School on Biomolecular Simulations

Membranes & MembraneProteins

Vani VemparalaThe Institute of Mathematical Sciences

Chennai

November 13 2007JNCASR, Bangalore

www.elsomresearch.com/.../nanosomes.htm

Cellular Environment

cytoplasm

extracellular

http://learn.genetics.utah.edu/units/basics/cell/

Plasma membrane

no membrane → no cell → no life

- acts as a compartment, only fewmolecules thick (60-100 Å)- lipid molecules are added/removed, asthe cell dimension changes- can self-heal- held together byhydrophobic/noncovalent interactions- has a fluid-like structure with rapid lipiddiffusion-electrical potential across membranes : -60 mV- lipid molecules are synthesized in ER

endoplasmic reticulum

Membranes - a closer look

- 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 likewater (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

Molecular Cell Biology, Fourth Edition W. H. FREEMAN, 2000

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

Lipid Structure

Hydrophilic head

Hydrophobic tail

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 ifhydrophobic molecules cluster ( e.g., oil coalesces to form a drop when dispersed inwater)

Conflicting forces experienced by amphipathic molecules resolved in theformation of bilayer - energetically most favourable

polar

nonpolar

saturated unsaturated

cholesterol phospholipids

Lipids to Cells

Free edges with exposedhydrophobic tails

- Self-healing property of lipids

- Free edges are energetically expensive

- overriding principle: free edges shouldbe eliminated

Sealed compartments

- profound effect: formation of closedcompartmental structures

- Amphipathic nature oflipids is fundamental

Head groupHead group

PhosphatePhosphate

GlycerolGlycerol

Fatt

y ac

id c

hain

Fatt

y ac

id c

hain

Fatt

y ac

id c

hain

Fatt

y ac

id c

hain

zwitterioniczwitterionic

chargedcharged

Pola

rPo

lar

Non

-pol

arN

on-p

olarPhospholipid Structure

Typical head groups:PC-phosphotidylcholinePE-phosphotidyletanolaminePG-phosphotidylglycerolFatty acid chain:14(myristic)-22(docosahexaenoic)carbon-may contain double bonds(unsaturated)-mostly even number of carbons

Charged lipids: ~ 10%

Choline - phosphatidyl choline. (PC) Ethanolamine - phosphatidyl ethanolamine. (PE)

Serine - phosphatidyl serine (PS) Glycerol - phosphatidyl glycerol.(PG)

PC, PE - neutral (zwitter-ionic)PS, PG- charged

Lipid: Head Groups

Oleic acid: monounsaturated C18(18:1)

Stearic acid: saturated C18(18:0)

Palmitic acid: saturated C16(16:0)

Docasahexaenoic acid: saturated C22(22:6)

Fatty acid chains

lipids can have two fatty acid chains of unequal lengthone or more chains can be unsaturatedLipids can have a rich variety by varying: fatty acid chainlength, degree of saturation, polar head group etc.,

Lipid: Fatty Acid Chains

effect on cell membrane fluidity

http://cellbio.utmb.edu/cellbio/membrane_intro.htm

http://courses.cm.utexas.edu/jrobertus/ch339k/overheads-2/ch11_cholesterol.jpg

Cholesterol is one of the most abundant lipidmolecules

Regulates the fluid-like nature of membranes,hence affects membrane dynamics

most cells (animal) have ~ 20-50%cholesterol

Cholesterol

Cholesterol: Lipid Rafts

Heterogeinity of lipids (saturated/unsaturated) has lead to mosaic-domain models (liquid-liquid 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 entryby accessing lipid rafts)

Membranes: Fluid Nature

lateral diffusion

rotation

flip-flop

Fluidity: ease with which lipidmolecules move within plane ofmembrane

- depends on lipid composition,temperature

- regular packing leads to less fluidity;unsaturation increases fluidity

saturated unsaturated

Double bond

Membrane fluidity plays role in: cellsignalling, movements of newly formed lipidmolecules, cell division, cell fusion etc,

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

O2, C2, N2,benzene

Smallhydrophobicmolecules

H2O,ethanol

Smalluncharged

polarmolecules

Aminoacids

Largeunchargedmolecules

ions

Na+, Cl-

Membranes: Permeability

Extra cellular

Intra cellular

Specialized transport proteins are required

Membrane Proteins

- Genomics – Membrane Proteins constitute ca. 25% to 30% of allgenes- 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

Trends Pharm Sci 22:23-26 (2001)

< 20 crystal structures knownKcsA KirBac1.1/3.1

Membrane Proteins

extra cellular domain

transmembrane domain

intra cellular domain

α-helices are most commonform in transmembrane domain

detergents used to separatemembrane proteins from

membrane

gating (~1 ms)

Filter

Pore

Gate

open closed

Ion Channels: Gating

Gating : stimulus-triggered

Stimulus: ligand, voltage, stress

Cavity

SelectivityFilter

Gate

Ion Channels: Selectivity

• Potassium selective -K+ radius = 1.33Å; Na+ radius = 0.95Å

Hydrophobic Mismatch

Thank You