membrane proteins

lipids

permeability barrier, establish compartments

proteins

responsible for most dynamic processes carried out by membranes

lipid composition 

the lipid composition of membranes is cell type specific and organelle specific

classes of membrane protein

• Peripheral membrane proteins

• Integral membrane proteins

• Lipid-anchored proteins

functional asymmetry

Orientation of proteins is asymmetric, sidedness of membrane

peripheral membranes proteins

• Relatively loosely attached to the membrane (often electrostatic/hydrogen bonds)

• Can be dissociated under mild conditions

integral membrane proteins

• Interact extensively with the lipid hydrocarbon chains

• Most span the lipid bilayer

• Can be extracted from the membrane only with detergents or other agents that disrupt the membrane

secondary protein structure

must ensure that the hydrophobic side chains of protein contact the lipid tails and these side chains shield the polar regions of the protein backbone

anti parallel beta sheets

• Curl to form a cylinder

• Acts as a pore or channel

• Outside surface non-polar, interacts with HC tails

• Inside surface that lines the pore is hydrophilic

porins

• Membrane proteins in outer membrane of gram-negative bacteria

• Also, in mitochondria and chloroplasts

• Channel-forming: entry of small solutes (nutrients)

• Often Trimers

gram negative bacteria

• Inner membrane acts as a permeability barrier

• Outer membrane permeable to small molecules through porins

alpha-helical membrane proteins

Most integral membrane proteins contain alpha-helical membrane-spanning domains

Example: Glycophorin A

Protein in erythrocyte membrane, contains a single membrane-spanning domain (alpha-helix)

bacteriorhodopsin

From halobacterium halobium

Light-driven proton pump

Contains 7 transmembrane helices

Helices are arranged perpendicular to the bilayer plane

Many membrane receptors also contain 7 transmembrane helices - G-protein-coupled receptors

Integral membrane proteins

Alpha-helical arrangement favoured in non-polar medium

Given the average membrane thickness of 30A, alpha helical transmembrane segments contain ~20 residues

Transmembrane helices can be accurately predicted from amino acid sequence

hydropathy plots

Predicts but doesn't prove, even soluble proteins have hydrophobic regions

membrane protein structure

Membrane protein structure is difficult to determine

Prediction methods and models were originally based on few structures, such as bacteriorhodopsin

Recently solved structures can look quite different from bacteriorhodopsin

• Example: bacterial Leucine transporter

Segments can be severely tilted rather than perpendicular to the membrane

Transmembrane helices can be split - unfolded in parts

lipid-anchored proteins

Some proteins are associated with the membrane via a covalent link to a lipid

Lipid serves as a membrane anchor

Protein component exposed either to cytoplasm or to exterior (sidedness)

Reversible attachment (important for signalling pathways)

examples

• Prenylated proteins

• Fatty acylated proteins

• Glycosyl phosphatidylinositol (GPI)-linked proteins

types of lipid anchored proteins

• Thioester-linked fatty acyl

• Amide-linked myristoyl

• Phenyl anchors

• Amide-linked glycosyl phosphatidylinositol (GPI)

Amide-linked myristoyl anchor

• Myristic acid (C14) is linked via amide bond to N-terminal glycine residue

• Reaction: N-myristylation

• Example: alpha subunit of G-proteins

thioester-linked fatty acyl anchors

• Covalent linkage of fatty acid via ester bond to cysteine (serine or threonine)

• Myristate, palmitate, stearate, and oleate (mainly C16 or C18)

• Examples: G-protein-coupled receptors, transferrin receptor

lipid anchored proteins

Prenyl anchors are derived from isoprene (C5 compound)

Isoprene is a lipid but can associate with them

Most common prenyl anchors: C15 (farnesyl) and C20 (geranylgeranyl)

Attachment site: C-terminal CAAX sequence

Proteolytic cleavage of the 3 C-terminal residues, Cys becomes the C-terminal residue

GPI anchored proteins

GPI linked proteins are all common in all eukaryotes

GPI-anchored proteins are exposed to the extracellular side of the membrane

Preferentially associate with lipid microdomains (lipid rafts)

core structure of GPI anchor 

• Phosphatidylinositol

• Tetra-saccharide

• Phosphoethanolamine

modification

additional sugars

Linked to carboxy-terminal amino acid of target protein via phosphoethanolamine

GPI anchors

Phosphatidylinositol (glycerol backbone connected to 2 FA chains and a phosphoryl group connected to the alcohol derivative, inositol) is glycosidically linked to a linear tetra-saccharide linked with a phosphodiester bond to phosphoethanolamine which in turn is amide linked to the protein's C-terminal carboxyl group.