by Keyword: Molecular dynamics simulation
Tampieri, F, Espona-Noguera, A, Labay, C, Ginebra, MP, Yusupov, M, Bogaerts, A, Canal, C, (2023). Does non-thermal plasma modify biopolymers in solution? A chemical and mechanistic study for alginate Biomaterials Science 11, 4845-4858 
The mutual interaction between reactive species generated by non-thermal plasma and biopolymers in solution causes oxidative modifications that can have an impact in biomedical applications.
JTD Keywords: atmospheric plasma, cellulose, dftb3, gas, oxidation, parameterization, simulations, water, Biopolymers, Hydrogen peroxide, Molecular dynamics simulation, Molecular-dynamics, Nitrites, Reactive oxygen species
Tuveri, GM, Ceccarelli, M, Pira, A, Bodrenko, IV, (2022). The Optimal Permeation of Cyclic Boronates to Cross the Outer Membrane via the Porin Pathway Antibiotics 11, 840
We investigated the diffusion of three cyclic boronates formulated as beta-lactamase inhibitors through the porin OmpF to evaluate their potential to cross OM via the porin pathway. The three nonbeta-lactam molecules diffuse through the porin eyelet region with the same mechanism observed for beta-lactam molecules and diazobicyclooctan derivatives, with the electric dipole moment aligned with the transversal electric field. In particular, the BOH group can interact with both the basic ladder and the acidic loop L3, which is characteristic of the size-constricted region of this class of porins. On one hand, we confirm that the transport of small molecules through enterobacter porins has a common general mechanism; on the other, the class of cyclic boronate molecules does not seem to have particular difficulties in diffusing through enterobacter porins, thus representing a good scaffold for new anti-infectives targeting Gram-negative bacteria research.
JTD Keywords: beta-lactamase inhibitors, cyclic boronates, diffusion current, metadynamics, molecular dynamics simulations, permeation, Antibiotics, Beta-lactamase inhibitors, Cyclic boronates, Diffusion, Diffusion current, Discovery, Electric-field, Metadynamics, Molecular dynamics simulations, Molecular-dynamics simulations, Nanopores, Permeability, Permeation, Porins, Rules, Translocation
Valle-Delgado, J. J., Liepina, I., Lapidus, D., Sabaté, R., Ventura, S., Samitier, J., Fernàndez-Busquets, X., (2012). Self-assembly of human amylin-derived peptides studied by atomic force microscopy and single molecule force spectroscopy Soft Matter 8, (4), 1234-1242
The self-assembly of peptides and proteins into amyloid fibrils of nanometric thickness and up to several micrometres in length, a phenomenon widely observed in biological systems, has recently aroused a growing interest in nanotechnology and nanomedicine. Here we have applied atomic force microscopy and single molecule force spectroscopy to study the amyloidogenesis of a peptide derived from human amylin and of its reverse sequence. The spontaneous formation of protofibrils and their orientation along well-defined directions on graphite and DMSO-coated graphite substrates make the studied peptides interesting candidates for nanotechnological applications. The measured binding forces between peptides correlate with the number of hydrogen bonds between individual peptides inside the fibril structure according to molecular dynamics simulations.
JTD Keywords: Amyloid fibril, Amyloidogenesis, Binding forces, Fibril structure, Graphite substrate, Molecular dynamics simulations, Nanometrics, Protofibrils, Single molecule force spectroscopy, Spontaneous formation, Atomic force microscopy, Atomic spectroscopy, Graphite, Hydrogen bonds, Medical nanotechnology, Molecular dynamics, Molecular physics, Self assembly, Thickness measurement, Peptides
