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Entropy 2013, 15(3), 1085-1099; doi:10.3390/e15031085
Article

Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

 and *
Received: 11 January 2013; in revised form: 18 February 2013 / Accepted: 12 March 2013 / Published: 18 March 2013
(This article belongs to the Special Issue Loop Entropy)
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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 molecular dynamics simulation; essential dynamics; collective motions; functional loop dynamics; triosephosphate isomerase; dihydroxyacetone phosphate; loop closure
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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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.

AMA Style

Kurkcuoglu Z, Doruker P. Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase. Entropy. 2013; 15(3):1085-1099.

Chicago/Turabian Style

Kurkcuoglu, Zeynep; Doruker, Pemra. 2013. "Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase." Entropy 15, no. 3: 1085-1099.


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