Adriano Amarante - Academia.edu (original) (raw)

Journal Articles by Adriano Amarante

Journal of the Brazilian Chemical Society

A combined molecular modeling and molecular dynamics simulation was carried out to obtain an impr... more 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 Å 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 Å. Moreover, the Ramachandran plot revealed no denaturation framework during the time of the simulation.

IEEE Sensors Journal, Jan 2014

Highly sensitive and selective functional nanobiosensors are being developed because they have s... more Highly sensitive and selective functional
nanobiosensors 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 functionalised to favour 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 AFM probe sensors has
been presented in this work.

Journal of Molecular Graphics & Modelling, Aug 16, 2013

The immobilization of enzymes on atomic force microscope tip (AFM tip) surface is a crucial step ... more 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.

Papers by Adriano Amarante

The combination of theoretical and experimental analysis has become a valuable tool to investigat... more The combination of theoretical and experimental analysis has become a valuable tool to investigate molecularly the mechanisms involved in biomolecular systems.1,2 Atomic Force Microscope assisted by computer simulations is able to estimate intermolecular forces with high specificity and selectivity by solving numerically interaction pathways. Since the immobilization process of enzymes on nanosurfaces is difficult to be controlled experimentally and it affects its biological activity, the proper orientation and binding site availability can be estimated through computer simulations. 3,4 Additionally, the unbinding process can be calculated through Steered Molecular Dynamics (SMD) and compared to AFM experiments.

Journal of molecular graphics & modelling, 2014

A stochastic simulation of adsorption processes was developed to simulate the coverage of an atom... more 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.

Materials Research, 2013

Atomic force spectroscopy, a technique derived from Atomic Force Microscopy (AFM), allowed us to ... more Atomic force spectroscopy, a technique derived from Atomic Force Microscopy (AFM), allowed us to distinguish nonspecific and specific interactions between the acetolactate synthase enzyme (ALS) and anti-atrazine antibody biomolecules and the herbicides imazaquin, metsulfuron-methyl and atrazine. The presence of specific interactions increased the adhesion force (F adh ) between the AFM tip and the herbicides, which made the modified tip a powerful biosensor. Increases of approximately 132% and 145% in the F adh values were observed when a tip functionalized with ALS was used to detect imazaquin and metsulfuron-methyl, respectively. The presence of specific interactions between the atrazine and the anti-atrazine antibody also caused an increase in the F adh values (approximately 175%) compared to those observed when using an unfunctionalized tip. The molecular modeling results obtained with the ALS enzyme suggest that the orientation of the biomolecule on the tip surface could be suitable for allowing interaction with the herbicides imazaquin and metsulfuron-methyl.

The atomic force microscopy (AFM) is a powerful for single-molecule force experiment that can cha... more The atomic force microscopy (AFM) is a powerful for single-molecule force experiment that can characterize physical and chemical properties of biological and polymeric matter at the nanometer scale. However, it does not reveal the molecular mechanisms behind the binding of ligands and conformational changes in biomolecules in atomic time scale. This information can only be addressed by molecular dynamics (DM) simulation, which simulates the AFM experiments through methodology called Steered Molecular Dynamics (SMD). The AFM simulation is usually obtained by integrating the mean force from an ensemble of configurations resulted from a molecular mechanics calculation. In this chapter, we shall concentrate on simulation of the atomic force spectroscopy (AFS), which procedure consist in perform a constant velocity molecular dynamics simulation, recording force and position at each time point, to reproduce and predict the atomic force curves. The AFM simulation showed to be very useful to provide qualitative and quantitative information about ligand binding pathways in enzymes and the mechanical properties of biological and synthetic polymers.

Book Chapters by Adriano Amarante

Journal of the Brazilian Chemical Society

A combined molecular modeling and molecular dynamics simulation was carried out to obtain an impr... more 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 Å 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 Å. Moreover, the Ramachandran plot revealed no denaturation framework during the time of the simulation.

IEEE Sensors Journal, Jan 2014

Highly sensitive and selective functional nanobiosensors are being developed because they have s... more Highly sensitive and selective functional
nanobiosensors 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 functionalised to favour 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 AFM probe sensors has
been presented in this work.

Journal of Molecular Graphics & Modelling, Aug 16, 2013

The immobilization of enzymes on atomic force microscope tip (AFM tip) surface is a crucial step ... more 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.

The combination of theoretical and experimental analysis has become a valuable tool to investigat... more The combination of theoretical and experimental analysis has become a valuable tool to investigate molecularly the mechanisms involved in biomolecular systems.1,2 Atomic Force Microscope assisted by computer simulations is able to estimate intermolecular forces with high specificity and selectivity by solving numerically interaction pathways. Since the immobilization process of enzymes on nanosurfaces is difficult to be controlled experimentally and it affects its biological activity, the proper orientation and binding site availability can be estimated through computer simulations. 3,4 Additionally, the unbinding process can be calculated through Steered Molecular Dynamics (SMD) and compared to AFM experiments.

Journal of molecular graphics & modelling, 2014

A stochastic simulation of adsorption processes was developed to simulate the coverage of an atom... more 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.

Materials Research, 2013

Atomic force spectroscopy, a technique derived from Atomic Force Microscopy (AFM), allowed us to ... more Atomic force spectroscopy, a technique derived from Atomic Force Microscopy (AFM), allowed us to distinguish nonspecific and specific interactions between the acetolactate synthase enzyme (ALS) and anti-atrazine antibody biomolecules and the herbicides imazaquin, metsulfuron-methyl and atrazine. The presence of specific interactions increased the adhesion force (F adh ) between the AFM tip and the herbicides, which made the modified tip a powerful biosensor. Increases of approximately 132% and 145% in the F adh values were observed when a tip functionalized with ALS was used to detect imazaquin and metsulfuron-methyl, respectively. The presence of specific interactions between the atrazine and the anti-atrazine antibody also caused an increase in the F adh values (approximately 175%) compared to those observed when using an unfunctionalized tip. The molecular modeling results obtained with the ALS enzyme suggest that the orientation of the biomolecule on the tip surface could be suitable for allowing interaction with the herbicides imazaquin and metsulfuron-methyl.

The atomic force microscopy (AFM) is a powerful for single-molecule force experiment that can cha... more The atomic force microscopy (AFM) is a powerful for single-molecule force experiment that can characterize physical and chemical properties of biological and polymeric matter at the nanometer scale. However, it does not reveal the molecular mechanisms behind the binding of ligands and conformational changes in biomolecules in atomic time scale. This information can only be addressed by molecular dynamics (DM) simulation, which simulates the AFM experiments through methodology called Steered Molecular Dynamics (SMD). The AFM simulation is usually obtained by integrating the mean force from an ensemble of configurations resulted from a molecular mechanics calculation. In this chapter, we shall concentrate on simulation of the atomic force spectroscopy (AFS), which procedure consist in perform a constant velocity molecular dynamics simulation, recording force and position at each time point, to reproduce and predict the atomic force curves. The AFM simulation showed to be very useful to provide qualitative and quantitative information about ligand binding pathways in enzymes and the mechanical properties of biological and synthetic polymers.