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Published on: May 13, 2020
Dimerization affects collective dynamics of triosephosphate isomerase
1Department of Chemical Engineering and Polymer Research Center, Bogazici University, Bebek, 34342, Istanbul, Turkey.
Biochemistry
|January 15, 2008
Summary
Dimerization of triosephosphate isomerase (TIM) enables collective motions, enhancing loop 6 closure crucial for enzyme activity. Monomeric TIM exhibits localized movements, lacking this coordinated dynamic.
Area of Science:
- Biochemistry
- Structural Biology
- Computational Biology
Background:
- Triosephosphate isomerase (TIM) functions as a homodimer, though subunit cooperativity is not evident.
- Loop 6 dynamics are critical for TIM's active site closure and catalytic function.
Purpose of the Study:
- To investigate the correlation between collective motions and loop 6 dynamics in apo-TIM.
- To compare the dynamic behaviors of dimeric and monomeric TIM structures.
Main Methods:
- Molecular dynamics (MD) simulations of 30-60 ns were conducted on dimeric and monomeric TIM.
- Simulations were performed in explicit water at 300 K and 1 bar.
Main Results:
- Dimeric TIM exhibited significant cross-correlations in residue fluctuations, driven by global subunit counter-rotations.
- The primary essential mode in the dimer strongly coupled loop 6 closure to active site dynamics.
- Monomeric TIM displayed localized loop motions without significant cross-correlations.
Conclusions:
- Dimerization induces collective motions at the nanosecond timescale in TIM.
- These collective motions are functionally relevant, coordinating loop 6 closure over the active site.
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