title: Dimerization affects collective dynamics of triosephosphate isomerase.
abstract: Molecular dynamics simulations (30-60 ns runs) are performed on free/apo triosephosphate isomerase (TIM) to determine any correlation between collective motions and loop 6 dynamics. Native TIM is reported to be active only as a homodimer even though cooperativity has not been observed between the two identical subunits. Both dimeric and monomeric (isolated from dimer) forms of TIM are simulated in explicit water at 300 K and 1 bar to inspect any differences between the structures in terms of fluctuation dynamics and functionally important loop 6 dynamics/closure. Significant cross-correlations between residue fluctuations are observed in the dimer, which result from the global counter-rotations of the two identical subunits in the essential modes of the dimer. Specifically, the first essential mode contributing to 34% of overall motion of the dimer is strongly coupled to the loop 6's closure over the active site. In contrast, such significant correlations cannot be observed in the monomeric structure, which maintains relatively localized motions of the loops in the essential modes. Thus, the onset of collective motions at ns time scale due to dimerization has functional implications as to the coordination of loop 6 closure.
authors.affiliation: Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
authors.forename: Sertan
authors.initials: S
authors.lastname: Cansu
authors.forename: Pemra
authors.initials: P
authors.lastname: Doruker
mesh_terms: D000818:Animals; D001051:Apoenzymes / Q000737:chemistry; D002645:Chickens; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019281:Dimerization; D008958:Models, Molecular; D014305:Triose-Phosphate Isomerase / Q000737:chemistry*
chemical_list: D001051:Apoenzymes; D014305:Triose-Phosphate Isomerase