4500: Phys Computational Biological Physics
Winter 2005
Lecture 15-16
Channel Proteins
Cell Membranes
Reading: Biochemistry by Stryer Chp I.12 Lipids & Cell Membranes
Channel Proteins
Reading: Biochemistry by Stryer Chp I.13 Membrane Channels and Pumps
Hands-on Tutorial: Building Gramicidin A ion channel
Why Do Living Cells Need Membranes?
Provide a barrier for: Conservation of materials inside the cell Protection against intrusion inside the cell of undesired materials
Extracellular (outside)
Cytoplasm (inside)
Cell Membranes are Built from Lipid Bilayers
Held together by hydrophobic interactions Self-assembly in water Tendency to close on themselves Self-sealing (a hole is unfavorable) Extensive: up to millimeters
Common Features of Cell Membranes
Sheetlike structure of lipid bilayers (60-100 thick) Asymmetric, fluid structures, held together by non-covalent bonding Electrically polarized (60mV transmembrane potential) Built from lipids and proteins (4:1 1:4 ratio), and also carbohydrates Barriers for the flow of ions and polar molecules Embedded proteins confer specific biological functions
P P A
Passive & Active Transport Across Cell Membranes
A P
Cell Membrane Permeability
Low permeability to charged and polar substances Water is an exception: small size, lack of charge, and its high concentration
Cell Membrane Proteins
Receptors, detecting the signals from outside: Light Odorant Taste Chemicals Hormones Neurotransmitters Drugs Channels, gates and pumps Electric/chemical potential Neurophysiology Energy Energy transduction: Photosynthesis Oxidative phosphorylation
Transport Through a Single Cannel
patch clamp technique
Gramicidin A an ion leak inside the membrane
Function: By altering the electrochecmical potential of the membrane, gramicidin A acts as an antibiotic. Small size suitable for long time MD simulations of ion permeation in channel proteins
Assembling Molecular Systems for NAMD: Gramicidin A
Tutorial by: Justin Gullingsrud Theoretical Biophysics Group University of Illinois
General Strategy
Determine the components of the simulation (protein, dna, water, ions, lipids, etc.) Prepare individual components, if necessary. Use psfgen or some other modeling program to add missing atoms, modify ionization states, graft functional groups onto particular residues, etc. Combine molecular components. Overlay pre-equilibrated solvent Generate solvent units on the fly Minimize
Example: Building Gramicidin A
Obtain GA structure from the PDB databank [1JNO] Deal with non-standard Nterminal and C-terminal residues Build a lipid membrane around the peptide Add water Equilibrate
Building the Protein Structure
Split the structure into connected segments Delete the hydrogens Positions can be obtained from the topology file Avoid naming problems Many atom names in the PDB file are different in the topology file - use psfgen's alias command to specify the mapping
Dealing with Residues
Your Unknown system may contain residues that aren't in your topology file In many cases the residue can be built as a chimera out of existing topology groups Exotic new groups may require quantum chemistry to parameterize accurately
Example: GA Protein Structure
D-Val and D-Leu residues Formyl group at Nterminus, ethanolamide group at C-terminus Created new topology, parameter entries by analogy with existing structures and terms.
Adding a Lipid Bilayer
Ab initio - surround the protein with lipids
obtained from an ideal structure. Lipid library -Take pre-equilibrated lipidwater pieces and fit them around the protein. Pre-existing membrane - Cut a hole in an existing membrane (equilibrated or not) and place the protein inside. Use the VMD membrane plugin
Example: Building a lipid bilayer for Gramicidin A
Start with idealized POPE structure, lipid tails straightened. Replicate the structure 16 times using psfgen. Position lipids geometrically using VMD. Position protein with the bilayer by eye.
Adding Water
Many modeling programs (e.g. MSI's Quanta) have a built-in solvate feature For membrane systems, take a preequilibrated block of water and add it to the system The solvate VMD plugin can automatically add water around a protein For adding counterions you may use the autoionize VMD plugin
Combining Simulation Components
Once you have all the components (protein, water, membrane, etc.), combine them into one structure. Load the structure into VMD, and use atom selections to create PDB files containing the atoms you want to keep. Use psfgen to assemble the new PDB files into a reasonable starting configuration.
Example: Solvating Gramicidin
Begin with a block of equilibrated water. Overlay the entire system with the water. Chop ...