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

J Mol Graph Model. 2014 Sep:53:100-104. doi: 10.1016/j.jmgm.2014.07.009. Epub 2014 Jul 23.

Abstract

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.

Keywords: ACC enzyme; AFM; Computational rigid model; Enzyme modeling; SMD; Stochastic adsorption.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetyl-CoA Carboxylase / antagonists & inhibitors
  • Acetyl-CoA Carboxylase / chemistry
  • Biosensing Techniques
  • Catalytic Domain
  • Enzymes, Immobilized / chemistry*
  • Microscopy, Atomic Force
  • Molecular Dynamics Simulation
  • Phenyl Ethers / chemistry
  • Propionates / chemistry
  • Protein Binding
  • Protein Structure, Quaternary
  • Saccharomyces cerevisiae Proteins / antagonists & inhibitors
  • Saccharomyces cerevisiae Proteins / chemistry
  • Stochastic Processes
  • Thermodynamics

Substances

  • 2-(4-(2,4-dichlorophenoxy)phenoxy)propionic acid
  • Enzymes, Immobilized
  • Phenyl Ethers
  • Propionates
  • Saccharomyces cerevisiae Proteins
  • Acetyl-CoA Carboxylase