Abstract
The binding/unbinding of the human thrombin and its 15-mer single stranded DNA aptamer, under the application of external stimulus in the form of electrostatic potential/electric field, is investigated by a combination of continuum analysis and atomistic molecular dynamics simulation. In agreement with the experiments that demonstrate the influence of electrostatic potential on the thrombin/aptamer complex, our computations show that the application of positive electric field successfully unbinds the thrombin from the aptamer. Results from umbrella sampling simulations reveal that there is a decrease in the free energy of binding between the thrombin and aptamer in presence of positive electric fields. Hydrogen bonding and non-bonded interaction energies, and hence the free energy of binding, between the thrombin and its aptamer reduce as the applied electric field is shifted from negative to positive values. Our analyses demonstrate that application of electrical stimulus modifies the molecular interactions within the complex and consequently, electrical field can be used to modulate the association between the thrombin and its aptamer.
Highlights
Structural and functional biotic-abiotic nanoscale interfaces are very promising for applications in highly sensitive, biocompatible and flexible bio-sensors and actuators
A positively charged molecule situated over a thrombin binding aptamer (TBA) layer at an electrode potential of (+) 300 mV will experience a repulsive force that is stronger compared to that at (+) 100 mV since the electric field becomes increasingly positive with increasing positive electrode potential
The simple, yet powerful, Poisson-Boltzmann theory based on a mean field model of the electrostatic interaction between particles reveals that at positive electrode potentials the DNA layer forms a repulsive region for the thrombin molecule, thereby acting as a deterrent to the complex formation
Summary
Structural and functional biotic-abiotic nanoscale interfaces are very promising for applications in highly sensitive, biocompatible and flexible bio-sensors and actuators Their potential use in biomedical and biomechanical sciences include, for instance, modulation of biological systems and biomolecular activity, disease detection as well as reprogramming of genetic information[1]. We investigate the effects of externally applied electrostatic potential on a film of TBA in salt solution using the Poisson Boltzmann equation (PBE) and calculate the free energy of binding between TBA and thrombin by MD simulations in presence of an applied electric field. We find that for positive electric fields the thrombin separates from the aptamer facilitated by a reduced free energy of binding
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