Membranes & Membrane Proteins

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1 School on Biomolecular Simulations Membranes & Membrane Proteins Vani Vemparala The Institute of Mathematical Sciences Chennai November JNCASR, Bangalore

2 Cellular Environment Plasma membrane extracellular cytoplasm endoplasmic reticulum - acts as a compartment, only few molecules thick ( 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/

3 Membranes - a closer look Molecular Cell Biology, Fourth Edition W. H. FREEMAN, 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

4 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

5 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

6 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

7 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

8 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

9 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.,

10 Cholesterol 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

11 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)

12 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

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14 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

15 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)

16 POPE entry: topology file

17 Lipid: Coarse Graining

18 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

19 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

20 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

21 Ion Channels: Gating open closed Filter Pore gating (~1 ms) Gate Gating : stimulus-triggered Stimulus: ligand, voltage, stress

22 Ion Channels: Selectivity Selectivity Filter Cavity Gate Potassium selective K+ radius = 1.33Å; Na+ radius = 0.95Å

23 Hydrophobic Mismatch

24 Thank You