title: Unbinding pathway energy of glyphosate from the EPSPs enzyme binding site characterized by Steered Molecular Dynamics and Potential of Mean Force.
abstract: The quantification of herbicides in the environment, like glyphosate, is extremely important to prevent contamination. Nanobiosensors stands out in the quantization process, because of the high selectivity, sensitivity and short response time of the method. In order to emulate the detection of glyphosate using a specific nanobiossensor through an Atomic Force Microscope (AFM), this work carried out Steered Molecular Dynamics simulations (SMD) in which the herbicide was unbinded from the active site of the enzyme 5- enolpyruvylshikimate 3 phosphate synthase (EPSPS) along three different directions.After the simulations, Potential of Mean Force calculations were carried, from a cumulant expansion of Jarzynski's equation to obtain the profile of free energy of interaction between the herbicide and the active site of the enzyme in the presence of shikimate-3 substrate phosphate (S3P). The set of values for external work, had a Gaussian distribution. The PMF values ranged according to the directions of the unbindong pahway of each simulation, displaying energy values of 10.7, 14.7 and 19.5KJmol-1. The results provide a theoretical support in order to assist the construction of a specific nanobiossensor to quantify the glyphosate herbicide.
authors.affiliation: Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil. Electronic address: jrmoca@gmail.com.
authors.forename: Moacir F
authors.initials: MF
authors.lastname: Ferreira
authors.affiliation: Instituto de Química, Universidade Federal de Uberlândia, 38408-100, Uberlândia, MG, Brazil.
authors.forename: Eduardo F
authors.initials: EF
authors.lastname: Franca
authors.affiliation: Universidade Federal de São Carlos, 18052-780, Sorocaba, SP, Brazil.
authors.forename: Fábio L
authors.initials: FL
authors.lastname: Leite
mesh_terms: D051229:3-Phosphoshikimate 1-Carboxyvinyltransferase / Q000737:chemistry* / Q000378:metabolism*; D001665:Binding Sites; D005998:Glycine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D006540:Herbicides / Q000737:chemistry / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D013816:Thermodynamics; D013997:Time Factors; D000097797:Glyphosate
chemical_list: D051229:3-Phosphoshikimate 1-Carboxyvinyltransferase; D005998:Glycine; D006540:Herbicides; D000097797:Glyphosate
keywords: AFM; EPSP; Glyphosate; Jarzynski’s equation; Potential mean of force; Steered molecular dynamics