title: Modeling the coverage of an AFM tip by enzymes and its application in nanobiosensors.
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.
authors.affiliation: Nanoneurobiophysics Research Group, Department of Physics, Chemistry and Mathematics, Federal University of São Carlos, 18052-780 Sorocaba, SP, Brazil.
authors.forename: Adriano M
authors.initials: AM
authors.lastname: Amarante
authors.affiliation: Nanoneurobiophysics Research Group, Department of Physics, Chemistry and Mathematics, Federal University of São Carlos, 18052-780 Sorocaba, SP, Brazil. Electronic address: guedmuller@gmail.com.
authors.forename: Guedmiller S
authors.initials: GS
authors.lastname: Oliveira
authors.affiliation: Nanoneurobiophysics Research Group, Department of Physics, Chemistry and Mathematics, Federal University of São Carlos, 18052-780 Sorocaba, SP, Brazil.
authors.forename: Carolina C
authors.initials: CC
authors.lastname: Bueno
authors.affiliation: Chemistry Institute, Federal University of Uberlândia, 38400-902 Uberlândia, MG, Brazil.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Cunha
authors.affiliation: Nanoneurobiophysics Research Group, Department of Physics, Chemistry and Mathematics, Federal University of São Carlos, 18052-780 Sorocaba, SP, Brazil.
authors.forename: Jéssica C M
authors.initials: JCM
authors.lastname: Ierich
authors.affiliation: Chemistry Department, Federal University of São Carlos, 13565-905 São Carlos, SP, Brazil.
authors.forename: Luiz C G
authors.initials: LCG
authors.lastname: Freitas
authors.affiliation: Chemistry Institute, Federal University of Uberlândia, 38400-902 Uberlândia, MG, Brazil.
authors.forename: Eduardo F
authors.initials: EF
authors.lastname: Franca
authors.affiliation: São Carlos Institute of Physics, University of São Paulo, 13566-590 São Carlos, SP, Brazil.
authors.forename: Osvaldo N
authors.initials: ON
authors.lastname: Oliveira
authors.affiliation: Nanoneurobiophysics Research Group, Department of Physics, Chemistry and Mathematics, Federal University of São Carlos, 18052-780 Sorocaba, SP, Brazil. Electronic address: fabioleite@ufscar.br.
authors.forename: Fábio L
authors.initials: FL
authors.lastname: Leite
mesh_terms: D000103:Acetyl-CoA Carboxylase / Q000037:antagonists & inhibitors / Q000737:chemistry; D015374:Biosensing Techniques; D020134:Catalytic Domain; D004800:Enzymes, Immobilized / Q000737:chemistry*; D018625:Microscopy, Atomic Force; D056004:Molecular Dynamics Simulation; D010647:Phenyl Ethers / Q000737:chemistry; D011422:Propionates / Q000737:chemistry; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D029701:Saccharomyces cerevisiae Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry; D013269:Stochastic Processes; D013816:Thermodynamics
chemical_list: C529887:2-(4-(2,4-dichlorophenoxy)phenoxy)propionic acid; D004800:Enzymes, Immobilized; D010647:Phenyl Ethers; D011422:Propionates; D029701:Saccharomyces cerevisiae Proteins; D000103:Acetyl-CoA Carboxylase
keywords: ACC enzyme; AFM; Computational rigid model; Enzyme modeling; SMD; Stochastic adsorption