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Density functional theory study of the relaxation and energy of iron surfaces
Abstract The relaxations and energies of the (1 0 0), (1 1 0) and (1 1 1) surfaces of (bcc) Fe have been calculated using density functional theory. A plane-wave pseudopotential method was employed.Expand
Interaction of small molecules with the SARS-CoV-2 main protease in silico and in vitro validation of potential lead compounds using an enzyme-linked immunosorbent assay
Findings indicate that hypericin and cyanidin-3-O-glucoside are suitable candidates for progress to in vitro and in vivo antiviral studies. Expand
Identification of Small Molecule Inhibitors of the Deubiquitinating Activity of the SARS-CoV-2 Papain-Like Protease: in silico Molecular Docking Studies and in vitro Enzymatic Activity Assay
The findings indicate that in particular hypericin, rutin, and cyanidin-3-O-glucoside, represent suitable candidates for subsequent evaluation as PLpro inhibitors, and deubiquitinating activity was validated in vitro using an enzymatic activity assay. Expand
Inhibition of peptide aggregation by lipids: insights from coarse-grained molecular simulations.
  • A. Hung, I. Yarovsky
  • Chemistry, Medicine
  • Journal of molecular graphics & modelling
  • 1 February 2011
Simulation of the aggregation of an amyloidogenic peptide in the absence and presence of a short-chained lipid suggests that the morphology of peptide aggregates is strongly dependent on their local lipid environment, with greater contacts with lipids resulting in the formation of more elongated aggregates. Expand
Density-functional theory studies of pyrite FeS2(100) and (110) surfaces
Abstract We have performed DFT calculations using both plane wave-pseudopotential and Gaussian basis set approaches on the (1 1 1) and (2 1 0) surfaces of pyrite (FeS2). Our calculations indicateExpand
Ordering surfaces on the nanoscale: implications for protein adsorption.
Results are in qualitative agreement with experimental results and suggest that Cyt C does not undergo significant structural disruption upon adsorption to MPMN surfaces, suggesting that proteins may be engineered to specifically interact with nanomaterials by targeted incorporation of unnatural amino acids possessing dual affinity to differing chemical motifs. Expand
Dicarba analogues of α-conotoxin RgIA. Structure, stability, and activity at potential pain targets.
Four RgIA analogues that replaced native disulfide pairs with nonreducible dicarba bridges may represent mechanistic probes to explore analgesia-related biological receptors and exhibited improved serum stability over the native peptide. Expand
A structural model for apolipoprotein C-II amyloid fibrils: experimental characterization and molecular dynamics simulations.
It is suggested that apoC-II monomers fold and self-assemble to form a stable cross-β-scaffold containing relatively unstructured connecting loops, and that charge clusters in the fibril rearrange to minimize the effects of same-charge interactions inherent in parallel in-register models. Expand
Identifying Key Amino Acid Residues That Affect α-Conotoxin AuIB Inhibition of α3β4 Nicotinic Acetylcholine Receptors*
Critical residues that mediate interactions between AuIB and its cognate nAChR subtype are identified and might help improve the design of analgesic conopeptides that selectively “avoid” nA ChR receptors while targeting receptors involved with nociception. Expand
First-principles study of metallic iron interfaces
Abstract Adhesion between clean, bulk-terminated bcc Fe(1 0 0) and Fe(1 1 0) matched and mismatched surfaces was simulated within the theoretical framework of the density functional theory. TheExpand