{"id":"https://openalex.org/W2945081200","doi":"https://doi.org/10.1021/acs.jcim.9b00098","title":"Effects of Metal Ions on A\u03b2<sub>42</sub> Peptide Conformations from Molecular Simulation Studies","display_name":"Effects of Metal Ions on A\u03b2<sub>42</sub> Peptide Conformations from Molecular Simulation Studies","publication_year":2019,"publication_date":"2019-05-16","ids":{"openalex":"https://openalex.org/W2945081200","doi":"https://doi.org/10.1021/acs.jcim.9b00098","mag":"2945081200","pmid":"https://pubmed.ncbi.nlm.nih.gov/31095382"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b00098","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00098","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/A5048994371","display_name":"Prabir Khatua","orcid":"https://orcid.org/0000-0002-5336-7645"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Prabir Khatua","raw_affiliation_strings":["Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India","institution_ids":["https://openalex.org/I145894827"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057115914","display_name":"Souvik Mondal","orcid":"https://orcid.org/0000-0001-5225-6233"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Souvik Mondal","raw_affiliation_strings":["Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India","institution_ids":["https://openalex.org/I145894827"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051434187","display_name":"Sanjoy Bandyopadhyay","orcid":"https://orcid.org/0000-0002-3267-6326"},"institutions":[{"id":"https://openalex.org/I145894827","display_name":"Indian Institute of Technology Kharagpur","ror":"https://ror.org/03w5sq511","country_code":"IN","type":"education","lineage":["https://openalex.org/I145894827"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Sanjoy Bandyopadhyay","raw_affiliation_strings":["Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India","Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India"],"raw_orcid":"https://orcid.org/0000-0002-3267-6326","affiliations":[{"raw_affiliation_string":"Centre for Computational and Data Sciences, Indian Institute of Technology, Kharagpur 721302, India","institution_ids":["https://openalex.org/I145894827"]},{"raw_affiliation_string":"Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India","institution_ids":["https://openalex.org/I145894827"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5051434187"],"corresponding_institution_ids":["https://openalex.org/I145894827"],"apc_list":null,"apc_paid":null,"fwci":0.8548,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.72543654,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"59","issue":"6","first_page":"2879","last_page":"2893"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9975000023841858,"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":0.9975000023841858,"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/T10570","display_name":"Drug Transport and Resistance Mechanisms","score":0.9932000041007996,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/T11419","display_name":"Supramolecular Self-Assembly in Materials","score":0.9866999983787537,"subfield":{"id":"https://openalex.org/subfields/2502","display_name":"Biomaterials"},"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/molecular-dynamics","display_name":"Molecular dynamics","score":0.7542463541030884},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.7198256254196167},{"id":"https://openalex.org/keywords/ion","display_name":"Ion","score":0.7097090482711792},{"id":"https://openalex.org/keywords/monomer","display_name":"Monomer","score":0.7011946439743042},{"id":"https://openalex.org/keywords/peptide","display_name":"Peptide","score":0.6883552670478821},{"id":"https://openalex.org/keywords/metal-ions-in-aqueous-solution","display_name":"Metal ions in aqueous solution","score":0.6067676544189453},{"id":"https://openalex.org/keywords/divalent","display_name":"Divalent","score":0.5901138782501221},{"id":"https://openalex.org/keywords/crystallography","display_name":"Crystallography","score":0.5868405699729919},{"id":"https://openalex.org/keywords/metal","display_name":"Metal","score":0.53709876537323},{"id":"https://openalex.org/keywords/helix","display_name":"Helix (gastropod)","score":0.48872804641723633},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.254422128200531},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.08427149057388306},{"id":"https://openalex.org/keywords/polymer","display_name":"Polymer","score":0.08104872703552246}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7542463541030884},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.7198256254196167},{"id":"https://openalex.org/C145148216","wikidata":"https://www.wikidata.org/wiki/Q36496","display_name":"Ion","level":2,"score":0.7097090482711792},{"id":"https://openalex.org/C166940927","wikidata":"https://www.wikidata.org/wiki/Q178827","display_name":"Monomer","level":3,"score":0.7011946439743042},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.6883552670478821},{"id":"https://openalex.org/C199164860","wikidata":"https://www.wikidata.org/wiki/Q6822745","display_name":"Metal ions in aqueous solution","level":3,"score":0.6067676544189453},{"id":"https://openalex.org/C74884574","wikidata":"https://www.wikidata.org/wiki/Q171407","display_name":"Divalent","level":2,"score":0.5901138782501221},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.5868405699729919},{"id":"https://openalex.org/C544153396","wikidata":"https://www.wikidata.org/wiki/Q11426","display_name":"Metal","level":2,"score":0.53709876537323},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.48872804641723633},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.254422128200531},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.08427149057388306},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.08104872703552246},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D010446","descriptor_name":"Peptide Fragments","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D012964","descriptor_name":"Sodium","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D012964","descriptor_name":"Sodium","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D012964","descriptor_name":"Sodium","qualifier_ui":"Q000494","qualifier_name":"pharmacology","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":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D015032","descriptor_name":"Zinc","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D055550","descriptor_name":"Protein Stability","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","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":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b00098","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b00098","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:31095382","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31095382","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":"Affordable and clean energy","score":0.8799999952316284,"id":"https://metadata.un.org/sdg/7"}],"awards":[{"id":"https://openalex.org/G1314386995","display_name":null,"funder_award_id":"18-12/2011(ii)EU-V","funder_id":"https://openalex.org/F4320320767","funder_display_name":"University Grants Commission"},{"id":"https://openalex.org/G7038681531","display_name":null,"funder_award_id":"09/081(1272)/2015-EMR-I","funder_id":"https://openalex.org/F4320320721","funder_display_name":"Council of Scientific and Industrial Research, India"}],"funders":[{"id":"https://openalex.org/F4320320721","display_name":"Council of Scientific and Industrial Research, India","ror":"https://ror.org/021wm7p51"},{"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":81,"referenced_works":["https://openalex.org/W230984257","https://openalex.org/W1506028353","https://openalex.org/W1632936309","https://openalex.org/W1897372423","https://openalex.org/W1968041782","https://openalex.org/W1976499671","https://openalex.org/W1979773315","https://openalex.org/W1980350354","https://openalex.org/W1980825524","https://openalex.org/W1981751229","https://openalex.org/W1981889004","https://openalex.org/W1985992988","https://openalex.org/W1986934575","https://openalex.org/W1992921903","https://openalex.org/W1997766662","https://openalex.org/W1998643862","https://openalex.org/W2005286629","https://openalex.org/W2006419295","https://openalex.org/W2007710639","https://openalex.org/W2009833553","https://openalex.org/W2011691446","https://openalex.org/W2011810121","https://openalex.org/W2013615657","https://openalex.org/W2015119496","https://openalex.org/W2017829285","https://openalex.org/W2018333394","https://openalex.org/W2024473468","https://openalex.org/W2025717854","https://openalex.org/W2027408247","https://openalex.org/W2028702957","https://openalex.org/W2029667189","https://openalex.org/W2031273125","https://openalex.org/W2032684305","https://openalex.org/W2038758364","https://openalex.org/W2040809566","https://openalex.org/W2042287552","https://openalex.org/W2049492779","https://openalex.org/W2050333027","https://openalex.org/W2051609969","https://openalex.org/W2057742133","https://openalex.org/W2058838294","https://openalex.org/W2063462994","https://openalex.org/W2067174909","https://openalex.org/W2070377130","https://openalex.org/W2072327749","https://openalex.org/W2073250936","https://openalex.org/W2076063919","https://openalex.org/W2077917242","https://openalex.org/W2081126811","https://openalex.org/W2083500052","https://openalex.org/W2087947213","https://openalex.org/W2091990417","https://openalex.org/W2094808560","https://openalex.org/W2095674336","https://openalex.org/W2096410114","https://openalex.org/W2106140689","https://openalex.org/W2110101020","https://openalex.org/W2115134759","https://openalex.org/W2118608964","https://openalex.org/W2121374178","https://openalex.org/W2121963977","https://openalex.org/W2122294662","https://openalex.org/W2137605538","https://openalex.org/W2141920771","https://openalex.org/W2149060580","https://openalex.org/W2150109193","https://openalex.org/W2150981663","https://openalex.org/W2160664224","https://openalex.org/W2165186407","https://openalex.org/W2165779834","https://openalex.org/W2240761048","https://openalex.org/W2314153262","https://openalex.org/W2320383960","https://openalex.org/W2400751364","https://openalex.org/W2414526397","https://openalex.org/W2527024095","https://openalex.org/W2531905581","https://openalex.org/W2625492010","https://openalex.org/W2751625684","https://openalex.org/W2783649277","https://openalex.org/W4388229418"],"related_works":["https://openalex.org/W2099163750","https://openalex.org/W1983113636","https://openalex.org/W2165143094","https://openalex.org/W2014190932","https://openalex.org/W2149247615","https://openalex.org/W2109467985","https://openalex.org/W4234765684","https://openalex.org/W1974727230","https://openalex.org/W2069857733","https://openalex.org/W2083798919"],"abstract_inverted_index":{"In":[0],"this":[1],"study,":[2],"we":[3],"investigate":[4],"the":[5,14,33,42,45,53,59,64,100,111,125,139,143,157,167,176,191,198],"conformational":[6,60],"characteristics":[7],"of":[8,16,41,47,55,116,120,127,138,146,161,170,178,190,200],"full-length":[9],"A\u03b242":[10],"peptide":[11,151,195],"monomers":[12,196],"in":[13,44,124,136,175,197],"presence":[15,46,54,126,177,199],"Na+":[17,128,184],"and":[18,84,94,109,213],"Zn2+":[19,147,180,201],"metal":[20,56],"ions":[21,57,129,181,202],"using":[22],"atomistic":[23],"molecular":[24],"dynamics":[25],"(MD)":[26],"simulations":[27],"with":[28,209],"an":[29],"aim":[30],"to":[31,98,134,149,206],"explore":[32],"possible":[34],"driving":[35],"forces":[36],"behind":[37],"enhanced":[38],"aggregation":[39,101,112,168],"rates":[40],"peptides":[43,172],"salts.":[48],"The":[49],"calculations":[50],"reveal":[51],"that":[52],"shifts":[58],"equilibrium":[61],"more":[62],"toward":[63],"compact":[65,70],"ordered":[66,71],"A\u03b2":[67,150,171,194],"structures.":[68,114],"Such":[69],"structures":[72],"stabilized":[73],"by":[74,107],"distant":[75,122],"nonlocal":[76],"contacts":[77,123],"between":[78],"two":[79,88],"crucial":[80],"hydrophobic":[81,90],"segments,":[82],"hp1":[83],"hp2,":[85],"primarily":[86],"through":[87],"important":[89],"aromatic":[91],"residues,":[92],"Phe-19":[93],"Phe-20,":[95],"are":[96],"expected":[97],"trigger":[99],"process":[102],"at":[103],"a":[104,117],"faster":[105],"rate":[106,169],"populating":[108],"stabilizing":[110],"prone":[113],"Formation":[115],"significant":[118,214],"number":[119],"such":[121],"has":[130,203],"also":[131],"been":[132,204],"found":[133,205],"result":[135],"breaking":[137,162],"N-terminal":[140,158],"helix.":[141],"On":[142],"contrary,":[144],"binding":[145,212],"ion":[148],"is":[152,173],"highly":[153],"specific,":[154],"which":[155],"stabilizes":[156],"helix":[159],"instead":[160],"it.":[163],"This":[164],"explains":[165],"why":[166],"higher":[174,187],"divalent":[179],"than":[182],"monovalent":[183],"ions.":[185],"Relatively":[186],"overall":[188],"stability":[189],"most":[192],"populated":[193],"be":[207],"associated":[208],"specific":[210],"Zn2+\u2013A\u03b2":[211],"free":[215],"energy":[216],"gain.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":6},{"year":2019,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}