Substrate Effect on Catalytic Loop and Global Dynamics of Triosephosphate Isomerase

Zeynep Kurkcuoglu,Pemra Doruker

doi:10.3390/e15031085

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.

Highlights

Flexibility and dynamics are crucial for the biological function of proteins
Each catalytic site is composed of residues N11, K13, H95 and E165 that belong to a single subunit
The root mean square deviations (RMSD) of the snapshots with respect to the initial structure are plotted in Figure S1 for each trajectory

Summary

Introduction

Flexibility and dynamics are crucial for the biological function of proteins. In certain enzymes, conformational changes, such as transformation between open and closed structures, are linked withEntropy 2013, 15 substrate binding and product release to/from the active site. TIM is a highly efficient enzyme, catalyzing the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP). It is a homodimer, with each subunit adopting the TIM-barrel fold. TIM is fully active as a dimer, even though there is no coupling between the two catalytic sites. Each catalytic site is composed of residues N11, K13, H95 and E165 (numbered based on chicken TIM) that belong to a single subunit. Residue E165 is located on the so-called catalytic loop 6 (E165-A176). Experiments have indicated that loop 6 closure is not ligand-gated, meaning that it is observed in the apo state [3]

Methods

Results

Conclusion