Antibody-mediated biorecognition of myelin oligodendrocyte glycoprotein: computational evidence of demyelination-related epitopes.

Antigen-antibody interaction is crucial in autoimmune disease pathogenesis, as multiple sclerosis and neuromyelitis optica. Given that, autoantibodies are essential biomolecules, of which the myelin oligodendrocyte glycoprotein (MOG) can figure as a target. Here we combined Molecular Dynamics (MD), Steered Molecular Dynamics (SMD), and Atomic Force Microscope (AFM) to detail MOG recognition by its specific antibody.

Immobilization and unbinding investigation of the antigen-antibody complex using theoretical and experimental techniques.

Experimental results for the antibody known as immunoglobulin G - IgG interacting with phenobarbital were obtained via atomic force microscopy (AFM) and thereafter investigated using computer simulation modeling tools. Using molecular dynamics simulation and docking calculations, the energetically stable configurations of an immobilized antibody over a silicon surface were searched. Six stable configurations of the immobilized antibody over the silicon nitride surface covered by linker molecules were found.

Chiral recognition of liquid phase dimers from gamma-valerolactone racemic mixture.

Gamma-valerolactone (GVL) is a cyclic ester that can be considered a green alternative in chemical processes due to its environmentally friendly physical and chemical properties and low production cost from biomass. Although GVL is a chiral solvent, it is usually used as a racemic mixture, instead of its homochiral forms, which might improve its performance in enantioselective synthesis and chiral separation chromatographic techniques. This report presents the development and validation of an atomistic force field optimized to reproduce GVL liquid-phase properties via Monte Carlo (MC) and molecular dynamics (MD) simulation methods.

Design of an Internal Model Control strategy for single-phase grid-connected PWM inverters and its performance analysis with a non-linear local load and weak grid.

This paper presents the design of a controller based on Internal Model Control (IMC) applied to a grid-connected single-phase PWM inverter. The mathematical modeling of the inverter and the LCL output filter, used to project the 1-DOF IMC controller, is presented and the decoupling of grid voltage by a Feedforward strategy is analyzed. A Proportional - Resonant Controller (P+Res) was used for the control of the same plant in the running of experimental results, thus moving towards the discussion of differences regarding IMC and P+Res performances, which arrived at the evaluation of the proposed control strategy.

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.

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.

Solvation of sodium octanoate micelles in concentrated urea solution studied by means of molecular dynamics simulations.

The effects of urea on self-assembling remains a challenging topic on surface chemistry, and computational modeling may have a role on the unraveling of the molecular mechanisms underlying these effects. Bearing that in mind, we performed a set of molecular dynamics simulations to assess the effects of urea on the self-assembling properties of sodium octanoate, an anionic surfactant, as compared to the aggregation of the same surfactant in pure water as the solvent. The concentration of free monomers increased 3-fold in the presence of urea, in agreement with the accepted view that urea should increase monomer solubility.

Designing an enzyme-based nanobiosensor using molecular modeling techniques.

Nanobiosensors can be built via functionalization of atomic force microscopy (AFM) tips with biomolecules capable of interacting with the analyte on a substrate, and the detection being performed by measuring the force between the immobilized biomolecule and the analyte. The optimization of such sensors may require multiple experiments to determine suitable experimental conditions for the immobilization and detection. In this study we employ molecular modeling techniques to assist in the design of nanobiosensors to detect herbicides.

Chitosan molecular structure as a function of N-acetylation.

Molecular dynamics simulations have been carried out to characterize the structure and solubility of chitosan nanoparticle-like structures as a function of the deacetylation level (0, 40, 60, and 100%) and the spatial distribution of the N-acetyl groups in the particles. The polysaccharide chains of highly N-deacetylated particles where the N-acetyl groups are uniformly distributed present a high flexibility and preference for the relaxed two-fold helix and five-fold helix motifs. When these groups are confined to a given region of the particle, the chains adopt preferentially a two-fold helix with ϕ and ψ values close to crystalline chitin.

Antimony-doped tin oxide nanocrystals: synthesis and solubility behavior in organic solvents.

This work focuses on the nonaqueous synthesis of antimony-doped tin oxide nanocrystals in the size range of 2-6 nm and the investigation of their solubility in organic solvents (CHCl(3) and THF) in the presence of amphiphilic molecules (oleic acid and oleylamine). To unravel the underlying processes, a set of molecular dynamics simulations is performed involving the compatibility of oleic acid and oleylamine in mixtures with both CHCl(3) and THF. The results show that the method is useful for obtaining the desired oxide, and that the interaction between amphiphilic molecules and solvents can be predicted by molecular dynamics simulations with very good qualitative agreement.

Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution.

Molecular dynamics simulations have been used to characterize the structure of single chitin and chitosan chains in aqueous solutions. Chitin chains, whether isolated or in the form of a β-chitin nanoparticle, adopt the 2-fold helix with ϕ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)···O5(n+1) responsible for the 2-fold helical motif in these polysaccharides is stabilized by hydrogen bonds with water molecules in a well-defined orientation.

Interaction between the CBM of Cel9A from Thermobifida fusca and cellulose fibers.

Molecular docking and molecular dynamics (MD) simulations were used to investigate the binding of a cellodextrin chain in a crystal-like conformation to the carbohydrate-binding module (CBM) of Cel9A from Thermobifida fusca. The fiber was found to bind to the CBM in a single and well-defined configuration in-line with the catalytic cleft, supporting the hypothesis that this CBM plays a role in the catalysis by feeding the catalytic domain (CD) with a polysaccharide chain. The results also expand the current known list of residues involved in the binding.

On the relative stabilities of the alkali cations 222 cryptates in the gas phase and in water-methanol solution.

The relative stabilities of the alkali [M subset 222]+ cryptates (M = Na, K, Rb and Cs) in the gas phase and in solution (80:20 v/v methanol:water mixture) at 298 K, are computed using a combination of ab initio quantum-chemical calculations (HF/6-31G and MP2/6-31+G*//HF/6-31+G*) and explicit-solvent Monte Carlo free-energy simulations. The results suggest that the relative stabilities of the cryptates in solution are due to a combination of steric effects (compression of large ions within the cryptand cavity), electronic effects (delocalization of the ionic charge onto the cryptand atoms) and solvent effects (dominantly the ionic dessolvation penalty). Thus, the relative stabilities in solution cannot be rationalized solely on the basis of a simple match or mismatch between the ionic radius and the cryptand cavity size as has been suggested previously.

Interaction of the disaccharide trehalose with a phospholipid bilayer: a molecular dynamics study.

The disaccharide trehalose is well known for its bioprotective properties. Produced in large amounts during stress periods in the life of organisms able to survive potentially damaging conditions, trehalose plays its protective role by stabilizing biostructures such as proteins and lipid membranes. In this study, molecular dynamics simulations are used to investigate the interaction of trehalose with a phospholipid bilayer at atomistic resolution.