Membrane proteins

Extrinsic (Peripheral) • Bind weakly and

reversibly• Electrostatic interactions• Sediment out with

membrane and removed with change in pH

• Can be important in signaling, endocytosis, lipid rafts, interaction with cytoskeleton

Cytochrome C

Amphitropic

• Activity is regulated by their change from water soluble form to membrane bound form.

• Most are inside the cell and involved in cell signaling, i.e. Phopholipase C and PKC

• Still some are exterior and involved in things like blood clotting and apolipoproteins involved in transport

Ankyrin

• A a 200 kDa protein that mediates the linkage of the cytoskeleton to the plasma membrane by binding to spectrin and other integral membrane proteins

Phospholipase A2

• Releases the sn-2 fatty acid that can be converted to AA for eicosanoid production.

Phospholipid membrane Phospholipase A2

Cyclooxygenases (COX)

Prostaglandins (PG) &Thromboxanes (TX)

Lipoxygenases (LOX)

Leukotrienes

O

HO

O

HOArachidonic acid Eicosapentaenoic acid

-poor substrate for cyclooxygenases-gives rise to series 5 leukotrienes

Structure of annexins• Involved in Ca2+ signaling• Large family of proteins that require Ca2+ to bind• Ability to bind Ca2+ is enhanced in the presence of lipids• Some participate in actin cytoskeleton attachment

Some peripheral proteins are Lipid-anchored proteins

• Lipid anchors target proteins to the membrane

• Lipids can be fatty acids, terpenes or glycosylphosphatidyllinositol

• Insertion of some lipids can cause curvature

0.5% of all eukaryotic proteins are linked with GPI

• In detergent resistant portion• May be a determinant of rafts

Different modes of binding amphoteric proteins to membranes

1) Electrostatic switch2) Lipid anchor3) Protein has a

binding pocket for a particular head group

4) Amphipathic helix in the interfacial region of the bilayer

Modulation of binding

• Reversing binding is crucial • Accomplished by kinases, altered levels of

ions or effector meolecules, or changes in local compositions of the membrane

• Common one is the “electrostatic switch” – with the addition of negative charges when the protein is phosphorylated on a serine or tyrosine in the membrane binding region

Effects of peripheral protein binding on lipid organization

• Reorganization of the lipids usually occurs because of binding affinity of the lipids to the protein

Classification of Intrinsic (Integral) membrane proteins

• Embedded in the membrane

• Requires disruption of membrane to solubilize them

• Nearly all type III are of two structural types:

1) bundles of α-helices 2) β - barrels

Monotopic proteins• Few examples of monotopic proteins• Some enzymes involved in lipid

metabolism access their substrates by integrating into one leaflet of the membrane

• i.e. Prostaglandin H2 synthase

AA Prostaglandin H2

• Another example is caveolins

Amino acids in intrinsic proteins1) Nonpolar amino

acids side chains typically point towards the hydrophobic interior

2) Acidic and basic residues remain uncharged, form ion pairs that neutralize their charge or play a special role

3) Hydrogen bonds often link side chain to backbone carbonyl group to cap the end helices or stabilize between helices

4) Glycine and proline often “break” the helix

5) Aromatic groups often interface the hyrodrophilic and nonpolar domains

Protein-Lipid Interaction

• Must maintain a tight seal

• Annular or boundary lipids are most conserved around an integral protein.

• Third type: Non-annular are tightly bound in crevices or between subunits of the proteins

• The relative association constants (Kr) between lipids and proteins.

• Increases from front to back.

Distortion of lipid bilayers due to hydrophobic mismatch

• Results when nonpolar region of the bilayer is thinner or thicker than the hydrophobic thickness required by integral protein

• Proteins with small number of helices are likely to tilt to accommodate thickness

• Larger proteins likely induce changes in thicknessLipids in the bilayer can can distort

to match thickness of proteins

Consequences of hydrophobic mismatch

EXTENTION, CONTRACTION OR TILTING

Bundles and barrels

Helical Bundles• Understood by early

information on bacteriorhodopsin

• From the purple membranes of the salt-loving bacterium Halobacter salinarum

• Became paradigm for ion transport proteins

Bacteriorhodopsin became the paradigm for ion transport & helical TM proteins

• Function to pump protons out of the cell in response to absorption of light

• Retinal helps convert light energy into electrochemical proton gradient to drive the formation of ATP

The structure of the photosynthetic reaction center of B. viridis

• 1988 prize in chemistry awarded to Hartmut Michel, Johan Deisenhofer and Robert Huber

• Membrane spanning surface is very hydrophobic

• TM consists of 5 helices from M, 5 from L and 1 from H

• Has 30-35 annular lipids

light harvesting complexesOther example of TM helical bundles…

• Crystal structure of LH2 of Rhodopseudomonas acidopha

• Projection of structure of 2 C-shaped LH1-RC complexes dimerize to an S shape

First x-ray structure of porin from Rhodobacter capsulatus (1991) confirmed

-barrel structure.

Porins are found in the outer membrane of Gram negative bacteria (and mitochondria and chloroplasts).

• 2 membranes separated by aqueous layer called periplasm

Porins• Function as passive diffusion channels to

allow rapid diffusion of their solutes• 2 classes:

1) general porins do not disciminate among solutes that are hydrophilic and under ≈600 Da

i.e. OmpF and OmpC2) specific porins are specific for their solutes

i.e. PhoE, LamB, ScrY, Tsx

Beta strands• Extended peptide

backbone needs only seven a.a. residues to cross the nonpolar domain

• Typically have 9 – 11 residues tilted at 45 degrees

• Must partner with other strand

• Interstrand H bonds make structure rigid and stable

• Even numbers strands vary from 8 – 24

• Amphipathic• Little to no α- helices

in beta barrels

An antiparallel β-sheet is formed with adjacent -strands running in opposite directions. Every other side chain extends above or below the sheet.

H-bonds are perpendicular to the chains and impart stability and rigidity.