Name
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. |
Year | DOI | Venue |
|---|---|---|
2013 | 10.3390/e15031085 | ENTROPY |
Keywords | Field | DocType |
molecular dynamics simulation,essential dynamics,collective motions,functional loop dynamics,triosephosphate isomerase,dihydroxyacetone phosphate,loop closure | Substrate (chemistry),Dihydroxyacetone phosphate,Mathematical optimization,Enzyme,Triosephosphate isomerase,DHAP,Molecular dynamics,Active site,Stereochemistry,Protein subunit,Mathematics | Journal |
Volume | Issue | ISSN |
15 | 3 | 1099-4300 |
Citations | PageRank | References |
0 | 0.34 | 6 |
Authors | ||
2 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Zeynep Kurkcuoglu | 1 | 6 | 1.63 |
| Pemra Doruker | 2 | 26 | 5.78 |