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Updated: Dec 25, 2025

Studying DNA Looping by Single-Molecule FRET
Published on: June 28, 2014
Sensitivity of Functional Loop Conformations on Long-Range Electrostatics: Implications for M20 Loop Dynamics in E.
C Satheesan Babu1, Carmay Lim1,2
1Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.
Abstract:
In E. coli dihydrofolate reductase, unusual conformational motions of a functional M20 loop that interacts with substrate and coenzyme have been construed as evidence for dynamical effects in enzyme catalysis. By computing this loop's conformational free energies in the apoenzyme, we show that it is sensitive to the treatment of long-range electrostatic interactions and the solvation box size in modeling/simulations. These results provide important guidelines for computing reaction/binding free energy profiles of proteins with functional loops.
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