Guedmiller S. Oliveira

Nanobiosensor for Diclofop Detection Based on Chemically Modified AFM Probes

Highly sensitive and selective functional nanobiobreaksensors are being developed because they have significant applications in the sustenance and conservation of natural resources and can be used in projects to identify degraded and contaminated areas (of both soil and water) and as environmental quality indicators. In the present study, a nanobiosensor was developed based on using theoretical models (molecular docking and molecular dynamics simulations) based on biomimicry of the action mechanism of herbicides in plants coupled with atomic force microscopy (AFM) tools. The herbicide molecules were detected at very low concentrations using a unique sensor construction: the AFM probes and the substrate were chemically functionalized to favor covalent bonding and promote molecular flexibility, as well as to achieve reproducible and accurate results. Computational methods were used to determine the binding energies associated with the enzyme-herbicide interactions, which were compared with experimental results for adhesion forces. The theoretical results showed that the diclofop herbicide could be assembled and attached onto the mica substrate surface and the ACCase enzyme on the AFM probe without damaging the diclofop molecule. The experimental results showed that using a specific agrochemical target molecule was more efficient than using other nonspecific agrochemicals. On average, there was a 90% difference between the values of specific recognition (diclofop) and nonspecific recognition (imazaquin, metsulfuron, and glyphosate). This result validated the selectivity and specificity of the nanobiosensor. The first evidence of diclofop detection by the AFM probe sensors has been presented in this paper.

Nanoneurobiophysics: new challenges for diagnosis and therapy of neurologic disorders

Nanoneurobiophysics Research Group Department of Physics Chemistry and Mathematics Federal University of Sao Carlos (UFSCar)

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

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.

Molecular modeling of enzyme attachment on AFM probes.

The immobilization of enzymes on atomic force microscope tip (AFM tip) surface is a crucial step in the development of nanobiosensors to be used in detection process. In this work, an atomistic modeling of the attachment of the acetyl coenzyme A carboxylase (ACC enzyme) on a functionalized AFM tip surface is proposed. Using electrostatic considerations, suitable enzyme-surface orientations with the active sites of the ACC enzyme available for interactions with bulk molecules were found. A 50 ns molecular dynamics trajectory in aqueous solution was obtained and surface contact area, hydrogen bonding and protein stability were analyzed. The enzyme-surface model proposed here with minor adjustment can be applied to study antigen-antibody interactions as well as enzyme immobilization on silica for chromatography applications.

A Computational Protein Structure Refinement of the Yeast Acetohydroxyacid Synthase

A combined molecular modeling and molecular dynamics simulation was carried out to obtain an improved description of the yeast acetohydroxyacid synthase (AHAS) in aqueous solution. After a thorough homology modeling, the AHAS catalytic dimer was subjected to a molecular dynamics (MD) simulation to analyze its behavior and optimize its geometry. The AHAS 3D molecular structure was analyzed according to the number of salt bridges and hydrogen bonds formed. During 20 ns of MD simulation, an average fluctuation of 3.9 A was obtained. The cofactor thiamine diphosphate makes a relevant contribution to the system stability; this hypothesis was confirmed by the decrease in the average fluctuation of 0.3 A. Moreover, the Ramachandran plot revealed no denaturation framework during the time of the simulation.

Molecular Modeling Applied to Nanobiosystems

Molecular modeling is an important tool for the study and development of new nanotechnologies. This technique is widely applied in the description and characterization of biological systems, aiding the research and development of new health-related technologies. This chapter provides the reader with basic—but fundamental—principles of computer simulation and the use of online biomolecule data repositories. The main programs for molecule manipulation and visualization and the theory underlying the main computational methods discussed are presented.

MODELAGEM MOLECULAR APLICADA A NANOBIOSSISTEMAS

A Modelagem Molecular e uma importante ferramenta para o estudo e o desenvolvimento de novas nanobiotecnologias. E amplamente aplicada na descricao e caracterizacao de sistemas biologicos, auxiliando a pesquisa e o desenvolvimento de novas tecnologias relacionadas com a saude, como novos tratamentos para cura de doencas. O presente capitulo fornece ao leitor os principios basicos, porem fundamentais, de simulacao computacional, do uso de bancos de dados e obtencao de estruturas enzimaticas online. Tambem sao apresentados os principais programas para manipulacao e visualizacao de moleculas, alem da teoria que rege cada um dos metodos de modelagem molecular abordados.