{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T15:56:41Z","timestamp":1759939001435,"version":"3.41.2"},"reference-count":56,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T00:00:00Z","timestamp":1614038400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81903601"],"award-info":[{"award-number":["81903601"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J of Molecular Recognition"],"published-print":{"date-parts":[[2021,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The specific regulation of PTPN18 protein to three HER2 phospho\u2010peptides has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the three HER2 phospho\u2010peptides binding to the PTPN18 catalytic domain is energetically favorable due to substrate specificity of PTPN18, and moreover, the PTPN18 protein have significantly higher affinity to pY1248 peptide (\u221245.22 kcal\/mol) than that of pY1112 (\u221225.3 kcal\/mol) and pY1196 (\u221231.86 kcal\/mol) peptides. Further, the binding of HER2 phospho\u2010peptides to PTPN18 have also caused the closure of WPD\u2010loop with the decrease of the centroid distances between the P\u2010loop and the WPD loop. The WPD\u2010loop closure of PTPN18 relates directly to the new hydrogen bond and hydrophobic interaction formations between the residues Tyr62, Asp64, Val65, Ala231, Arg235, and Ala273 in PTPN18 and Tyr(PO3) in the HER2 phospho\u2010peptides, which suggests that these key residues would contribute to the specific regulation of PTPN18 to the substrates. The correlation analysis revealed the allosteric communication networks from the pY binding loop to the WPD loop through the structural change and the residue interactions in PTPN18. These results will be helpful to understand the specific regulation through the allosteric communication network in the PTPN18 catalytic domain.<\/jats:p>","DOI":"10.1002\/jmr.2890","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T11:54:24Z","timestamp":1614081264000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Molecular dynamics simulation studies on the specific regulation of <scp>PTPN18<\/scp> to the <scp>HER2<\/scp> phospho\u2010peptides"],"prefix":"10.1002","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7052-1018","authenticated-orcid":false,"given":"Mingqiong","family":"Tong","sequence":"first","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Liu","sequence":"additional","affiliation":[{"name":"The Office of Academic Affairs Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wan","family":"Sun","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jing","family":"Liu","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Na","family":"Fan","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyue","family":"Wang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhongyu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinfeng","family":"Song","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chao","family":"Lv","sequence":"additional","affiliation":[{"name":"Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing Dezhou University  Dezhou China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yan","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry Beijing Normal University  Beijing China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2021,2,23]]},"reference":[{"doi-asserted-by":"publisher","key":"e_1_2_10_2_1","DOI":"10.1073\/pnas.1418402111"},{"doi-asserted-by":"publisher","key":"e_1_2_10_3_1","DOI":"10.1016\/j.abb.2004.05.024"},{"doi-asserted-by":"publisher","key":"e_1_2_10_4_1","DOI":"10.1021\/acs.molpharmaceut.9b00426"},{"doi-asserted-by":"publisher","key":"e_1_2_10_5_1","DOI":"10.1021\/acscombsci.9b00152"},{"doi-asserted-by":"publisher","key":"e_1_2_10_6_1","DOI":"10.1016\/j.athoracsur.2011.12.056"},{"doi-asserted-by":"publisher","key":"e_1_2_10_7_1","DOI":"10.18632\/oncotarget.3588"},{"doi-asserted-by":"publisher","key":"e_1_2_10_8_1","DOI":"10.1038\/nature12308"},{"doi-asserted-by":"publisher","key":"e_1_2_10_9_1","DOI":"10.1016\/j.cell.2011.02.003"},{"doi-asserted-by":"publisher","key":"e_1_2_10_10_1","DOI":"10.1371\/journal.pone.0085592"},{"doi-asserted-by":"publisher","key":"e_1_2_10_11_1","DOI":"10.1016\/j.cell.2011.02.030"},{"doi-asserted-by":"publisher","key":"e_1_2_10_12_1","DOI":"10.1016\/j.ejmech.2020.112657"},{"doi-asserted-by":"publisher","key":"e_1_2_10_13_1","DOI":"10.1002\/jcp.27378"},{"doi-asserted-by":"publisher","key":"e_1_2_10_14_1","DOI":"10.1146\/annurev.pharmtox.42.083001.144616"},{"doi-asserted-by":"publisher","key":"e_1_2_10_15_1","DOI":"10.1021\/acs.biochem.8b00656"},{"doi-asserted-by":"publisher","key":"e_1_2_10_16_1","DOI":"10.1039\/D0CC04714G"},{"doi-asserted-by":"publisher","key":"e_1_2_10_17_1","DOI":"10.1016\/j.cell.2008.11.038"},{"doi-asserted-by":"publisher","key":"e_1_2_10_18_1","DOI":"10.1016\/j.celrep.2016.04.016"},{"doi-asserted-by":"publisher","key":"e_1_2_10_19_1","DOI":"10.1074\/jbc.M412211200"},{"doi-asserted-by":"publisher","key":"e_1_2_10_20_1","DOI":"10.1016\/j.cellsig.2020.109554"},{"doi-asserted-by":"publisher","key":"e_1_2_10_21_1","DOI":"10.1111\/j.1600-065X.2008.00747.x"},{"doi-asserted-by":"publisher","key":"e_1_2_10_22_1","DOI":"10.1073\/pnas.0706233104"},{"doi-asserted-by":"publisher","key":"e_1_2_10_23_1","DOI":"10.1038\/ng1323"},{"doi-asserted-by":"publisher","key":"e_1_2_10_24_1","DOI":"10.1074\/jbc.M309527200"},{"doi-asserted-by":"publisher","key":"e_1_2_10_25_1","DOI":"10.1016\/S0092-8674(00)80938-1"},{"doi-asserted-by":"publisher","key":"e_1_2_10_26_1","DOI":"10.1016\/j.celrep.2015.08.037"},{"doi-asserted-by":"publisher","key":"e_1_2_10_27_1","DOI":"10.1038\/aps.2014.80"},{"doi-asserted-by":"publisher","key":"e_1_2_10_28_1","DOI":"10.1021\/acs.biochem.8b00655"},{"doi-asserted-by":"publisher","key":"e_1_2_10_29_1","DOI":"10.1038\/cr.2014.99"},{"doi-asserted-by":"publisher","key":"e_1_2_10_30_1","DOI":"10.3390\/ijms19010060"},{"doi-asserted-by":"publisher","key":"e_1_2_10_31_1","DOI":"10.1002\/prot.10470"},{"doi-asserted-by":"publisher","key":"e_1_2_10_32_1","DOI":"10.1002\/jcc.10349"},{"doi-asserted-by":"publisher","key":"e_1_2_10_33_1","DOI":"10.1002\/jcc.20035"},{"doi-asserted-by":"publisher","key":"e_1_2_10_34_1","DOI":"10.1002\/jcc.10262"},{"doi-asserted-by":"publisher","key":"e_1_2_10_35_1","DOI":"10.1007\/s00894-005-0028-4"},{"volume-title":"Amber 9","year":"2006","author":"Case DA","key":"e_1_2_10_36_1"},{"doi-asserted-by":"publisher","key":"e_1_2_10_37_1","DOI":"10.1371\/journal.pone.0035159"},{"doi-asserted-by":"publisher","key":"e_1_2_10_38_1","DOI":"10.1039\/C5RA11234F"},{"doi-asserted-by":"publisher","key":"e_1_2_10_39_1","DOI":"10.1002\/jmr.2300"},{"doi-asserted-by":"publisher","key":"e_1_2_10_40_1","DOI":"10.1080\/07391102.1998.10508245"},{"doi-asserted-by":"publisher","key":"e_1_2_10_41_1","DOI":"10.1021\/ar000033j"},{"doi-asserted-by":"publisher","key":"e_1_2_10_42_1","DOI":"10.1021\/ja981307p"},{"doi-asserted-by":"publisher","key":"e_1_2_10_43_1","DOI":"10.1021\/ja981844"},{"doi-asserted-by":"publisher","key":"e_1_2_10_44_1","DOI":"10.1371\/journal.pone.0053841"},{"doi-asserted-by":"publisher","key":"e_1_2_10_45_1","DOI":"10.1002\/jmr.1146"},{"doi-asserted-by":"publisher","key":"e_1_2_10_46_1","DOI":"10.1002\/jmr.2756"},{"doi-asserted-by":"publisher","key":"e_1_2_10_47_1","DOI":"10.1021\/ja060830y"},{"doi-asserted-by":"publisher","key":"e_1_2_10_48_1","DOI":"10.1002\/jcc.10379"},{"doi-asserted-by":"publisher","key":"e_1_2_10_49_1","DOI":"10.1016\/j.str.2006.01.014"},{"doi-asserted-by":"publisher","key":"e_1_2_10_50_1","DOI":"10.1021\/jm000241h"},{"doi-asserted-by":"publisher","key":"e_1_2_10_51_1","DOI":"10.1021\/jm050306m"},{"doi-asserted-by":"publisher","key":"e_1_2_10_52_1","DOI":"10.1021\/ja907795q"},{"doi-asserted-by":"publisher","key":"e_1_2_10_53_1","DOI":"10.1021\/ja003834q"},{"doi-asserted-by":"publisher","key":"e_1_2_10_54_1","DOI":"10.1016\/S0022-2836(02)00919-1"},{"doi-asserted-by":"publisher","key":"e_1_2_10_55_1","DOI":"10.1002\/prot.22806"},{"doi-asserted-by":"publisher","key":"e_1_2_10_56_1","DOI":"10.1002\/pro.5560020413"},{"doi-asserted-by":"publisher","key":"e_1_2_10_57_1","DOI":"10.1006\/jmbi.1993.1598"}],"container-title":["Journal of Molecular Recognition"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jmr.2890","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jmr.2890","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jmr.2890","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T16:31:50Z","timestamp":1693413110000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/jmr.2890"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,2,23]]},"references-count":56,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2021,7]]}},"alternative-id":["10.1002\/jmr.2890"],"URL":"https:\/\/doi.org\/10.1002\/jmr.2890","archive":["Portico"],"relation":{},"ISSN":["0952-3499","1099-1352"],"issn-type":[{"type":"print","value":"0952-3499"},{"type":"electronic","value":"1099-1352"}],"subject":[],"published":{"date-parts":[[2021,2,23]]},"assertion":[{"value":"2020-10-12","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-01-26","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2021-02-23","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2890"}}