{"id":"https://openalex.org/W3012027247","doi":"https://doi.org/10.1021/acs.jcim.0c00023","title":"Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study","display_name":"Role of Glycosaminoglycans in Procathepsin B Maturation: Molecular Mechanism Elucidated by a Computational Study","publication_year":2020,"publication_date":"2020-03-10","ids":{"openalex":"https://openalex.org/W3012027247","doi":"https://doi.org/10.1021/acs.jcim.0c00023","mag":"3012027247","pmid":"https://pubmed.ncbi.nlm.nih.gov/32155059"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00023","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00023","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00023","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00023","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030746059","display_name":"Krzysztof K. Bojarski","orcid":"https://orcid.org/0000-0002-2066-1522"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Krzysztof K. Bojarski","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, Wita Stwosza 63, 80-308 Gda\u0144sk, Poland"],"raw_orcid":"https://orcid.org/0000-0002-2066-1522","affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016490968","display_name":"Agnieszka Karczy\u0144ska","orcid":"https://orcid.org/0000-0003-2327-9537"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Agnieszka S. Karczy\u0144ska","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, Wita Stwosza 63, 80-308 Gda\u0144sk, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086671958","display_name":"Sergey A. Samsonov","orcid":"https://orcid.org/0000-0002-5166-4849"},"institutions":[{"id":"https://openalex.org/I40413290","display_name":"University of Gda\u0144sk","ror":"https://ror.org/011dv8m48","country_code":"PL","type":"education","lineage":["https://openalex.org/I40413290"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Sergey A. Samsonov","raw_affiliation_strings":["Faculty of Chemistry, University of Gda\u0144sk, Wita Stwosza 63, 80-308 Gda\u0144sk, Poland"],"raw_orcid":"https://orcid.org/0000-0002-5166-4849","affiliations":[{"raw_affiliation_string":"Faculty of Chemistry, University of Gda\u0144sk, Wita Stwosza 63, 80-308 Gda\u0144sk, Poland","institution_ids":["https://openalex.org/I40413290"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5030746059","https://openalex.org/A5086671958"],"corresponding_institution_ids":["https://openalex.org/I40413290"],"apc_list":null,"apc_paid":null,"fwci":0.5656,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.56137453,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"60","issue":"4","first_page":"2247","last_page":"2256"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10620","display_name":"Protease and Inhibitor Mechanisms","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10620","display_name":"Protease and Inhibitor Mechanisms","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11131","display_name":"Proteoglycans and glycosaminoglycans research","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/T11617","display_name":"Enzyme Production and Characterization","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1305","display_name":"Biotechnology"},"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/cathepsin","display_name":"Cathepsin","score":0.7391014695167542},{"id":"https://openalex.org/keywords/glycosaminoglycan","display_name":"Glycosaminoglycan","score":0.6366968750953674},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5724891424179077},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.5562357306480408},{"id":"https://openalex.org/keywords/proteolysis","display_name":"Proteolysis","score":0.5241922736167908},{"id":"https://openalex.org/keywords/proteases","display_name":"Proteases","score":0.48448917269706726},{"id":"https://openalex.org/keywords/extracellular-matrix","display_name":"Extracellular matrix","score":0.4815390706062317},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.48040392994880676},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.318875253200531},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28073498606681824}],"concepts":[{"id":"https://openalex.org/C167844969","wikidata":"https://www.wikidata.org/wiki/Q426245","display_name":"Cathepsin","level":3,"score":0.7391014695167542},{"id":"https://openalex.org/C153074725","wikidata":"https://www.wikidata.org/wiki/Q407553","display_name":"Glycosaminoglycan","level":2,"score":0.6366968750953674},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5724891424179077},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.5562357306480408},{"id":"https://openalex.org/C2781307694","wikidata":"https://www.wikidata.org/wiki/Q33123","display_name":"Proteolysis","level":3,"score":0.5241922736167908},{"id":"https://openalex.org/C182220744","wikidata":"https://www.wikidata.org/wiki/Q7251226","display_name":"Proteases","level":3,"score":0.48448917269706726},{"id":"https://openalex.org/C189165786","wikidata":"https://www.wikidata.org/wiki/Q193825","display_name":"Extracellular matrix","level":2,"score":0.4815390706062317},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.48040392994880676},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.318875253200531},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28073498606681824}],"mesh":[{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001686","descriptor_name":"Biological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002401","descriptor_name":"Cathepsin B","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002401","descriptor_name":"Cathepsin B","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002401","descriptor_name":"Cathepsin B","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002403","descriptor_name":"Cathepsins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002403","descriptor_name":"Cathepsins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002403","descriptor_name":"Cathepsins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004792","descriptor_name":"Enzyme Precursors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004792","descriptor_name":"Enzyme Precursors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004792","descriptor_name":"Enzyme Precursors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006025","descriptor_name":"Glycosaminoglycans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.0c00023","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00023","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00023","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32155059","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32155059","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},{"id":"pmh:oai:pubmedcentral.nih.gov:7588040","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7588040","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,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.0c00023","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00023","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.0c00023","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1700977524","display_name":null,"funder_award_id":"UMO-2017/26/M/ST4/00044","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G240473628","display_name":null,"funder_award_id":"UMO-2018/30/E/ST4/00037","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"},{"id":"https://openalex.org/G6236698138","display_name":null,"funder_award_id":"UMO-2018/31/N/ST4/01677","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3012027247.pdf"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W58102331","https://openalex.org/W130890307","https://openalex.org/W200753288","https://openalex.org/W630005112","https://openalex.org/W1512048530","https://openalex.org/W1548119734","https://openalex.org/W1913565270","https://openalex.org/W1967502057","https://openalex.org/W1968321554","https://openalex.org/W1971971965","https://openalex.org/W1977260572","https://openalex.org/W1977812451","https://openalex.org/W1980653863","https://openalex.org/W1980692898","https://openalex.org/W1986012385","https://openalex.org/W1990328562","https://openalex.org/W1996795546","https://openalex.org/W2012748696","https://openalex.org/W2015151182","https://openalex.org/W2017686863","https://openalex.org/W2023041802","https://openalex.org/W2025880126","https://openalex.org/W2029667189","https://openalex.org/W2030340060","https://openalex.org/W2031527740","https://openalex.org/W2035163490","https://openalex.org/W2035266068","https://openalex.org/W2043344837","https://openalex.org/W2045674145","https://openalex.org/W2049891971","https://openalex.org/W2054732153","https://openalex.org/W2058616210","https://openalex.org/W2061394683","https://openalex.org/W2074331165","https://openalex.org/W2075503331","https://openalex.org/W2078366002","https://openalex.org/W2080442263","https://openalex.org/W2087030184","https://openalex.org/W2091164805","https://openalex.org/W2098943363","https://openalex.org/W2111270835","https://openalex.org/W2112154906","https://openalex.org/W2117672117","https://openalex.org/W2130440034","https://openalex.org/W2147129952","https://openalex.org/W2147805425","https://openalex.org/W2157925921","https://openalex.org/W2158534713","https://openalex.org/W2164071805","https://openalex.org/W2164401552","https://openalex.org/W2173247062","https://openalex.org/W2320727223","https://openalex.org/W2404280981","https://openalex.org/W2462618639","https://openalex.org/W2471683236","https://openalex.org/W2559950162","https://openalex.org/W2772791582","https://openalex.org/W2782990227","https://openalex.org/W2802007263","https://openalex.org/W2803873050","https://openalex.org/W2914504056","https://openalex.org/W2926834221","https://openalex.org/W2954153470","https://openalex.org/W4230476373"],"related_works":["https://openalex.org/W64651649","https://openalex.org/W2020525831","https://openalex.org/W2193246976","https://openalex.org/W2052842511","https://openalex.org/W1691503547","https://openalex.org/W2185690955","https://openalex.org/W169919519","https://openalex.org/W363277453","https://openalex.org/W167723665","https://openalex.org/W2080254866"],"abstract_inverted_index":{"High":[0],"Resolution":[1],"Image":[2],"Download":[3],"MS":[4],"PowerPoint":[5],"Slide":[6],"Procathepsins":[7],"are":[8,230],"an":[9],"inactive,":[10],"immature":[11],"form":[12],"of":[13,46,92,102,125,141,157,195,199],"cathepsins,":[14,85],"predominantly":[15],"cysteine":[16],"proteases":[17],"present":[18],"in":[19,25,32,61,66,94,127,139,233,236],"the":[20,80,89,99,106,116,123,155,158,163,168,181,184,196,203],"extracellular":[21],"matrix":[22],"(ECM)":[23],"and":[24,74,145,170,235],"lysosomes":[26],"that":[27,63,151,172,229],"play":[28],"a":[29,191,220],"key":[30],"role":[31,124],"various":[33],"biological":[34,68],"processes":[35,69],"such":[36,70],"as":[37,71,219],"bone":[38],"resorption":[39],"or":[40],"intracellular":[41],"proteolysis.":[42],"The":[43],"enzymatic":[44],"activity":[45],"cathepsins":[47],"can":[48,87,153,217],"be":[49,208],"mediated":[50],"by":[51],"glycosaminoglycans":[52],"(GAGs),":[53],"long":[54],"unbranched":[55],"periodic":[56],"negatively":[57],"charged":[58],"polysaccharides":[59],"found":[60],"ECM":[62],"take":[64],"part":[65],"many":[67],"anticoagulation,":[72],"angiogenesis,":[73],"tissue":[75],"regeneration.":[76],"In":[77,112],"addition":[78],"to":[79,121,177,210],"known":[81],"effects":[82],"on":[83,226],"mature":[84],"GAGs":[86,126,152,173],"mediate":[88],"maturation":[90,197],"process":[91,129,198],"procathepsins,":[93],"particular,":[95],"procathepsin":[96,136,159,178,200],"B.":[97],"However,":[98],"detailed":[100],"mechanism":[101],"this":[103,113,128],"mediation":[104],"at":[105],"molecular":[107],"level":[108],"is":[109],"still":[110],"unknown.":[111],"study,":[114],"for":[115,167,223],"first":[117],"time,":[118],"we":[119],"aimed":[120],"unravel":[122],"using":[130],"computational":[131],"approaches.":[132],"We":[133,149],"rigorously":[134],"analyzed":[135],"B\u2013GAG":[137],"complexes":[138],"terms":[140],"their":[142],"dynamics,":[143],"energetics,":[144],"potential":[146],"allosteric":[147],"regulation.":[148],"revealed":[150],"stabilize":[154],"conformation":[156],"B":[160,179],"structure":[161],"with":[162],"active":[164,186],"site":[165],"accessible":[166],"substrate":[169],"concluded":[171],"most":[174],"probably":[175],"bind":[176],"once":[180],"zymogen":[182],"adopts":[183],"enzymatically":[185],"conformation.":[187],"Our":[188],"data":[189,216],"provided":[190],"novel":[192],"mechanistic":[193],"view":[194],"B,":[201],"while":[202],"approaches":[204],"elaborated":[205],"here":[206],"might":[207],"useful":[209],"study":[211],"other":[212],"procathepsins.":[213],"Furthermore,":[214],"our":[215],"serve":[218],"rational":[221],"guide":[222],"experimental":[224],"work":[225],"procathepsin\u2013GAG":[227],"systems":[228],"not":[231],"characterized":[232],"vivo":[234],"vitro":[237],"yet.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}