{"id":"https://openalex.org/W2097917449","doi":"https://doi.org/10.1371/journal.pcbi.1004061","title":"Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2","display_name":"Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2","publication_year":2015,"publication_date":"2015-04-07","ids":{"openalex":"https://openalex.org/W2097917449","doi":"https://doi.org/10.1371/journal.pcbi.1004061","mag":"2097917449","pmid":"https://pubmed.ncbi.nlm.nih.gov/25849117"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1004061","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004061","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004061&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004061&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011210508","display_name":"Tom\u00e1\u0161 Trnka","orcid":"https://orcid.org/0000-0002-9273-3820"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":false,"raw_author_name":"Tom\u00e1\u0161 Trnka","raw_affiliation_strings":["Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Faculty of Science-National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","Faculty of Science\u2014National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Faculty of Science-National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Faculty of Science\u2014National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083099713","display_name":"Stanislav Kozmon","orcid":"https://orcid.org/0000-0002-0946-3453"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I207624831","display_name":"Slovak Academy of Sciences","ror":"https://ror.org/03h7qq074","country_code":"SK","type":"government","lineage":["https://openalex.org/I207624831"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ","SK"],"is_corresponding":false,"raw_author_name":"Stanislav Kozmon","raw_affiliation_strings":["Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Faculty of Science-National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic; On leave from the Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic","Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","Faculty of Science\u2014National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","On leave from the Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Faculty of Science-National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic; On leave from the Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Faculty of Science\u2014National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]},{"raw_affiliation_string":"On leave from the Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic","institution_ids":["https://openalex.org/I207624831"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006856491","display_name":"Igor Tvaro\u0161ka","orcid":"https://orcid.org/0000-0003-2740-944X"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I207624831","display_name":"Slovak Academy of Sciences","ror":"https://ror.org/03h7qq074","country_code":"SK","type":"government","lineage":["https://openalex.org/I207624831"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ","SK"],"is_corresponding":false,"raw_author_name":"Igor Tvaro\u0161ka","raw_affiliation_strings":["Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic","Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic","institution_ids":["https://openalex.org/I207624831"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061853775","display_name":"Jaroslav Ko\u010da","orcid":"https://orcid.org/0000-0002-2780-4901"},"institutions":[{"id":"https://openalex.org/I1310815967","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]},{"id":"https://openalex.org/I4210090417","display_name":"Central European Institute of Technology \u2013 Masaryk University","ror":"https://ror.org/009nz6031","country_code":"CZ","type":"education","lineage":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"]}],"countries":["CZ"],"is_corresponding":true,"raw_author_name":"Jaroslav Ko\u010da","raw_affiliation_strings":["Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Faculty of Science-National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","Faculty of Science\u2014National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic; Faculty of Science-National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967"]},{"raw_affiliation_string":"Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I4210090417"]},{"raw_affiliation_string":"Faculty of Science\u2014National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061853775"],"corresponding_institution_ids":["https://openalex.org/I1310815967","https://openalex.org/I21449261","https://openalex.org/I4210090417"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.963,"has_fulltext":true,"cited_by_count":27,"citation_normalized_percentile":{"value":0.74550317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"11","issue":"4","first_page":"e1004061","last_page":"e1004061"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","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/T10602","display_name":"Glycosylation and Glycoproteins Research","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/T10835","display_name":"Carbohydrate Chemistry and Synthesis","score":0.9984999895095825,"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"}},{"id":"https://openalex.org/T12827","display_name":"Biochemical and Molecular Research","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"}}],"keywords":[{"id":"https://openalex.org/keywords/qm/mm","display_name":"QM/MM","score":0.7211982011795044},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.5848217010498047},{"id":"https://openalex.org/keywords/potential-energy-surface","display_name":"Potential energy surface","score":0.5506411194801331},{"id":"https://openalex.org/keywords/glycosyltransferase","display_name":"Glycosyltransferase","score":0.5358314514160156},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"Umbrella sampling","score":0.44647398591041565},{"id":"https://openalex.org/keywords/nucleophile","display_name":"Nucleophile","score":0.42252233624458313},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.3967936038970947},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.35617631673812866},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.35185155272483826},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.2710200548171997},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.15489935874938965},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.1203262209892273},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.085804283618927}],"concepts":[{"id":"https://openalex.org/C20803032","wikidata":"https://www.wikidata.org/wiki/Q207900","display_name":"QM/MM","level":3,"score":0.7211982011795044},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.5848217010498047},{"id":"https://openalex.org/C125277925","wikidata":"https://www.wikidata.org/wiki/Q2572687","display_name":"Potential energy surface","level":3,"score":0.5506411194801331},{"id":"https://openalex.org/C161019410","wikidata":"https://www.wikidata.org/wiki/Q67201373","display_name":"Glycosyltransferase","level":3,"score":0.5358314514160156},{"id":"https://openalex.org/C128747166","wikidata":"https://www.wikidata.org/wiki/Q7881414","display_name":"Umbrella sampling","level":3,"score":0.44647398591041565},{"id":"https://openalex.org/C178907741","wikidata":"https://www.wikidata.org/wiki/Q745930","display_name":"Nucleophile","level":3,"score":0.42252233624458313},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.3967936038970947},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.35617631673812866},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.35185155272483826},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.2710200548171997},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.15489935874938965},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.1203262209892273},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.085804283618927}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002384","descriptor_name":"Catalysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006031","descriptor_name":"Glycosylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011134","descriptor_name":"Polysaccharides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000648","qualifier_name":"ultrastructure","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016695","descriptor_name":"Glycosyltransferases","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1004061","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004061","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004061&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:25849117","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25849117","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4388629","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4388629","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1004061","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004061","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:1461800a6fcf4375b35b7bbf9aa16e19","is_oa":false,"landing_page_url":"https://doaj.org/article/1461800a6fcf4375b35b7bbf9aa16e19","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,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 11, Iss 4, p e1004061 (2015)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/1369698","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/_Stepwise_Catalytic_Mechanism_via_Short_Lived_Intermediate_Inferred_from_Combined_QM_MM_MERP_and_PES_Calculations_on_Retaining_Glycosyltransferase_ppGalNAcT2_/1369698","pdf_url":null,"source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:is.muni.cz:1300938","is_oa":true,"landing_page_url":"https://is.muni.cz/repo/1300938","pdf_url":null,"source":{"id":"https://openalex.org/S4306400102","display_name":"Ve\u0159ejn\u00e9 slu\u017eby Informa\u010dn\u00edho syst\u00e9mu (Masarykiana Brunensis Universitas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1004061","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1004061","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004061&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8899999856948853}],"awards":[{"id":"https://openalex.org/G119949705","display_name":null,"funder_award_id":"CZ.1.05/1.1.00/02.0070","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1376288820","display_name":null,"funder_award_id":"CZ.1.05/1.100","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1516336186","display_name":null,"funder_award_id":"LM2010005","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1849335853","display_name":null,"funder_award_id":"CZ.1.05/1.100/02.0068","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G1884311943","display_name":null,"funder_award_id":"CZ.1.05/1.1.00/02.0068.","funder_id":"https://openalex.org/F4320323870","funder_display_name":"Central European Institute of Technology"},{"id":"https://openalex.org/G4620337067","display_name":null,"funder_award_id":"LM2010005","funder_id":"https://openalex.org/F4320323870","funder_display_name":"Central European Institute of Technology"},{"id":"https://openalex.org/G4638083868","display_name":null,"funder_award_id":"CZ.1.05/1.1.00/02.0070","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G5305951045","display_name":null,"funder_award_id":"CZ.1.05/1.1.00/02","funder_id":"https://openalex.org/F4320323870","funder_display_name":"Central European Institute of Technology"},{"id":"https://openalex.org/G6475306530","display_name":null,"funder_award_id":"CZ.1.05/1.1.00/02.0068","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G8755899154","display_name":null,"funder_award_id":"1.05/1.1.00/02.0068","funder_id":"https://openalex.org/F4320335322","funder_display_name":"European Regional Development Fund"},{"id":"https://openalex.org/G8833518822","display_name":"Synergies of Life and Material Sciences to Create a New Future","funder_award_id":"286154","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G919868476","display_name":null,"funder_award_id":"CZ.1.05/1.1.00/02.0068","funder_id":"https://openalex.org/F4320312330","funder_display_name":"Slovensk\u00e1 Akad\u00e9mia Vied"}],"funders":[{"id":"https://openalex.org/F4320312330","display_name":"Slovensk\u00e1 Akad\u00e9mia Vied","ror":"https://ror.org/03h7qq074"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320323641","display_name":"Vedeck\u00e1 Grantov\u00e1 Agent\u00fara M\u0160VVa\u0160 SR a SAV","ror":"https://ror.org/044gwpv05"},{"id":"https://openalex.org/F4320323870","display_name":"Central European Institute of Technology","ror":"https://ror.org/01p7k1986"},{"id":"https://openalex.org/F4320331617","display_name":"National Supercomputing Centre Singapore","ror":null},{"id":"https://openalex.org/F4320335322","display_name":"European Regional Development Fund","ror":"https://ror.org/00k4n6c32"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2097917449.pdf","grobid_xml":"https://content.openalex.org/works/W2097917449.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W1518196605","https://openalex.org/W1826102023","https://openalex.org/W1862479421","https://openalex.org/W1965466877","https://openalex.org/W1967236984","https://openalex.org/W1967783415","https://openalex.org/W1970000657","https://openalex.org/W1973050454","https://openalex.org/W1973960622","https://openalex.org/W1981368803","https://openalex.org/W1981491642","https://openalex.org/W1982414593","https://openalex.org/W1985583109","https://openalex.org/W1992607565","https://openalex.org/W2000500972","https://openalex.org/W2004911982","https://openalex.org/W2006831634","https://openalex.org/W2008423326","https://openalex.org/W2008819551","https://openalex.org/W2010965811","https://openalex.org/W2020114693","https://openalex.org/W2022946259","https://openalex.org/W2030687437","https://openalex.org/W2031430816","https://openalex.org/W2036420977","https://openalex.org/W2037535298","https://openalex.org/W2038581884","https://openalex.org/W2044028691","https://openalex.org/W2044135718","https://openalex.org/W2044340366","https://openalex.org/W2051812123","https://openalex.org/W2054704030","https://openalex.org/W2058373167","https://openalex.org/W2067787044","https://openalex.org/W2080780084","https://openalex.org/W2085336624","https://openalex.org/W2086513155","https://openalex.org/W2086957099","https://openalex.org/W2087271883","https://openalex.org/W2092157292","https://openalex.org/W2098943363","https://openalex.org/W2099428582","https://openalex.org/W2101773487","https://openalex.org/W2104113433","https://openalex.org/W2111705896","https://openalex.org/W2112921913","https://openalex.org/W2116373706","https://openalex.org/W2118020631","https://openalex.org/W2119412579","https://openalex.org/W2122199548","https://openalex.org/W2131458606","https://openalex.org/W2133465431","https://openalex.org/W2138605813","https://openalex.org/W2142775793","https://openalex.org/W2150345533","https://openalex.org/W2150697053","https://openalex.org/W2151324716","https://openalex.org/W2156495637","https://openalex.org/W2159075520","https://openalex.org/W2159330251","https://openalex.org/W2162331387","https://openalex.org/W2163630189","https://openalex.org/W2176969324","https://openalex.org/W2314158661","https://openalex.org/W3034519476","https://openalex.org/W4233785154","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W1845968178","https://openalex.org/W294973217","https://openalex.org/W2611893394","https://openalex.org/W4392897086","https://openalex.org/W2920920027","https://openalex.org/W2171509264","https://openalex.org/W1575818491","https://openalex.org/W2756247685","https://openalex.org/W2725278195","https://openalex.org/W1971290752"],"abstract_inverted_index":{"The":[0,173,219,261],"glycosylation":[1],"of":[2,13,26,32,44,59,63,109,129,134,145,164,170,182,194,238,249,263],"cell":[3,18],"surface":[4,80],"proteins":[5],"plays":[6],"a":[7,11,77,88,114,130,211,252,264],"crucial":[8],"role":[9],"in":[10,82,202,230],"multitude":[12],"biological":[14],"processes,":[15],"such":[16],"as":[17,271],"adhesion":[19],"and":[20,87],"recognition.":[21],"To":[22],"understand":[23],"the":[24,29,33,41,56,64,95,120,127,146,160,179,187,190,197,203,224,233,236,239,247,258,274],"process":[25,248],"protein":[27],"glycosylation,":[28],"reaction":[30,42,91,225,275],"mechanisms":[31],"participating":[34],"enzymes":[35],"need":[36],"to":[37,113,158,168,257],"be":[38,140],"known.":[39],"However,":[40],"mechanism":[43,58],"retaining":[45,65],"glycosyltransferases":[46],"has":[47],"not":[48],"yet":[49],"been":[50,156],"sufficiently":[51],"explained.":[52],"Here":[53],"we":[54,154],"investigated":[55],"catalytic":[57],"human":[60,183],"isoform":[61,184],"2":[62],"glycosyltransferase":[66],"polypeptide":[67],"UDP-GalNAc":[68],"transferase":[69],"by":[70,273],"coupling":[71],"two":[72,83],"different":[73],"QM/MM-based":[74],"approaches,":[75],"namely":[76],"potential":[78,147,165],"energy":[79,90,101,148,231,237,276],"scan":[81,102,116],"distance":[84],"difference":[85],"dimensions":[86],"minimum":[89],"path":[92,123],"optimisation":[93,124],"using":[94,279],"Nudged":[96],"Elastic":[97],"Band":[98],"method.":[99],"Potential":[100],"studies":[103],"often":[104],"suffer":[105],"from":[106],"inadequate":[107],"sampling":[108,128],"reactive":[110],"processes":[111],"due":[112],"predefined":[115],"coordinate":[117],"system.":[118],"At":[119],"same":[121],"time,":[122],"methods":[125],"enable":[126],"virtually":[131],"unlimited":[132],"number":[133],"dimensions,":[135],"but":[136],"their":[137],"results":[138],"cannot":[139],"unambiguously":[141],"interpreted":[142],"without":[143],"knowledge":[144],"surface.":[149],"By":[150],"combining":[151],"these":[152,171],"methods,":[153],"have":[155],"able":[157],"eliminate":[159],"most":[161],"significant":[162],"sources":[163],"errors":[166],"inherent":[167],"each":[169],"approaches.":[172],"structural":[174],"model":[175],"is":[176,226,242,254,269],"based":[177],"on":[178],"crystal":[180],"structure":[181],"2.":[185],"In":[186],"QM/MM":[188],"method,":[189],"QM":[191],"region":[192],"consists":[193],"275":[195],"atoms,":[196],"remaining":[198],"5776":[199],"atoms":[200],"were":[201],"MM":[204],"region.":[205],"We":[206],"found":[207],"that":[208],"ppGalNAcT2":[209],"catalyzes":[210],"same-face":[212],"nucleophilic":[213,250],"substitution":[214],"with":[215],"internal":[216],"return":[217],"(SNi).":[218],"optimized":[220],"transition":[221],"state":[222],"for":[223],"13.8":[227],"kcal/mol":[228,244],"higher":[229],"than":[232],"reactant":[234],"while":[235],"product":[240],"complex":[241],"6.7":[243],"lower.":[245],"During":[246],"attack,":[251],"proton":[253],"synchronously":[255],"transferred":[256],"leaving":[259],"phosphate.":[260],"presence":[262],"short-lived":[265],"metastable":[266],"oxocarbenium":[267],"intermediate":[268],"likely,":[270],"indicated":[272],"profiles":[277],"obtained":[278],"high-level":[280],"density":[281],"functionals.":[282]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}