Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors

• A stochastic modeling of enzyme attachment on a functionalized AFM tip surface was proposed.
• Enzyme arrangement over the surface, and the average number of enzyme–substract interaction was obtained.
• Enzyme–substract interaction energy was obtained by using Steered Molecular Dynamics calculation.
• The theoretical results obtained are in good agreement with experiments.

A stochastic simulation of adsorption processes was developed to simulate the coverage of an atomic force microscope (AFM) tip with enzymes represented as rigid polyhedrons. From geometric considerations of the enzyme structure and AFM tip, we could estimate the average number of active sites available to interact with substrate molecules in the bulk. The procedure was exploited to determine the interaction force between acetyl-CoA carboxylase enzyme (ACC enzyme) and its substrate diclofop, for which steered molecular dynamics (SMD) was used. The theoretical force of (1.6 ± 0.5) nN per enzyme led to a total force in remarkable agreement with the experimentally measured force with AFM, thus demonstrating the usefulness of the procedure proposed here to assist in the interpretation of nanobiosensors experiments.

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