School on Biomolecular Simulations Membranes & Membrane Proteins Vani Vemparala The Institute of Mathematical Sciences Chennai November 13 2007 JNCASR, Bangalore
Cellular Environment Plasma membrane extracellular cytoplasm endoplasmic reticulum - acts as a compartment, only few molecules thick (60-100 Å) - lipid molecules are added/removed, as the cell dimension changes - can self-heal - held together by hydrophobic/noncovalent interactions - has a fluid-like structure with rapid lipid diffusion -electrical potential across membranes : - 60 mv - lipid molecules are synthesized in ER no membrane no cell no life ww.elsomresearch.com/.../nanosomes.htm ttp://learn.genetics.utah.edu/units/basics/cell/
Membranes - a closer look Molecular Cell Biology, Fourth Edition W. H. FREEMAN, 2000 - Cellular lipid membranes are heterogeneous systems with a variety of lipids, cholesterol and proteins - permeable to non-polar molecules (O2, CO2) and small polar molecules like water (osmosis); non-permeable to: ions, charged molecules (glucose), macromolecules (proteins) - membrane proteins can participate in cell recognition (through glycoproteins) - many different types of lipid molecules
Membranes - Components - membranes mostly contain lipids and proteins - membrane lipids contain hydrophobic and hydrophilic moieties - form barriers to free flow of charged species - ~30% of proteins are membrane proteins -~50% of current drug targets are membrane proteins
cholesterol Lipid Structure phospholipids Hydrophilic head polar Hydrophobic tail nonpolar saturated unsaturated Lipid molecules are amphipathic Hydrophilic molecules readily dissolve in water (forming favourable electrostatic / hydrogen bond interactions) Hydrophobic molecules are insoluble in water. Energetic cost minimized if hydrophobic molecules cluster ( e.g., oil coalesces to form a drop when dispersed in water) Conflicting forces experienced by amphipathic molecules resolved in the formation of bilayer - energetically most favourable
Lipids to Cells Free edges with exposed hydrophobic tails - Self-healing property of lipids - Free edges are energetically expensive - overriding principle: free edges should be eliminated - profound effect: formation of closed compartmental structures - Amphipathic nature of lipids is fundamental Sealed compartments
Phospholipid Structure Polar Head group Phosphate zwitterionic charged Charged lipids: ~ 10% Non-polar Glycerol Fatty acid chain Fatty acid chain Typical head groups: PC-phosphotidylcholine PE-phosphotidyletanolamine PG-phosphotidylglycerol Fatty acid chain: 14(myristic)-22(docosahexaenoi carbon -may contain double bonds (unsaturated) -mostly even number of carbons
Lipid: Head Groups Choline - phosphatidyl choline. (PC) Ethanolamine - phosphatidyl ethanolamine. (PE) Serine - phosphatidyl serine (PS) Glycerol - phosphatidyl glycerol.(pg) PC, PE - neutral (zwitter-ionic) PS, PG- charged
Fatty acid chains Lipid: Fatty Acid Chains Oleic acid: monounsaturated C18 (18:1) Palmitic acid: saturated C16 (16:0) Stearic acid: saturated C18 (18:0) Docasahexaenoic acid: saturated C22 (22:6) lipids can have two fatty acid chains of unequal length one or more chains can be unsaturated Lipids can have a rich variety by varying: fatty acid chain length, degree of saturation, polar head group etc.,
Cholesterol http://courses.cm.utexas.edu/jrobertus/ch339k/overheads-2/ch11_cholesterol.jpg http://cellbio.utmb.edu/cellbio/membrane_intro.htm Cholesterol is one of the most abundant lipid molecules Regulates the fluid-like nature of membranes, hence affects membrane dynamics most cells (animal) have ~ 20-50% cholesterol effect on cell membrane fluidity
Cholesterol: Lipid Rafts Heterogeinity of lipids (saturated/unsaturated) has lead to mosaic-domain models (liquidliquid immiscibility) Domains rich in sphingolipids and cholesterol - lipid rafts Role of Rafts proposed in function of trafficking and sorting newly formed lipids Rafts implicated in diseases such as HIV, Alzheimer s (pathogens may gain cellular entry by accessing lipid rafts)
Membranes: Fluid Nature luidity: ease with which lipid molecules move within plane of membrane lateral diffusion depends on lipid composition, emperature regular packing leads to less fluidity; nsaturation increases fluidity rotation Double bond Membrane fluidity plays role in: cell signalling, movements of newly formed lipid molecules, cell division, cell fusion etc, saturated unsaturated
Membrane: Analysis - average area/lipid - membrane thickness - electron density profile - order parameters - tilt angle of hydrocarbon chains - pressure profiles - permeation of various small molecules across membranes - diffusion of lipid molecules - surface tension across membranes - electrostatic potential change
Membrane: Setup - unlike proteins, no initial coordinates available - make your own structures or look for existing bilayer patches - hack into existing lipid topologies to build new ones - CHARMM 27 force field has lipid topologies/parameter files - VMD has membrane plugin (very limited)
POPE entry: topology file
Lipid: Coarse Graining
Membranes: Permeability Small hydrophobic molecules O 2, C 2, N 2, benzene Small uncharged polar molecules H 2 O, ethanol Large uncharged molecules Amino acids ions Na +, Cl - Extra cellular Intra cellular Specialized transport proteins are required
Membrane Proteins Trends Pharm Sci 22:23-26 (2001) < 20 crystal structures known KcsA KirBac1.1/3.1 - Genomics Membrane Proteins constitute ca. 25% to 30% of all genes - Membrane Proteins are implicated in many diseases: Diabetes, Parkinson s, drug resistance (tumours & bacteria) - Membrane Proteins are major drug targets - ~50% of current drug targets are membrane proteins Nobel Prize in Chemistry 2003
Membrane Proteins extra cellular domain transmembrane domain intra cellular domain α-helices are most common form in transmembrane domain detergents used to separate membrane proteins from membrane
Ion Channels: Gating open closed Filter Pore gating (~1 ms) Gate Gating : stimulus-triggered Stimulus: ligand, voltage, stress
Ion Channels: Selectivity Selectivity Filter Cavity Gate Potassium selective K+ radius = 1.33Å; Na+ radius = 0.95Å
Hydrophobic Mismatch
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