{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T02:48:52Z","timestamp":1792291732180,"version":"4.4.0"},"reference-count":59,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2023,6,24]],"date-time":"2023-06-24T00:00:00Z","timestamp":1687564800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institute of General Medical Sciences of the National Institutes of Health","doi-asserted-by":"publisher","award":["SC2GM130470"],"award-info":[{"award-number":["SC2GM130470"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institute of General Medical Sciences of the National Institutes of Health","doi-asserted-by":"publisher","award":["90922-09 07"],"award-info":[{"award-number":["90922-09 07"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018321","name":"Queens College Startup fund","doi-asserted-by":"publisher","award":["SC2GM130470"],"award-info":[{"award-number":["SC2GM130470"]}],"id":[{"id":"10.13039\/100018321","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100018321","name":"Queens College Startup fund","doi-asserted-by":"publisher","award":["90922-09 07"],"award-info":[{"award-number":["90922-09 07"]}],"id":[{"id":"10.13039\/100018321","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>The specificity loop of Matrix Metalloproteinases (MMPs) is known to regulate recognition of their substrates, and the S1\u2032\u2212site surrounded by the loop is a unique place to address the selectivity of ligands toward each MMP. Molecular dynamics (MD) simulations of apo\u2212MMP\u221213 and its complex forms with various ligands were conducted to identify the role of the specificity loop for the ligand binding to MMP\u221213. The MD simulations showed the dual role of T247 as a hydrogen bond donor to the ligand, as well as a contributor to the formation of the van der Waal surface area, with T245 and K249 on the S1\u2032\u2212site. The hydrophobic surface area mediated by T247 blocks the access of water molecules to the S1\u2032\u2212site of MMP\u221213 and stabilizes the ligand in the site. The F252 residue is flexible in order to search for the optimum location in the S1\u2032\u2212site of the apo\u2212MMP\u221213, but once a ligand binds to the S1\u2032\u2212site, it can form offset \u03c0\u2212\u03c0 or edge\u2212to\u2212\u03c0 stacking interactions with the ligand. Lastly, H222 and Y244 provide the offset \u03c0\u2212\u03c0 and \u03c0\u2212CH(C\u03b2) interactions on each side of the phenyl ring of the ligand, and this sandwiched interaction could be critical for the ligand binding to MMP\u221213.<\/jats:p>","DOI":"10.3390\/ijms241310577","type":"journal-article","created":{"date-parts":[[2023,6,26]],"date-time":"2023-06-26T01:42:32Z","timestamp":1687743752000},"page":"10577","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["Molecular Dynamics Simulations of Matrix Metalloproteinase 13 and the Analysis of the Specificity Loop and the S1\u2032\u2212Site"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8218-6440","authenticated-orcid":false,"given":"Jun Yong","family":"Choi","sequence":"first","affiliation":[{"name":"Department of Chemistry and Biochemistry, Queens College, Flushing, NY 11367, USA"},{"name":"Ph.D. Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eugene","family":"Chung","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry, Queens College, Flushing, NY 11367, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2023,6,24]]},"reference":[{"key":"ref_1","first-page":"712","article-title":"Matrix Metalloproteinases: From Molecular Mechanisms to Physiology, Pathophysiology, and Pharmacology","volume":"74","author":"Thode","year":"2022","journal-title":"Pharmacol. 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