{"id":"https://openalex.org/W4403171686","doi":"https://doi.org/10.1021/acs.jcim.4c01050","title":"Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation","display_name":"Simulation-Guided Molecular Modeling of Nisin and Lipid II Assembly and Membrane Pore Formation","publication_year":2024,"publication_date":"2024-10-07","ids":{"openalex":"https://openalex.org/W4403171686","doi":"https://doi.org/10.1021/acs.jcim.4c01050","pmid":"https://pubmed.ncbi.nlm.nih.gov/39370850"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01050","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01050","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/A5108265743","display_name":"Hugo A. Perez","orcid":null},"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":"Hugo A. Perez","raw_affiliation_strings":["Department of Physics, Florida International University, Miami, Florida 33199, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407678","display_name":"Zhe Wang","orcid":"https://orcid.org/0000-0003-3762-3167"},"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":"Zhe Wang","raw_affiliation_strings":["Department of Physics, Florida International University, Miami, Florida 33199, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063623074","display_name":"Bernard S. Gerstman","orcid":"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":["Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States","Department of Physics, Florida International University, Miami, Florida 33199, United States"],"raw_orcid":"https://orcid.org/0000-0003-4258-529X","affiliations":[{"raw_affiliation_string":"Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"Department of Physics, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047137763","display_name":"Jin He","orcid":"https://orcid.org/0000-0002-2633-9809"},"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":"Jin He","raw_affiliation_strings":["Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States","Department of Physics, Florida International University, Miami, Florida 33199, United States"],"raw_orcid":"https://orcid.org/0000-0002-2633-9809","affiliations":[{"raw_affiliation_string":"Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"Department of Physics, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071186045","display_name":"Prem P. Chapagain","orcid":"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":true,"raw_author_name":"Prem P. Chapagain","raw_affiliation_strings":["Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States","Department of Physics, Florida International University, Miami, Florida 33199, United States"],"raw_orcid":"https://orcid.org/0000-0002-0999-4975","affiliations":[{"raw_affiliation_string":"Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]},{"raw_affiliation_string":"Department of Physics, Florida International University, Miami, Florida 33199, United States","institution_ids":["https://openalex.org/I19700959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5071186045"],"corresponding_institution_ids":["https://openalex.org/I19700959"],"apc_list":null,"apc_paid":null,"fwci":0.9331,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.74335823,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"64","issue":"20","first_page":"7977","last_page":"7986"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9998000264167786,"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/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.9998000264167786,"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":0.9980999827384949,"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/T10120","display_name":"Bacterial Genetics and Biotechnology","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/nisin","display_name":"Nisin","score":0.8870226144790649},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5687346458435059},{"id":"https://openalex.org/keywords/lipid-ii","display_name":"Lipid II","score":0.5172812938690186},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.45452913641929626},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.27448031306266785},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.1252916157245636},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.0653289258480072}],"concepts":[{"id":"https://openalex.org/C2778457984","wikidata":"https://www.wikidata.org/wiki/Q415798","display_name":"Nisin","level":3,"score":0.8870226144790649},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5687346458435059},{"id":"https://openalex.org/C2780183148","wikidata":"https://www.wikidata.org/wiki/Q21099571","display_name":"Lipid II","level":4,"score":0.5172812938690186},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.45452913641929626},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.27448031306266785},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.1252916157245636},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.0653289258480072},{"id":"https://openalex.org/C4937899","wikidata":"https://www.wikidata.org/wiki/Q68541106","display_name":"Antimicrobial","level":2,"score":0.0},{"id":"https://openalex.org/C2776634448","wikidata":"https://www.wikidata.org/wiki/Q206920","display_name":"Peptidoglycan","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D009561","descriptor_name":"Nisin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010714","descriptor_name":"Phosphatidylethanolamines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010714","descriptor_name":"Phosphatidylethanolamines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010714","descriptor_name":"Phosphatidylethanolamines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000031","qualifier_name":"analogs & derivatives","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014538","descriptor_name":"Uridine Diphosphate N-Acetylmuramic Acid","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D055503","descriptor_name":"Protein Multimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055503","descriptor_name":"Protein Multimerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055503","descriptor_name":"Protein Multimerization","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},{"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.4c01050","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01050","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:39370850","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39370850","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1678313994","https://openalex.org/W1968125869","https://openalex.org/W1980145079","https://openalex.org/W2000693118","https://openalex.org/W2007807255","https://openalex.org/W2021520922","https://openalex.org/W2024665809","https://openalex.org/W2036108598","https://openalex.org/W2052779789","https://openalex.org/W2054031517","https://openalex.org/W2082351355","https://openalex.org/W2083344288","https://openalex.org/W2117510530","https://openalex.org/W2121552999","https://openalex.org/W2130771866","https://openalex.org/W2133179696","https://openalex.org/W2145315186","https://openalex.org/W2146325980","https://openalex.org/W2148521301","https://openalex.org/W2148851922","https://openalex.org/W2150152340","https://openalex.org/W2153668434","https://openalex.org/W2155398486","https://openalex.org/W2158412800","https://openalex.org/W2206954826","https://openalex.org/W2487854154","https://openalex.org/W2557882133","https://openalex.org/W2560839684","https://openalex.org/W2777561590","https://openalex.org/W2889597951","https://openalex.org/W2914776516","https://openalex.org/W2945405656","https://openalex.org/W2969414466","https://openalex.org/W2971185209","https://openalex.org/W2996508375","https://openalex.org/W3032471731","https://openalex.org/W3088690197","https://openalex.org/W4210522538","https://openalex.org/W4289638129","https://openalex.org/W4317617267","https://openalex.org/W4396577018","https://openalex.org/W4396721167"],"related_works":["https://openalex.org/W2163834922","https://openalex.org/W2146325980","https://openalex.org/W2232114200","https://openalex.org/W2415414695","https://openalex.org/W2345563846","https://openalex.org/W4396577018","https://openalex.org/W4319937678","https://openalex.org/W2512469025","https://openalex.org/W2951987835","https://openalex.org/W1981255596"],"abstract_inverted_index":{"The":[0],"lantibiotic":[1],"pore-forming":[2],"peptide":[3,56],"nisin":[4,39,105,128,151],"is":[5,52,60],"a":[6,112,134,144],"promising":[7],"candidate":[8],"in":[9,26,48,64,91,111,164],"the":[10,49,66,85,92,148,154,159,165],"fight":[11],"against":[12],"multidrug-resistant":[13],"bacteria":[14,25],"due":[15],"to":[16,23,62,83,119,137],"its":[17],"unique":[18],"structure,":[19],"which":[20],"allows":[21],"it":[22],"disrupt":[24],"two":[27],"distinct":[28],"ways\u2500Lipid":[29],"II":[30,42,89,132,163],"trafficking":[31],"and":[32,40,87,116,156],"transmembrane":[33,122],"pore":[34,46],"formation.":[35],"However,":[36],"exactly":[37],"how":[38],"Lipid":[41,131,162],"assemble":[43],"into":[44,58,158],"oligomeric":[45,169],"structures":[47],"bacterial":[50],"membrane":[51,93,155],"not":[53],"known.":[54],"Spontaneous":[55],"assembly":[57],"pores":[59],"difficult":[61],"observe":[63],"even":[65],"very":[67],"long-time":[68],"scale":[69,98],"molecular":[70],"dynamics":[71],"(MD)":[72],"simulations.":[73],"In":[74],"this":[75],"study,":[76],"we":[77,102],"adopted":[78],"an":[79],"MD-guided":[80],"modeling":[81],"approach":[82],"investigate":[84],"nisin-nisin":[86],"nisin-Lipid":[88],"associations":[90],"environment.":[94],"Through":[95],"extensive":[96],"microsecond-time":[97],"all-atom":[99],"MD":[100],"simulations,":[101],"established":[103],"that":[104,126],"monomers":[106,152],"dimerize":[107],"by":[108],"forming":[109],"\u03b2-sheets":[110],"POPE:POPG":[113],"lipid":[114],"bilayer":[115],"oligomerize":[117],"further":[118],"form":[120],"stable":[121],"channels.":[123],"We":[124],"determined":[125],"these":[127],"dimers":[129],"use":[130],"as":[133],"dimer":[135],"interface":[136],"incur":[138],"enhanced":[139],"stability.":[140],"Our":[141],"results":[142],"provide":[143],"clearer":[145],"understanding":[146],"of":[147,150,161,168],"self-assembly":[149],"within":[153],"insights":[157],"role":[160],"structural":[166],"integrity":[167],"structures.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}