{"id":"https://openalex.org/W4409623267","doi":"https://doi.org/10.1021/acs.jcim.5c00401","title":"Methyl\u2022\u2022\u2022Methyl Interactions in Proteins: Insights from Structural and Computational Studies","display_name":"Methyl\u2022\u2022\u2022Methyl Interactions in Proteins: Insights from Structural and Computational Studies","publication_year":2025,"publication_date":"2025-04-21","ids":{"openalex":"https://openalex.org/W4409623267","doi":"https://doi.org/10.1021/acs.jcim.5c00401","pmid":"https://pubmed.ncbi.nlm.nih.gov/40256983"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00401","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00401","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/A5010706623","display_name":"Juhi Dutta","orcid":"https://orcid.org/0000-0001-6078-794X"},"institutions":[{"id":"https://openalex.org/I163389970","display_name":"National Institute of Science Education and Research","ror":"https://ror.org/02r2k1c68","country_code":"IN","type":"education","lineage":["https://openalex.org/I163389970","https://openalex.org/I200207707"]},{"id":"https://openalex.org/I200207707","display_name":"Homi Bhabha National Institute","ror":"https://ror.org/02bv3zr67","country_code":"IN","type":"education","lineage":["https://openalex.org/I200207707"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Juhi Dutta","raw_affiliation_strings":["Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India"],"affiliations":[{"raw_affiliation_string":"Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","institution_ids":["https://openalex.org/I200207707"]},{"raw_affiliation_string":"School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India","institution_ids":["https://openalex.org/I163389970"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035490501","display_name":"Akshay Kumar Sahu","orcid":"https://orcid.org/0000-0002-9041-0112"},"institutions":[{"id":"https://openalex.org/I163389970","display_name":"National Institute of Science Education and Research","ror":"https://ror.org/02r2k1c68","country_code":"IN","type":"education","lineage":["https://openalex.org/I163389970","https://openalex.org/I200207707"]},{"id":"https://openalex.org/I200207707","display_name":"Homi Bhabha National Institute","ror":"https://ror.org/02bv3zr67","country_code":"IN","type":"education","lineage":["https://openalex.org/I200207707"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Akshay Kumar Sahu","raw_affiliation_strings":["Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India"],"affiliations":[{"raw_affiliation_string":"Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","institution_ids":["https://openalex.org/I200207707"]},{"raw_affiliation_string":"School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India","institution_ids":["https://openalex.org/I163389970"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070588518","display_name":"Subhrakant Jena","orcid":"https://orcid.org/0000-0001-9474-821X"},"institutions":[{"id":"https://openalex.org/I163389970","display_name":"National Institute of Science Education and Research","ror":"https://ror.org/02r2k1c68","country_code":"IN","type":"education","lineage":["https://openalex.org/I163389970","https://openalex.org/I200207707"]},{"id":"https://openalex.org/I200207707","display_name":"Homi Bhabha National Institute","ror":"https://ror.org/02bv3zr67","country_code":"IN","type":"education","lineage":["https://openalex.org/I200207707"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Subhrakant Jena","raw_affiliation_strings":["Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India"],"affiliations":[{"raw_affiliation_string":"Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","institution_ids":["https://openalex.org/I200207707"]},{"raw_affiliation_string":"School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India","institution_ids":["https://openalex.org/I163389970"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000779109","display_name":"Himansu S. Biswal","orcid":"https://orcid.org/0000-0003-0791-2259"},"institutions":[{"id":"https://openalex.org/I163389970","display_name":"National Institute of Science Education and Research","ror":"https://ror.org/02r2k1c68","country_code":"IN","type":"education","lineage":["https://openalex.org/I163389970","https://openalex.org/I200207707"]},{"id":"https://openalex.org/I200207707","display_name":"Homi Bhabha National Institute","ror":"https://ror.org/02bv3zr67","country_code":"IN","type":"education","lineage":["https://openalex.org/I200207707"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Himansu S. Biswal","raw_affiliation_strings":["Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India"],"affiliations":[{"raw_affiliation_string":"Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India","institution_ids":["https://openalex.org/I200207707"]},{"raw_affiliation_string":"School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, Bhubaneswar PIN 752050, India","institution_ids":["https://openalex.org/I163389970"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000779109"],"corresponding_institution_ids":["https://openalex.org/I163389970","https://openalex.org/I200207707"],"apc_list":null,"apc_paid":null,"fwci":0.8073,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.71114646,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"65","issue":"9","first_page":"4729","last_page":"4739"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9983000159263611,"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":0.9983000159263611,"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/T10798","display_name":"Crystallography and molecular interactions","score":0.9911999702453613,"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"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.9890999794006348,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4709290862083435},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.41974738240242004},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3252517879009247}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4709290862083435},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.41974738240242004},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3252517879009247}],"mesh":[{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","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":"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00401","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00401","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:40256983","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40256983","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":[{"display_name":"Zero hunger","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/2"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320768","display_name":"Department of Atomic Energy, Government of India","ror":"https://ror.org/02m388s04"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":99,"referenced_works":["https://openalex.org/W135786528","https://openalex.org/W1187950418","https://openalex.org/W1487413481","https://openalex.org/W1568111217","https://openalex.org/W1964277385","https://openalex.org/W1966949133","https://openalex.org/W1969169061","https://openalex.org/W1973021508","https://openalex.org/W1986191798","https://openalex.org/W1987392154","https://openalex.org/W1988982985","https://openalex.org/W1989474096","https://openalex.org/W1993077801","https://openalex.org/W1999680479","https://openalex.org/W2000975220","https://openalex.org/W2001404485","https://openalex.org/W2008995741","https://openalex.org/W2009292272","https://openalex.org/W2013030049","https://openalex.org/W2016373164","https://openalex.org/W2017985925","https://openalex.org/W2020865957","https://openalex.org/W2021163287","https://openalex.org/W2021200484","https://openalex.org/W2023232001","https://openalex.org/W2023795624","https://openalex.org/W2024163549","https://openalex.org/W2025759763","https://openalex.org/W2027270560","https://openalex.org/W2029667189","https://openalex.org/W2033558148","https://openalex.org/W2044591029","https://openalex.org/W2045529907","https://openalex.org/W2055125957","https://openalex.org/W2056158778","https://openalex.org/W2060248710","https://openalex.org/W2060287713","https://openalex.org/W2060412313","https://openalex.org/W2079017121","https://openalex.org/W2093981928","https://openalex.org/W2094779541","https://openalex.org/W2096747776","https://openalex.org/W2104919283","https://openalex.org/W2107676206","https://openalex.org/W2117813821","https://openalex.org/W2120402304","https://openalex.org/W2126342963","https://openalex.org/W2130479394","https://openalex.org/W2132525235","https://openalex.org/W2134036374","https://openalex.org/W2143981217","https://openalex.org/W2170402416","https://openalex.org/W2185372522","https://openalex.org/W2265596863","https://openalex.org/W2283384996","https://openalex.org/W2319800489","https://openalex.org/W2324145887","https://openalex.org/W2518751208","https://openalex.org/W2586299966","https://openalex.org/W2605402476","https://openalex.org/W2739354641","https://openalex.org/W2752619161","https://openalex.org/W2758698892","https://openalex.org/W2764287601","https://openalex.org/W2788835357","https://openalex.org/W2796309353","https://openalex.org/W2804428227","https://openalex.org/W2890100083","https://openalex.org/W2897197650","https://openalex.org/W2915077077","https://openalex.org/W2983142403","https://openalex.org/W2983680023","https://openalex.org/W2990537375","https://openalex.org/W3013302298","https://openalex.org/W3016161630","https://openalex.org/W3042838583","https://openalex.org/W3080639832","https://openalex.org/W3111819906","https://openalex.org/W3112612284","https://openalex.org/W3190366419","https://openalex.org/W3208006447","https://openalex.org/W3210226264","https://openalex.org/W4221019465","https://openalex.org/W4233998925","https://openalex.org/W4240035468","https://openalex.org/W4280535719","https://openalex.org/W4292493013","https://openalex.org/W4312114024","https://openalex.org/W4363609397","https://openalex.org/W4381798972","https://openalex.org/W4383335015","https://openalex.org/W4387622872","https://openalex.org/W4388013848","https://openalex.org/W4388622814","https://openalex.org/W4389347920","https://openalex.org/W4391592788","https://openalex.org/W4393866906","https://openalex.org/W4394716207","https://openalex.org/W4406905282"],"related_works":["https://openalex.org/W4387497383","https://openalex.org/W2948807893","https://openalex.org/W2899084033","https://openalex.org/W2778153218","https://openalex.org/W2748952813","https://openalex.org/W1531601525","https://openalex.org/W4391375266","https://openalex.org/W2078814861","https://openalex.org/W2527526854","https://openalex.org/W1976181487"],"abstract_inverted_index":{"The":[0],"low":[1],"affinity":[2],"of":[3,12,29,37,53,58,67,72,81,124,140,171],"nonpolar":[4,43],"groups":[5],"for":[6,129,167],"water":[7],"gave":[8],"birth":[9],"to":[10,98,106],"one":[11],"the":[13,26,34,54,63,121,130,157],"significant":[14,35],"supramolecular":[15],"forces":[16,40],"known":[17],"as":[18,21,23],"hydrophobic":[19],"interaction":[20,93],"early":[22],"1937.":[24],"While":[25],"precise":[27],"origins":[28],"this":[30],"phenomenon":[31],"remain":[32],"debated,":[33],"role":[36],"London":[38],"dispersion":[39,107],"in":[41],"stabilizing":[42],"complexes":[44],"is":[45,127,144],"well-established.":[46],"This":[47],"article":[48],"presents":[49],"a":[50,70,111],"comprehensive":[51],"investigation":[52],"nature":[55],"and":[56,76,134,156,174,178],"strength":[57,177],"CH<sub>3</sub>\u2022\u2022\u2022H<sub>3</sub>C":[59,117,172],"(methyl-methyl)":[60],"interactions":[61,89,118,126,143,173],"within":[62],"amino":[64],"acid":[65],"residues":[66],"proteins,":[68],"employing":[69],"combination":[71],"quantum":[73],"mechanical":[74],"calculations":[75],"custom":[77],"Python":[78],"code.":[79],"Analysis":[80],"isolated":[82],"mimetic":[83],"dipeptide":[84],"models":[85],"reveals":[86],"that":[87,152],"these":[88,141],"are":[90,103,119],"weak,":[91,120],"with":[92],"energies":[94,102],"ranging":[95],"from":[96],"-2.40":[97],"-6.94":[99],"kJ/mol.":[100],"These":[101],"primarily":[104],"attributed":[105],"forces,":[108],"supplemented":[109],"by":[110],"minor":[112],"electrostatic":[113],"contribution.":[114],"Even":[115],"though":[116],"cumulative":[122],"effect":[123],"such":[125],"vital":[128],"flexible":[131],"enzymatic":[132],"center":[133],"drug-protein":[135],"interactions.":[136],"Although":[137],"experimental":[138],"characterization":[139],"weak":[142],"challenging,":[145],"our":[146],"computational":[147],"studies,":[148],"presented":[149],"herein,":[150],"suggest":[151],"solution-phase":[153],"<sup>13</sup>C":[154],"NMR":[155],"recently":[158],"developed":[159],"gas-phase":[160],"terahertz":[161],"(THz)":[162],"spectroscopy":[163],"offer":[164],"promising":[165],"avenues":[166],"obtaining":[168],"spectroscopic":[169],"signatures":[170],"elucidating":[175],"their":[176],"molecular":[179],"origin.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
