Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains' pathogenicity level.

The Helicobacter pylori cytotoxin-associated gene A (CagA) is known for causing gastroduodenal diseases, such as atrophic gastritis and peptic ulcerations. Furthermore Helicobacter pylori CagA positive strains has been reported as one of the main risk factors for gastric cancer (Parsonnet et al., 1997). Structural variations in the CagA structure can alter its affinity with the host proteins, inducing differences in the pathogenicity of H. pylori. CagA N-terminal region is characterized for be conserved among all H. pylori strains since the C-terminal region is characterized by an intrinsically disorder behavior. We generated complete structural models of CagA using different conformations of the C-terminal region for two H. pylori strains. These models contain the same EPIYA (ABC1C2) motifs but different level of pathogenicity: gastric cancer and duodenal ulcer. Using these structural models we evaluated the pathogenicity level of the H. pylori strain, based on the affinity of the interaction with SHP-2 and Grb2 receptors and on the number of interactions with the EPIYA motif. We found that the main differences in the interaction was due to the contributions of certain types of energies from each strain and not from the total energy of the molecule. Specifically, the electrostatic energy, helix dipole energy, Wander Waals clashes, torsional clash, backbone clash and cis bond energy allowed a separation between severe and mild pathology for the interaction of only CagA with SHP2.

Peptides design based on transmembrane Escherichia coli's OmpA protein through molecular dynamics simulations in water-dodecane interfaces.

Recent research efforts have focused on the production of environmentally nonthreatening products, including identifying biosurfactants that can replace conventional surfactants. In order to utilize biosurfactants in different industries such as cosmetic, food or petroleum, it is necessary to understand the underpinnings behind the interactions that could take place for biosurfactants which display potential for interface activity. This work aimed to use molecular dynamics simulations to understand the interactions of rationally obtained peptide sequences from the original sequence of the OmpA gene in Escherichia coli, based on the free energy change (ΔG) during peptide insertion at the water-dodecane interface. Seventeen OmpA-based peptide sequences were selected and analyzed based on their hydropathy index profiles. We found that free energy change due to Columbic interactions and SASA (ΔGCoul/SASA), total free energy change and MW (ΔG/MW), and free energy change due to Coulombic and van der Waals interactions (ΔGCoul/ΔGvdW) ratios could provide a better understating in the contribution of the free energy decrease at the interface. The results indicated that the peptide sequences GKNHDTGVSPVFA and THENQLGAGAFG display biosurfactant potential based on low ΔG per square nanometer, high ΔGCoul/ΔGvdW ratio, clearly defined moieties along its hydrophobic surface and sequence, and the presence of charged residues in the polar head. Clearly defined moieties and SASA were determinant for electrostatic interactions between oil-water interfaces. Experimental validations exhibited that the emulsions prepared remained stable between 3 and 27h, respectively. Even though the peptide GKNHDTGVSPVFA displays strong interactions at the interface, stabilization times showed that the peptide THENQLGAGAFG exhibited the best performance suggesting that the stability can be better described by kinetic rather than thermodynamic criteria once the emulsion is formed.

Molecular dynamics approach to investigate the coupling of the hydrophilic-lipophilic balance with the configuration distribution function in biosurfactant-based emulsions.

Emulsion stability has been characterized by macroscopic variables such as the hydrophilic-lipophilic balance, with the aim being to predict the surfactant properties of molecules. Nevertheless, this parameter does not take the topology of the molecule into account, as it only considers its lipophilic degree. On the other hand, the classical Derjaguin-Landau-Verwey-Overbeek approach (based on the continuum model), which has been widely utilized to evaluate the stabilities of colloids, polymers, and surfactants, takes some bulk macroscopic parameters such as the shear viscosity coefficient and the dielectric permittivity into account. In the work reported here, molecular dynamics simulations were used to elucidate the mechanism of layer formation and micellar structure for different combinations of valine-aspartic acid peptides in dodecane-water emulsions, as well as their associations with the hydrophilic-lipophilic balance. The peptide-dodecane radial distribution function showed that the first peak intensity was inversely correlated with the hydrophilic-lipophilic balance; moreover, the oscillatory structural forces became increasingly prominent when the hydrophilic-lipophilic balance was decreased. Our results seem to indicate that the radial distribution function could be utilized to evaluate the stabilities of emulsions of peptides via molecular simulations.