{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,2]],"date-time":"2025-11-02T19:56:05Z","timestamp":1762113365712,"version":"build-2065373602"},"reference-count":27,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2013,3,18]],"date-time":"2013-03-18T00:00:00Z","timestamp":1363564800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Entropy"],"abstract":"<jats:p>The opening\/closure of the catalytic loop 6 over the active site in apo triosephosphate isomerase (TIM) has been previously shown to be driven by the global motions of the enzyme, specifically the counter-clockwise rotation of the subunits. In this work, the effect of the substrate dihydroxyacetone phosphate (DHAP) on TIM dynamics is assessed using two apo and two DHAP-bound molecular dynamics (MD) trajectories  (each 60 ns long). Multiple events of catalytic loop opening\/closure take place during 60 ns runs for both apo TIM and its DHAP-complex. However, counter-clockwise rotation observed in apo TIM is suppressed and bending-type motions are linked to loop dynamics in the presence of DHAP. Bound DHAP molecules also reduce the overall mobility of the enzyme and change the pattern of orientational cross-correlations, mostly those within each subunit. The fluctuations of pseudodihedral angles of the loop 6 residues are enhanced towards the C-terminus, when DHAP is bound at the active site.<\/jats:p>","DOI":"10.3390\/e15031085","type":"journal-article","created":{"date-parts":[[2013,3,18]],"date-time":"2013-03-18T13:58:38Z","timestamp":1363615118000},"page":"1085-1099","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase"],"prefix":"10.3390","volume":"15","author":[{"given":"Zeynep","family":"Kurkcuoglu","sequence":"first","affiliation":[{"name":"Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul 34342, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pemra","family":"Doruker","sequence":"additional","affiliation":[{"name":"Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul 34342, Turkey"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2013,3,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"3961","DOI":"10.1007\/s00018-010-0473-9","article-title":"Triosephosphate isomerase: A highly evolved biocatalyst","volume":"67","author":"Wierenga","year":"2010","journal-title":"Cell. 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