{"id":"https://openalex.org/W2061910182","doi":"https://doi.org/10.1063/1.4752247","title":"Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization","display_name":"Lattice model simulations of the effects of the position of a peptide trigger segment on helix folding and dimerization","publication_year":2012,"publication_date":"2012-09-13","ids":{"openalex":"https://openalex.org/W2061910182","doi":"https://doi.org/10.1063/1.4752247","mag":"2061910182","pmid":"https://pubmed.ncbi.nlm.nih.gov/22979897"},"language":"en","primary_location":{"id":"doi:10.1063/1.4752247","doi":"https://doi.org/10.1063/1.4752247","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.4752247","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"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-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},"volume":null,"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/A5002220991","display_name":"Yuba R. Bhandari","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuba R. Bhandari","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199, USA","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071186045","display_name":"Prem P. Chapagain","orcid":"https://orcid.org/0000-0002-0999-4975","observed_orcids":["https://orcid.org/0000-0002-0999-4975"]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Prem P. Chapagain","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199, USA","FLORIDA INTERNATIONAL UNIVERSITY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199, USA","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"FLORIDA INTERNATIONAL UNIVERSITY","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063623074","display_name":"Bernard S. Gerstman","orcid":"https://orcid.org/0000-0003-4258-529X","observed_orcids":["https://orcid.org/0000-0003-4258-529X"]},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bernard S. Gerstman","raw_affiliation_strings":["Florida International University Department of Physics, , University Park, Miami, Florida 33199, USA","FLORIDA INTERNATIONAL UNIVERSITY"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Florida International University Department of Physics, , University Park, Miami, Florida 33199, USA","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"FLORIDA INTERNATIONAL UNIVERSITY","institution_ids":["https://openalex.org/I19700959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I19700959"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":null,"fwci":0.107,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.42160177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"137","issue":"10","first_page":"105103","last_page":"105103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9980000257492065,"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":0.9980000257492065,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.0005000000237487257,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic 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/alpha-helix-folding","display_name":"alpha-helix folding","score":0.7540000081062317},{"id":"https://openalex.org/keywords/protein-dimerization","display_name":"protein dimerization","score":0.9210000038146973},{"id":"https://openalex.org/keywords/salt-bridges","display_name":"salt bridges","score":0.8080000281333923},{"id":"https://openalex.org/keywords/interhelical-interactions","display_name":"interhelical interactions","score":0.9399999976158142},{"id":"https://openalex.org/keywords/folding-kinetics","display_name":"folding kinetics","score":0.8330000042915344},{"id":"https://openalex.org/keywords/folding-free-energy","display_name":"folding free energy","score":0.7459999918937683},{"id":"https://openalex.org/keywords/heat-capacity","display_name":"heat capacity","score":0.8650000095367432},{"id":"https://openalex.org/keywords/dimer-stability","display_name":"dimer stability","score":0.8659999966621399},{"id":"https://openalex.org/keywords/protein-design","display_name":"protein design","score":0.5450000166893005},{"id":"https://openalex.org/keywords/lattice-model","display_name":"lattice model","score":0.8420000076293945}],"concepts":[{"id":"https://openalex.org/C2779546866","wikidata":"https://www.wikidata.org/wiki/Q531306","display_name":"Dimer","level":2,"score":0.842024564743042},{"id":"https://openalex.org/C2776545253","wikidata":"https://www.wikidata.org/wiki/Q5464292","display_name":"Folding (DSP implementation)","level":2,"score":0.6567885875701904},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.5899043679237366},{"id":"https://openalex.org/C204328495","wikidata":"https://www.wikidata.org/wiki/Q847556","display_name":"Protein folding","level":2,"score":0.5796864628791809},{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.550892174243927},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.544292151927948},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.524997353553772},{"id":"https://openalex.org/C2779281246","wikidata":"https://www.wikidata.org/wiki/Q172847","display_name":"Peptide","level":2,"score":0.521307647228241},{"id":"https://openalex.org/C2778530040","wikidata":"https://www.wikidata.org/wiki/Q1937315","display_name":"Helix (gastropod)","level":3,"score":0.4826350808143616},{"id":"https://openalex.org/C135889238","wikidata":"https://www.wikidata.org/wiki/Q46276","display_name":"Kinetic energy","level":2,"score":0.42754215002059937},{"id":"https://openalex.org/C2781204021","wikidata":"https://www.wikidata.org/wiki/Q6497091","display_name":"Lattice (music)","level":2,"score":0.424642413854599},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.41719287633895874},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.37669119238853455},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.23290258646011353},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.22961565852165222},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"score":0.08250850439071655},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0756915807723999},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C2779965526","wikidata":"https://www.wikidata.org/wiki/Q308841","display_name":"Snail","level":2,"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/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D013816","descriptor_name":"Thermodynamics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017510","descriptor_name":"Protein Folding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019281","descriptor_name":"Dimerization","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":true}],"locations_count":2,"locations":[{"id":"doi:10.1063/1.4752247","doi":"https://doi.org/10.1063/1.4752247","is_oa":false,"landing_page_url":"https://doi.org/10.1063/1.4752247","pdf_url":null,"source":{"id":"https://openalex.org/S77047749","display_name":"The Journal of Chemical Physics","issn_l":"0021-9606","issn":["0021-9606","1089-7690","1520-9032"],"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-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320257","host_organization_name":"American Institute of Physics","host_organization_lineage":["https://openalex.org/P4310320257"],"host_organization_lineage_names":["American Institute of Physics"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The Journal of Chemical Physics","raw_type":"journal-article"},{"id":"pmid:22979897","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22979897","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":"The Journal of chemical physics","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":43,"referenced_works":["https://openalex.org/W1538731614","https://openalex.org/W1961177618","https://openalex.org/W1964521402","https://openalex.org/W1971314619","https://openalex.org/W1973766927","https://openalex.org/W1977312918","https://openalex.org/W1977803857","https://openalex.org/W1983612150","https://openalex.org/W1991451475","https://openalex.org/W1991999468","https://openalex.org/W1996905580","https://openalex.org/W1998875094","https://openalex.org/W2001818491","https://openalex.org/W2015546050","https://openalex.org/W2016162029","https://openalex.org/W2021843093","https://openalex.org/W2022859590","https://openalex.org/W2029691162","https://openalex.org/W2032092670","https://openalex.org/W2032892814","https://openalex.org/W2037169923","https://openalex.org/W2037349497","https://openalex.org/W2040660768","https://openalex.org/W2042172415","https://openalex.org/W2051039246","https://openalex.org/W2055290772","https://openalex.org/W2058067565","https://openalex.org/W2079677554","https://openalex.org/W2080851686","https://openalex.org/W2091492447","https://openalex.org/W2091582055","https://openalex.org/W2092424728","https://openalex.org/W2094364221","https://openalex.org/W2095130514","https://openalex.org/W2100447226","https://openalex.org/W2100784948","https://openalex.org/W2104121136","https://openalex.org/W2121911824","https://openalex.org/W2122627381","https://openalex.org/W2133792795","https://openalex.org/W2142857418","https://openalex.org/W2158303080","https://openalex.org/W2165499430"],"related_works":["https://openalex.org/W224865965","https://openalex.org/W1991451475","https://openalex.org/W2010225110","https://openalex.org/W2618334148","https://openalex.org/W1543703735","https://openalex.org/W345795906","https://openalex.org/W2044006724","https://openalex.org/W2021380050","https://openalex.org/W1996905580","https://openalex.org/W1996466860"],"abstract_inverted_index":{"The":[0,156,168,212,228,249],"folding":[1,153,166,252],"and":[2,58,94,117,138,143,154,170,253],"dimerization":[3,47,181],"of":[4,12,18,35,44,61,74,91,97,113,132,141,152,158,183,201,209,214,217,237],"proteins":[5,261],"is":[6,161,187,196,225],"greatly":[7],"facilitated":[8,51],"by":[9,52,163],"the":[10,33,36,41,72,89,95,98,111,114,122,125,133,150,159,174,180,184,190,202,207,210,215,218,221,235,238],"presence":[11],"a":[13,16,23,78,232,242],"trigger":[14,115,134,222,264],"site,":[15],"segment":[17,116,191],"amino":[19],"acids":[20],"that":[21,179,245,262],"has":[22],"higher":[24],"propensity":[25,43,195],"for":[26,259],"forming":[27],"\u03b1-helix":[28],"structure":[29],"as":[30,56,204],"compared":[31,205],"to":[32,40,108,148,177,206,240],"rest":[34],"chain.":[37,211],"In":[38,64],"addition":[39],"helical":[42,194],"each":[45],"chain,":[46],"can":[48,230],"also":[49,226],"be":[50],"interhelical":[53],"interactions":[54,76,87],"such":[55],"saltbridges,":[57],"interfacial":[59],"contacts":[60],"different":[62,86,130],"strengths.":[63],"this":[65],"work,":[66],"we":[67],"are":[68,146],"interested":[69],"in":[70,77,234],"understanding":[71],"interplay":[73],"these":[75,85],"model":[79,105,185],"peptide":[80],"system.":[81],"We":[82,102],"investigate":[83,109],"how":[84,110],"influence":[88],"kinetics":[90,157],"dimer":[92,219,239,254],"formation":[93],"stability":[96,216,229,255],"fully":[99],"formed":[100],"dimer.":[101],"use":[103],"lattice":[104],"computer":[106],"simulations":[107,175],"effectiveness":[112],"its":[118],"saltbridges":[119],"depends":[120],"on":[121,220,251],"location":[123],"along":[124],"protein":[126],"primary":[127],"sequence.":[128],"For":[129],"positions":[131],"segment,":[135],"heat":[136],"capacity":[137],"free":[139],"energy":[140],"unfolded":[142],"folded":[144],"configurations":[145],"calculated":[147],"study":[149],"thermodynamics":[151],"dimerization.":[155],"process":[160,182],"investigated":[162],"calculating":[164],"characteristic":[165],"times.":[167],"thermodynamic":[169],"kinetic":[171],"data":[172],"from":[173],"combine":[176],"show":[178],"system":[186],"faster":[188],"when":[189],"with":[192],"high":[193],"located":[197],"near":[198],"either":[199],"end":[200],"peptide,":[203],"middle":[208],"dependence":[213],"segment's":[223],"position":[224],"studied.":[227],"play":[231],"role":[233],"ability":[236],"perform":[241],"biological":[243],"function":[244],"involves":[246],"partial":[247],"unzipping.":[248],"results":[250],"provide":[256],"important":[257],"insights":[258],"designing":[260],"involve":[263],"sites.":[265]},"counts_by_year":[{"year":2017,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}