{"id":"https://openalex.org/W4298007971","doi":"https://doi.org/10.1016/j.bpr.2022.100080","title":"Importance of molecular dynamics equilibrium protocol on protein-lipid interaction near channel pore","display_name":"Importance of molecular dynamics equilibrium protocol on protein-lipid interaction near channel pore","publication_year":2022,"publication_date":"2022-09-29","ids":{"openalex":"https://openalex.org/W4298007971","doi":"https://doi.org/10.1016/j.bpr.2022.100080","pmid":"https://pubmed.ncbi.nlm.nih.gov/36425669","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/9680783"},"language":"en","primary_location":{"id":"doi:10.1016/j.bpr.2022.100080","doi":"https://doi.org/10.1016/j.bpr.2022.100080","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.bpr.2022.100080","pdf_url":null,"source":{"id":"https://openalex.org/S4210240234","display_name":"Biophysical Reports","issn_l":"2667-0747","issn":["2667-0747"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","ki-jl-1","medline","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Reports","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.bpr.2022.100080","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056421111","display_name":"Wenjuan Jiang","orcid":"https://orcid.org/0000-0002-6360-3875","observed_orcids":["https://orcid.org/0000-0002-6360-3875"]},"institutions":[{"id":"https://openalex.org/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Wenjuan Jiang","raw_affiliation_strings":["College of Pharmacy, Western University of Health Sciences, Pomona, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmacy, Western University of Health Sciences, Pomona, California","institution_ids":["https://openalex.org/I93393672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019413362","display_name":"J\u00e9r\u00f4me J. Lacroix","orcid":"https://orcid.org/0000-0001-5687-0652","observed_orcids":["https://orcid.org/0000-0001-5687-0652"]},"institutions":[{"id":"https://openalex.org/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jerome Lacroix","raw_affiliation_strings":["Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California","institution_ids":["https://openalex.org/I93393672"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101602550","display_name":"Yun Luo","orcid":"https://orcid.org/0000-0003-3581-754X","observed_orcids":["https://orcid.org/0000-0003-3581-754X","https://orcid.org/0000-0002-1948-5832"]},"institutions":[{"id":"https://openalex.org/I93393672","display_name":"Western University of Health Sciences","ror":"https://ror.org/05167c961","country_code":"US","type":"education","lineage":["https://openalex.org/I93393672"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yun Lyna Luo","raw_affiliation_strings":["College of Pharmacy, Western University of Health Sciences, Pomona, California"],"raw_orcid":"https://orcid.org/0000-0003-3581-754X","affiliations":[{"raw_affiliation_string":"College of Pharmacy, Western University of Health Sciences, Pomona, California","institution_ids":["https://openalex.org/I93393672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5056421111","https://openalex.org/A5101602550"],"corresponding_institution_ids":["https://openalex.org/I93393672"],"apc_list":{"value":2000,"currency":"USD","value_usd":2000},"apc_paid":{"value":2000,"currency":"USD","value_usd":2000},"fwci":0.816,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.67506774,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"2","issue":"4","first_page":"100080","last_page":"100080"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.7271000146865845,"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":0.7271000146865845,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.241799995303154,"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/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.009200000204145908,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/protein-lipid-interactions","display_name":"protein-lipid interactions","score":0.7730000019073486},{"id":"https://openalex.org/keywords/ion-channel-pore","display_name":"ion channel pore","score":0.8479999899864197},{"id":"https://openalex.org/keywords/piezo1","display_name":"Piezo1","score":0.7689999938011169},{"id":"https://openalex.org/keywords/mechanosensitive-channels","display_name":"mechanosensitive ion channels","score":0.8159999847412109},{"id":"https://openalex.org/keywords/lipid-density","display_name":"lipid density","score":0.671999990940094}],"concepts":[{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.7820913791656494},{"id":"https://openalex.org/C39944091","wikidata":"https://www.wikidata.org/wiki/Q423279","display_name":"Lipid bilayer","level":3,"score":0.6571173667907715},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5978708863258362},{"id":"https://openalex.org/C12554922","wikidata":"https://www.wikidata.org/wiki/Q7100","display_name":"Biophysics","level":1,"score":0.5766847133636475},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.50389164686203},{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.4390289783477783},{"id":"https://openalex.org/C24530287","wikidata":"https://www.wikidata.org/wiki/Q424204","display_name":"Transmembrane protein","level":3,"score":0.4350912570953369},{"id":"https://openalex.org/C82160515","wikidata":"https://www.wikidata.org/wiki/Q5377201","display_name":"Energy profile","level":3,"score":0.43238216638565063},{"id":"https://openalex.org/C118892022","wikidata":"https://www.wikidata.org/wiki/Q7834587","display_name":"Transmembrane domain","level":3,"score":0.4147428274154663},{"id":"https://openalex.org/C159467904","wikidata":"https://www.wikidata.org/wiki/Q2001702","display_name":"Chemical physics","level":1,"score":0.3996034264564514},{"id":"https://openalex.org/C8010536","wikidata":"https://www.wikidata.org/wiki/Q160398","display_name":"Crystallography","level":1,"score":0.39490947127342224},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.19666287302970886},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.13009098172187805},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10140103101730347},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.09276026487350464},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.08579644560813904},{"id":"https://openalex.org/C170493617","wikidata":"https://www.wikidata.org/wiki/Q208467","display_name":"Receptor","level":2,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1016/j.bpr.2022.100080","doi":"https://doi.org/10.1016/j.bpr.2022.100080","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.bpr.2022.100080","pdf_url":null,"source":{"id":"https://openalex.org/S4210240234","display_name":"Biophysical Reports","issn_l":"2667-0747","issn":["2667-0747"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","ki-jl-1","medline","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Reports","raw_type":"journal-article"},{"id":"doi:10.1101/2021.11.28.470286","doi":"https://doi.org/10.1101/2021.11.28.470286","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2021.11.28.470286","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/09/19/2021.11.28.470286.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nd","license_id":"https://openalex.org/licenses/cc-by-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:9680783","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9680783","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophys Rep (N Y)","raw_type":"Text"},{"id":"pmid:36425669","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36425669","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":"Biophysical reports","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:efd01807a31a413fb5825105b3903477","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/efd01807a31a413fb5825105b3903477","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Biophysical Reports, Vol 2, Iss 4, Pp 100080- (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.bpr.2022.100080","doi":"https://doi.org/10.1016/j.bpr.2022.100080","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.bpr.2022.100080","pdf_url":null,"source":{"id":"https://openalex.org/S4210240234","display_name":"Biophysical Reports","issn_l":"2667-0747","issn":["2667-0747"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","ki-jl-1","medline","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biophysical Reports","raw_type":"journal-article"},"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"score":0.5899999737739563,"id":"https://metadata.un.org/sdg/6","display_name":"Clean water and sanitation"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G6858339838","display_name":null,"funder_award_id":"ACI-154862","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7234137079","display_name":null,"funder_award_id":"MCB160119","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7355564437","display_name":"Breakthrough Molecular Dynamics Research via an Anton2 Supercomputer","funder_award_id":"R01GM116961","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000860883","display_name":"PHARMACOLOGICAL MODULATION OF PIEZO1 CHANNELS","funder_award_id":"R01GM130834","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1976499671","https://openalex.org/W1981021420","https://openalex.org/W1984853348","https://openalex.org/W1990815583","https://openalex.org/W1999720993","https://openalex.org/W2003217611","https://openalex.org/W2020579993","https://openalex.org/W2021520922","https://openalex.org/W2024012749","https://openalex.org/W2024762727","https://openalex.org/W2029667189","https://openalex.org/W2044832274","https://openalex.org/W2060872117","https://openalex.org/W2072604508","https://openalex.org/W2077954341","https://openalex.org/W2101532349","https://openalex.org/W2106140689","https://openalex.org/W2119267663","https://openalex.org/W2129213941","https://openalex.org/W2149079172","https://openalex.org/W2155554859","https://openalex.org/W2160544821","https://openalex.org/W2272911234","https://openalex.org/W2314292783","https://openalex.org/W2327174080","https://openalex.org/W2343601000","https://openalex.org/W2460255279","https://openalex.org/W2584847871","https://openalex.org/W2774142732","https://openalex.org/W2776294243","https://openalex.org/W2779962245","https://openalex.org/W2783466581","https://openalex.org/W2785150634","https://openalex.org/W2804041046","https://openalex.org/W2921245417","https://openalex.org/W2969829558","https://openalex.org/W2971793051","https://openalex.org/W2979208253","https://openalex.org/W2996862388","https://openalex.org/W3036538529","https://openalex.org/W3037395564","https://openalex.org/W3103439995","https://openalex.org/W3122270077","https://openalex.org/W3131830629","https://openalex.org/W3137205495","https://openalex.org/W3170736331","https://openalex.org/W4224012209","https://openalex.org/W4253695859"],"related_works":["https://openalex.org/W4211097445","https://openalex.org/W2052299042","https://openalex.org/W2047022491","https://openalex.org/W2042527516","https://openalex.org/W2047668074","https://openalex.org/W3095343287","https://openalex.org/W3082468152","https://openalex.org/W3005056000","https://openalex.org/W4407498705","https://openalex.org/W1978457126"],"abstract_inverted_index":{"ABSTRACT":[0],"Multiscale":[1],"molecular":[2,206],"dynamics":[3,207],"(MD)":[4],"simulations":[5,90,208,243],"using":[6],"Martini":[7],"coarse-grained":[8,239],"(CG)":[9],"and":[10,47,63,87,107,141,166,192,235,240,262],"all-atom":[11,241],"(AA)":[12],"forcer":[13],"fields":[14],"are":[15],"commonly":[16],"used":[17],"in":[18,66,100,150,233,246],"membrane":[19,40],"protein":[20,41,45],"studies.":[21],"In":[22],"particular,":[23],"reverse-mapping":[24],"an":[25,30,34,211],"equilibrated":[26],"CG":[27,133,140,163],"model":[28,32],"to":[29,122,136,266],"AA":[31,89,142,153,180],"offers":[33],"efficient":[35],"way":[36],"for":[37,186,214],"preparing":[38],"large":[39],"systems":[42],"with":[43,71,179,202],"complex":[44],"shapes":[46],"lipid":[48,61,143,174,190,203,248],"compositions.":[49],"Here,":[50],"we":[51,81,228],"report":[52],"that":[53,112,168,230],"this":[54,79,184,260,268],"hybrid":[55],"CG-equilibrium-AA-production":[56],"protocol":[57,170],"may":[58],"artificially":[59],"increase":[60],"density":[62,105],"decrease":[64],"hydration":[65,118,177],"ion":[67],"channel":[68,99,225,252],"pores":[69],"walled":[70],"transmembrane":[72],"gaps.":[73],"To":[74],"understand":[75],"the":[76,92,96,113,124,137,151,172,216,251,256],"origin":[77],"of":[78,84,91,95,115,189,218,259],"conundrum,":[80],"conducted":[82],"replicas":[83],"CG,":[85],"AA,":[86],"reverse-mapped":[88],"pore":[93,117,125,130,146,176],"domain":[94],"mechanosensitive":[97,223],"Piezo1":[98,224],"a":[101,169],"non-conducting":[102],"conformation.":[103],"Lipid/water":[104],"analysis":[106],"free":[108,158],"energy":[109],"calculations":[110],"reveal":[111],"lack":[114],"initial":[116],"allows":[119],"adjacent":[120],"lipids":[121,147],"enter":[123],"lumen":[126],"through":[127],"gaps":[128],"between":[129,139,238],"helices":[131],"during":[132],"simulation.":[134],"Due":[135],"mismatch":[138],"kinetics,":[144],"these":[145],"remain":[148],"trapped":[149],"subsequent":[152],"simulations,":[154],"despite":[155],"unfavorable":[156],"binding":[157],"energy.":[159],"We":[160,254],"tested":[161],"several":[162],"equilibrium":[164,236],"protocols":[165,237,265],"found":[167,229],"restraining":[171],"whole":[173],"produces":[175],"consistent":[178],"results,":[181],"thus":[182],"eliminating":[183],"artifact":[185],"further":[187],"studies":[188],"gating":[191],"protein-lipid":[193,220],"interactions.":[194,221],"WHY":[195],"IT":[196],"MATTERS":[197],"Membrane-embedded":[198],"proteins":[199],"constantly":[200],"interact":[201],"molecules.":[204],"Computational":[205],"have":[209],"become":[210],"indispensable":[212],"tool":[213],"investigating":[215],"role":[217],"such":[219],"Using":[222],"as":[226],"model,":[227],"subtle":[231],"differences":[232],"solvation":[234],"MD":[242],"can":[244],"result":[245],"different":[247],"densities":[249],"inside":[250],"pore.":[253],"identify":[255],"underlying":[257],"cause":[258],"discrepancy":[261],"propose":[263],"alternative":[264],"avoid":[267],"artifact.":[269]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2022-10-01T00:00:00"}