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Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions
Published on: November 21, 2017
Cooperativity in drug-DNA recognition: a molecular dynamics study.
S A Harris1, E Gavathiotis, M S Searle
1School of Pharmaceutical Sciences, University Park, Nottingham NG7 2RD, UK.
Molecular dynamics simulations reveal that while structural and energetic factors alone do not explain Hoechst 33258 binding cooperativity to DNA, incorporating configurational entropy accurately predicts the observed experimental results.
Area of Science:
- Molecular Biophysics
- Computational Chemistry
- Structural Biology
Background:
- Nuclear Magnetic Resonance (NMR) studies show the minor groove-binding ligand Hoechst 33258 binds DNA cooperatively.
- No intermediate 1:1 complex is detected, and static NMR structures of free and 2:1 complex DNA do not fully explain this cooperativity.
Purpose of the Study:
- To investigate the origins of cooperativity in Hoechst 33258 DNA binding using molecular dynamics (MD) simulations.
- To calculate thermodynamic parameters for molecular recognition events.
Main Methods:
- Performed MD simulations on free DNA, 1:1 complex, and 2:1 complex.
- Calculated enthalpic, hydration, and configurational entropy factors.
Main Results:
- MD simulations indicate structural factors alone do not explain cooperativity; enthalpic and hydration factors suggest slight anticooperativity.
- Including configurational entropy changes results in calculated cooperativity that aligns well with experimental observations.
Conclusions:
- Molecular dynamics simulations provide insights into DNA-ligand interactions difficult to explain with static models.
- The study demonstrates "allostery without conformational change" by accounting for entropic contributions.
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