Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics.

To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site.

Morphological Changes of 3T3 Cells under Simulated Microgravity.

Background: Cells are sensitive to changes in gravity, especially the cytoskeletal structures that determine cell morphology. The aim of this study was to assess the effects of simulated microgravity (SMG) on 3T3 cell morphology, as demonstrated by a characterization of the morphology of cells and nuclei, alterations of microfilaments and microtubules, and changes in cycle progression.

Methods: 3T3 cells underwent induced SMG for 72 h with Gravite, while the control group was under 1G.

Identification of potential anti-hyperglycemic compounds in ethyl acetate extract: and studies.

has been long known for valuable health benefits by folk experience and was recently reported with diabetes-tackling evidences, thus deserving extending efforts on screening for component-activity relationship. In this study, experiments were carried out to find the evidence, justification, and input for computations on the potential against diabetes-related protein structures: PDB-4W93, PDB-3W37, and PDB-4A3A. Liquid chromatography identified 14 bioactive compounds in the ethyl acetate extract (-) and quantified the contents of cordycepin (0.

Hexavalent Chromium Inhibited Zebrafish Embryo Development by Altering Apoptosis- and Antioxidant-Related Genes.

This study aimed to assess the effects of hexavalent chromium on zebrafish () embryo development. The zebrafish embryos were treated with solutions containing chromium at different concentrations (0.1, 1, 3.

Identification of potential inhibitors against Alzheimer-related proteins in ethanol extract: experimental evidence and computational analyses.

Unlabelled: Laboratory experiments were carried out to identify the chemical composition of and reveal the first evidence of their Alzheimer-related potential. Liquid chromatography-mass spectrometry analysis identified 21 bioactive compounds in the ethanol extract (). High-performance liquid chromatography quantified the content of cordycepin (0.