descriptor_name":"Myosins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/ja901276n","doi":"https://doi.org/10.1021/ja901276n","is_oa":false,"landing_page_url":"https://doi.org/10.1021/ja901276n","pdf_url":null,"source":{"id":"https://openalex.org/S111155417","display_name":"Journal of the American Chemical Society","issn_l":"0002-7863","issn":["0002-7863","1520-5126","1943-2984"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["cwts-core","dongbi-a","jufo-3","ki-jl-3","medline","norway-2","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":"Journal of the American Chemical Society","raw_type":"journal-article"},{"id":"pmid:19621963","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19621963","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 the American Chemical Society","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W149567199","https://openalex.org/W1487346929","https://openalex.org/W1489910389","https://openalex.org/W1490071206","https://openalex.org/W1502592231","https://openalex.org/W1546896179","https://openalex.org/W1592871544","https://openalex.org/W1596745037","https://openalex.org/W1965008769","https://openalex.org/W1968386558","https://openalex.org/W1974956783","https://openalex.org/W1976391576","https://openalex.org/W1976499671","https://openalex.org/W1979484963","https://openalex.org/W1987159249","https://openalex.org/W1993177346","https://openalex.org/W1994956527","https://openalex.org/W1995270225","https://openalex.org/W2002447487","https://openalex.org/W2006576662","https://openalex.org/W2008336420","https://openalex.org/W2011537276","https://openalex.org/W2014811165","https://openalex.org/W2016045733","https://openalex.org/W2018693480","https://openalex.org/W2021131040","https://openalex.org/W2022888287","https://openalex.org/W2024943432","https://openalex.org/W2025717854","https://openalex.org/W2026381296","https://openalex.org/W2027408247","https://openalex.org/W2029663475","https://openalex.org/W2040796759","https://openalex.org/W2043383780","https://openalex.org/W2044027436","https://openalex.org/W2047220879","https://openalex.org/W2048351441","https://openalex.org/W2050775475","https://openalex.org/W2053590485","https://openalex.org/W2054516131","https://openalex.org/W2059695325","https://openalex.org/W2061095840","https://openalex.org/W2063156348","https://openalex.org/W2063666710","https://openalex.org/W2063801137","https://openalex.org/W2077782280","https://openalex.org/W2081440105","https://openalex.org/W2086429541","https://openalex.org/W2086691291","https://openalex.org/W2090614666","https://openalex.org/W2096921126","https://openalex.org/W2100190064","https://openalex.org/W2103243650","https://openalex.org/W2110791164","https://openalex.org/W2112154906","https://openalex.org/W2129858246","https://openalex.org/W2135412355","https://openalex.org/W2142212546","https://openalex.org/W2145215567","https://openalex.org/W2150981663","https://openalex.org/W2470665661","https://openalex.org/W3005445942"],"related_works":["https://openalex.org/W2090243244","https://openalex.org/W2097985410","https://openalex.org/W1991026841","https://openalex.org/W2071581377","https://openalex.org/W2884393083","https://openalex.org/W2083372974","https://openalex.org/W3194596948","https://openalex.org/W4251812211","https://openalex.org/W2056408100","https://openalex.org/W2013298964"],"abstract_inverted_index":{"Changes":[0],"in":[1,18,77,81,157,165],"the":[2,13,42,49,74,93,116,147,166],"free":[3,52],"energy":[4,53],"barrier":[5,142],"(DeltaE),":[6],"entropy,":[7],"and":[8,44,115,119,144],"motional":[9,107],"parameters":[10,108,126],"associated":[11],"with":[12],"rotation":[14],"of":[15,30,47,73,92],"methyl":[16,50,75,94,110,122],"groups":[17,76,95,152],"a":[19,25,97,138],"protein":[20,167],"(calmodulin":[21],"(CaM))":[22],"on":[23,87,100,163,171],"binding":[24,149],"ligand":[26,64],"(the":[27,109],"calmodulin-binding":[28],"domain":[29],"smooth-muscle":[31],"myosin":[32],"(smMLCKp))":[33],"are":[34,59,69,104,159],"investigated":[35],"using":[36],"molecular":[37],"dynamics":[38],"simulation.":[39],"In":[40],"both":[41],"bound":[43],"uncomplexed":[45],"forms":[46],"CaM,":[48],"rotational":[51,90,111,124,141],"barriers":[54],"follow":[55],"skewed-Gaussian":[56],"distributions":[57],"that":[58,153],"not":[60],"altered":[61],"significantly":[62],"upon":[63],"binding.":[65,88,172],"However,":[66],"site-specific":[67],"perturbations":[68],"found.":[70],"Around":[71],"11%":[72],"CaM":[78],"exhibit":[79,96,154],"changes":[80,143,156],"DeltaE":[82,158],"greater":[83],"than":[84],"0.7":[85],"kcal/mol":[86],"The":[89,102],"entropies":[91],"nonlinear":[98],"dependence":[99],"DeltaE.":[101,120],"relations":[103],"examined":[105],"between":[106,140],"NMR":[112],"order":[113,125],"parameter":[114],"relaxation":[117],"time)":[118],"Low-barrier":[121],"group":[123],"deviate":[127],"from":[128],"ideal":[129],"tetrahedrality":[130],"by":[131],"up":[132],"to":[133,146,161],"approximately":[134],"20%.":[135],"There":[136],"is":[137],"correlation":[139],"proximity":[145],"protein-peptide":[148],"interface.":[150],"Methyl":[151],"large":[155],"found":[160],"report":[162],"elements":[164],"undergoing":[168],"structural":[169],"change":[170]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}