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Lecture 19:
Membrane Proteins
Architecture of Membrane Proteins
Fluid Mosaic Model
Protein Targeting
Membrane Proteins are Responsible for Most Membrane Functions
Lipid bilayers can form closed compartments.
Biological membranes have specific functions and
these are carried out by membrane proteins.
Approximately one-third of genomes code for
membrane proteins.
Lipid Bilayer
Biological Membrane
Different Membranes have Different Protein Compositions
SDS-PAGE gel of three
different membranes
The different capabilities of membranes are
conferred by membrane proteins associated
with that membrane.
Some membrane protein functions:
Pumps and Channels:
Transport or diffusion of substances
across membranes.
Receptors:
Receive extracellular signals (eg hormones)
and transmit information across membranes.
Transducers:
Interconvert energy from one form to
another.
Enzymes:
Carry out chemical reactions.
A: Erythrocyte plasma membrane
B: Photoreceptor membranes of retina
C: Muscle sarcoplasmic reticulum
Bilayer-Protein Associations
Membrane proteins can be associated with the lipid bilayer in various ways.
The two sides of a membrane are different- membrane proteins are oriented.
Proteins can span the membrane (transmembrane proteins) or be
associated with one side through interactions with other proteins
or with lipids.
Peripheral membrane proteins (d,e) are
loosely associated with membrane or other
proteins through polar and charged
interactions. These can be solubilized by
disrupting such interactions, eg by salt or
pH changes.
Integral membrane proteins (a,b,c) are
tightly associated with bilayer through
hydrophobic interactions with lipids and
can only be removed by detergents or
organic solvents. They are insoluble in
water.
Structural Basis of Membrane Protein-Bilayer Interactions
The absence of hydrogen-bonding groups inside the bilayer limits the
types of structure that can exist there. Membrane proteins must
satisfy their own hydrogen-bonding groups.
Transmembrane a-helices: Some transmembrane proteins
have alpha-helices that are sufficiently long to span
the membrane. The outer surfaces of these helices interact with
the lipid core of the membrane.
Transmembrane b-strands: Membranes can also be spanned
by beta-sheets in which case the outside of the sheet interacts
with the lipids of the bilayer.
Hydrophobic surfaces: Some proteins associate with the bilayer
through hydrophobic areas on their surfaces which protrude
into the bilayer but do not span it.
Covalent attachment of hydrophobic “anchor”: Otherwise soluble
proteins are sometimes tethered to membranes by covalent
attachment of a hydrophobic group.
Transmembrane a-Helices
Transmembrane a-helices are the most common type of structure in
membrane proteins.
With a rise of 1.5 Angstrom/residue, approximately 30 helical residues
are required to span a ~45 Angstrom membrane.
The hydrocarbon core of the membrane is ~30 Angstroms,
requiring 20 helical residues to span it.
Transmembrane a-helices are comprised primarily of hydrophobic residues.
Buried polar residues are unfavorable.
Transmembrane helix
Whole Bilayer
~40 Angstroms
~27 residues
~ 7-8 turns
Hydrocarbon
Core
~30 Angstroms
~20 residues
~5-6 turns
Bacteriorhodopsin
Bacteriorhodopsin absorbs light energy and uses it to pump protons
across the plasma membrane of halophilic bacteria, moving ions from
a lower concentration to an area of higher concentration.
It consists of a bundle of 7 hydrophobic helices.
Light
energy
H+
H+
Higher
Concentration
H+
Membrane
Lower
Concentration
H+
Helical regions are in yellow- charged residues are pink.
Transmembrane b-Sheets
Another common architecture of membrane proteins is the b-barrel, in
which the polypeptide backbone repeatedly crosses the bilayer as part of a
b-sheet.
With a 3.5 Angstrom distance between Ca positions, a b-strand would
require a minimum of about 9 residues to cross the hydrophobic core
of a lipid bilayer.
However, in most barrels the strands are not oriented perpendicular to
the membrane so more residues are required to span it.
Transmembrane b-strand
Whole Bilayer
~40 Angstroms
11-12 residues
Hydrocarbon
Core
~30 Angstroms
~9 residues
Porin
Higher
Concentration
Membrane
Lower
Concentration
This porin is an example of a b-barrel membrane
protein. It forms a continuous b-sheet of 16
transmembrane strands.
The interior is a water-filled channel or pore that
allows small molecules to diffuse passively
through the membrane.
The interior is lined with hydrophilic residues
whereas the side of the sheet facing the
lipids is hydrophobic.
Hydrophobic residues in yellow.
Hydrophobic Surfaces
Proteins can associate with membranes through hydrophobic patches or
protrusions that insert into the hydrocarbon core of the lipid bilayer.
Polar part
Hydrophobic
part
In general, the parts of membrane proteins that interact with the
hydrocarbon core of membranes are covered with hydrophobic side-chains
and the parts that are in contact with the surrounding aqueous solution
are covered with hydrophilic side-chains.
The lack of hydrogen bonding groups in the membrane interior makes
it very unfavorable to have buried but unsatisfied hydrogen-bonding
groups.
Prostaglandin H2 synthase
Prostaglandin H2 synthase-1 converts the fatty acid arachidonic acid
(generated by hydrolysis of lipids) into Prostaglandin H2, which is
a precursor of other prostaglandins involved in the inflammatory
response, pain and fever.
The enzyme is firmly attached to the membrane though an alpha-helical
“knob” lined with hydrophobic residues that protrudes into the
hydrocarbon core.
Arachidonate can enter the active site of the enzyme through a
hydrophobic channel in this “knob”.
This enzyme is the site of action of aspirin, which acetylates a serine
residue in the interior of this channel, blocking the entry of arachidonate
and preventing the formation of prostaglandin H2.
In turn the inflammatory response is inhibited.
Covalent Attachment of Hydrophobic Anchors:
Soluble
protein
Membrane
anchor
Otherwise soluble proteins can be tethered
to the membrane by covalent attachment
of hydrophobic groups to the protein.
An example is the attachment of a palmitoyl
group through a thioester bond to cysteine
side-chains.
Specific enzymes carry out these modifications
by recognizing specific target sequences near
the modification site.
Detection of Transmembrane Helices by Sequence Analysis
Membrane proteins comprise perhaps a third of all proteins.
But analysis of the their structures is difficult.
Of ~27,000 protein structures known, only about 30 are membrane
proteins.
To a greater extent than for globular proteins, we must rely on
sequence analysis to predict structural features of membrane
proteins.
The location of transmembrane helices in a membrane
protein can often be predicted from sequence information.
Polarity Scales
To quantify the likelihood of a given residue being
found in a transmembrane helix, one way is to
determine the difference in energy between a
side-chain in the membrane interior and the same
side-chain in water.
The more hydrophilic the side-chain, the more
favorable the transfer.
Since many residues in a row must be hydrophobic
in a transmembrane helix, summing the energy
for all the residues in a contiguous segment gives
a fairly reliable estimate of whether that segment
is likely to contain a transmembrane helix.
Plotting such a sum in a “sliding window” over the
length of the chain gives a hydropathy plot.
Glycophorin contains
a single transmembrane
helix.
A hydropathy plot for glycophorin
shows a significant peak near the
sequence position of this
transmembrane helix.
By contrast a hydropathy plot for porin, which has no transmembrane
helices, does not show a significant peak anywhere.
Lipids Can Diffuse Freely in the Plane of the Membrane
Lipids have high mobility in the plane of the membrane but rarely cross
to the other side of the bilayer.
Studies with fluorescently labeled lipids in which a local area is
photobleached show that new fluorescent lipids rapidly diffuse
into the bleached area.
Membrane Fluidity
Membranes must remain fluid and flexible for membrane proteins to function
properly. However, at low temperatures, lipids can undergo a phase transition
in which they “freeze” into an ordered and rigid state.
Lipids with longer hydrocarbon chains tend to have higher transition
temperatures, and unsaturated hydrocarbon chains with cis double bonds
tend to have lower transition temperatures due less favorable packing.
Bacteria control the fluidity of their membranes by regulating the fraction
of lipids with longer hydrocarbon chains or cis double bonds.
Animals regulate the cholesterol content of their membranes to achieve
similar control over membrane fluidity.
The Fluid Mosaic Model
The fluid mosaic model proposes that biological membranes are
asymmetric 2-dimensional fluids. The lipids are free to diffuse in the
plane of the membrane and serve as a solvent for hydrophobic membrane
proteins, which can also diffuse in the plane of the membrane. At the
same time the membrane is a permeability barrier for polar and charged
substances.
Proteins are Targeted to Different Cellular Compartments by Signal Sequences
The amino acid sequences of proteins contain specific sequences
which are recognized by receptors and pores on particular
membranes which lead to their being imported into a given
compartment or embedded in that membrane.
Lysozome
Mitochondria
Golgi complex
Endoplasmic
Reticulum
Peroxisome
Nucleus
Plasma
membrane
Placing a nuclear localization sequence on a cytoplasmic protein
causes it to be imported into the nucleus. Specific proteins
recognize the localization sequences and bind them, initiating
the import process.
Proper targeting of proteins is necessary for them to perform
their functions.
Summary:
Different membranes have different protein contents which confer their
different capabilities.
Membrane proteins associate with lipid bilayers in a variety of ways. In
some cases the amino acid sequence can suggest structural features
in such proteins.
Proteins have internal sequence codes for the organelle to which they
should be targeted.
Key Concepts:
Peripheral and Integral membrane proteins
Architecture of membrane proteins
Hydropathy plots
Fluid mosaic model
Targeting sequences