title: Electrical Stimulus Controlled Binding/Unbinding of Human Thrombin-Aptamer Complex.
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.
authors.affiliation: Department of Mechanical Engineering and Iowa State University, Ames, IA 50011, USA.
authors.forename: Agnivo
authors.initials: A
authors.lastname: Gosai
authors.affiliation: Department of Mechanical Engineering and Iowa State University, Ames, IA 50011, USA.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
authors.affiliation: Department of Mechanical Engineering and Iowa State University, Ames, IA 50011, USA.|Microelectronics Research Center, Iowa State University, Ames, IA 50011, USA.
authors.forename: Ganesh
authors.initials: G
authors.lastname: Balasubramanian
authors.affiliation: Department of Mechanical Engineering and Iowa State University, Ames, IA 50011, USA.
authors.forename: Pranav
authors.initials: P
authors.lastname: Shrotriya
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D018360:Crystallography, X-Ray; D004277:DNA, Single-Stranded; D004558:Electric Stimulation; D004566:Electrodes; D006801:Humans; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D055672:Static Electricity; D013816:Thermodynamics; D013917:Thrombin / Q000737:chemistry / Q000378:metabolism*
chemical_list: D052157:Aptamers, Nucleotide; D004277:DNA, Single-Stranded; C081676:thrombin aptamer; D013917:Thrombin