Internal membranes for organelles Bilayer Permeability • Low permeability to charged and polar substances • Water is an exception: small size, lack of charge, and its high concentration • Shedding solvation shells for ions is very unlikelyCommon Features of Biological Membranes Sheet-like structure TWO-molecule thick (60-100A) Lipids, Proteins, and carbohydrates Lipids form the barrier.
Proteins mediate distinct functions.Non-covalent assemblies (self-assembly, protein-lipid interaction) Asymmetric (always) Fluid structures: 2-dimensional solution of oriented lipids and proteins Electrically polarized (inside negative ~-60mV) Spontaneously forming in water Protein/lipid ratio = 1/4 – 4/1 Carbohydrate moieties are always outside the cell Protein/Lipid ratio • Pure lipid: insulation (neuronal cells) • Other membranes: on average 50% • Energy transduction membranes (75%) Internal membranes of mitocondria and Each atom i at position ri, is treated as a point with a mass mi and a fixed charge qi. What is the Force Field? In molecular dynamics a molecule is described as a series of charged points (atoms) linked by springs (bonds). To describe the time evolution of bond lengths, bond angles and torsions, also the non-bonding van der Waals and elecrostatic interactions between atoms, one uses a force field. The force field is a collection of equations and associated constants designed to reproduce molecular geometry and selected properties of tested structures. Energy Terms Described in the CHARMm Force Field