Computational protocol: Cholesterol accelerates the binding of Alzheimer's β-amyloid peptide to ganglioside GM1 through a universal hydrogen-bond-dependent sterol tuning of glycolipid conformation

Similar protocols

Protocol publication

[…] The starting structure of Aβ1-40 (Di Scala et al., ) and of Aβ5-16 (Fantini and Yahi, ) were derived from a NMR structure of Aβ1-40 in solution in a water–micelle environment (Coles et al., ), using the PDB entry 1BA4. Geometry optimization was first achieved using the unconstrained optimization rendered by the Polak–Ribière conjugate gradient algorithm. Molecular dynamics simulations were then performed for various periods of times ranging from 10 ps to 10 ns in vacuo with the Bio+ (CHARMM) force field (Singh et al., ) of the Hyperchem software suite (ChemCad, Obernay, France). The energy of interaction was determined with the Molegro Molecular Viewer (Thomsen and Christensen, ). Galactose-cholesterol and GM1-cholesterol models were obtained with the Hyperchem program as described previously (Yahi et al., ), by analogy with the GSL structures published by Pasher and Sundell (). Lipid-protein complexes were visualized with the PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC. […]

Pipeline specifications

Software tools CCP4, CHARMM, PyMOL
Application Protein structure analysis
Diseases Alzheimer Disease
Chemicals Cholesterol, G(M1) Ganglioside, Hydrogen, Phosphatidylcholines