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The binding model of adenosine-specific DNA aptamer: Umbrella sampling study
Ruslan R Ramasanoff1, Petr A Sokolov2
1Sevastopol State University, Universitetskaya 33, 299053, Sevastopol, Russia.
Journal of Molecular Graphics & Modelling
|October 6, 2022
Summary
This study reveals how adenosine monophosphate (AMP) selectively binds to DNA aptamers. An induced-fit model explains the binding mechanism, supported by molecular dynamics simulations.
Area of Science:
- Biochemistry
- Molecular Biology
- Computational Chemistry
Background:
- Adenosine-specific DNA aptamers are crucial for molecular recognition.
- Understanding their binding mechanisms is key to aptamer-based technologies.
Purpose of the Study:
- To elucidate the selective binding mechanism of adenosine-specific DNA aptamers.
- To investigate the role of aptamer structure in molecular specificity and stabilization.
Main Methods:
- Umbrella sampling molecular dynamics (MD) calculations.
- Utilized the parmbsc1 force field for simulations.
- Analyzed free energy landscapes of AMP dissociation.
Main Results:
- Identified a disordered internal loop in the unbound aptamer with specific guanine packing hindering ligand entry.
- Observed a stabilizing hydrogen bond network in the unbound aptamer's binding cavity.
- Proposed a sequential binding model where the first AMP induces ordering, followed by a second, lower-energy binding event.
Conclusions:
- The adenosine-specific DNA aptamer employs an induced-fit binding model.
- This model aligns with experimental data from NMR and calorimetry.
- Structural dynamics of the aptamer are critical for its high specificity and affinity.
