Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

Entropy

Zeynep Kurkcuoglu¹ 

[1] Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, Istanbul 34342, Turkey; E-Mail

关键词: molecular dynamics simulation;    essential dynamics;    collective motions;    functional loop dynamics;    triosephosphate isomerase;    dihydroxyacetone phosphate;    loop closure;   

DOI  :  10.3390/e15031085

来源: mdpi

【 摘 要 】

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.

【 授权许可】

CC BY   
© 2013 by the authors; licensee MDPI, Basel, Switzerland.