The interactions between HAAO and human serum albumin (HSA) were studied by multiple spectroscopic methods and molecular modeling procedures.
Mixed monolayers of the surface-active lipopeptide surfactin-C15 and various lipids differing by their chain length (DMPC, DPPC, DSPC) and polar headgroup (DPPC, DPPE, DPPS) were investigated by atomic force microscopy (AFM) in combination with molecular modeling (Hypermatrix procedure) and surface pressure-area isotherms.
Information on compound synthesis, chemical data, and the molecular modeling method, detailed results, the experimental procedures for SPR, DNA-binding activity/EMSA, immunoprecipitation and immunoblotting, and Cyquant cell proliferation assays.
All molecular modeling was conducted using a stochastic global energy optimization procedure in Internal Coordinate Mechanics (ICM) using the ICM-Pro package version 3.7 (MolSoft LLC, San Diego, CA) (Abagyan et al., 2010; Abagyan et al., 1994).
The results obtained suggest that the finite element-based procedure yields the results, which are very similar to their molecular modeling counterparts for small-size nano-valves, for which both types of analyses are feasible.
All modeling procedures and computations, including energy minimizations in molecular mechanics, were performed using HyperChem 8.0.8 Molecular Modeling System (Hypercube Inc., Gainesville, Florida, USA) and ChemBio3D Ultra 11.0 (CambridgeSoft Corporation,Cambridge, UK).
Thus, we asked whether MT2 interacts with any of those TrkA residues and chose to conduct molecular modeling studies, in which docking was performed as a global energy optimization by means of the biased probability Monte Carlo stochastic procedure.
(b) Box modeling procedure.
Figure 1 Modeling procedure.
(a) ARMA(2n,2n – 1) modeling procedure.
