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Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase
Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul 34342, Turkey
* Author to whom correspondence should be addressed.
Received: 11 January 2013; in revised form: 18 February 2013 / Accepted: 12 March 2013 / Published: 18 March 2013
Abstract: 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.
Keywords: molecular dynamics simulation; essential dynamics; collective motions; functional loop dynamics; triosephosphate isomerase; dihydroxyacetone phosphate; loop closure
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MDPI and ACS Style
Kurkcuoglu, Z.; Doruker, P. Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. Entropy 2013, 15, 1085-1099.
Kurkcuoglu Z, Doruker P. Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. Entropy. 2013; 15(3):1085-1099.
Kurkcuoglu, Zeynep; Doruker, Pemra. 2013. "Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase." Entropy 15, no. 3: 1085-1099.