Download Lecture 15 Membrane Proteins I

Lecture 15
Membrane Proteins I
Introduction
What are membrane proteins and where do they exist?
Proteins consist of three main classes which are classified as globular, fibrous and membrane
proteins. A cell is enveloped by a membrane which makes the boundary of a cell and enables it
to maintain the distinction between cytosolic and extracellular milieu. Cells consist of various
organelles such as golgi body, endoplasmic reticulum, mitochondria and several other membrane
bound organelles. The difference between cytosol and these organelles are maintained by
individual membranes. These biological membranes are made up of mainly lipid bilayers
whereas functions are carried out by membrane proteins.
Classification of membrane proteins:
Membrane associated proteins can be classified in the following two ways:
1. Mode of interaction with the membranes
2. Cellular locations
According to the literature, the membrane proteins can be categorized as follows:
1. Type I membrane proteins
2. Type II membrane proteins
3. Multipass transmembrane proteins
4. Lipid chain anchored-membrane proteins
5. GPI-anchored-membrane proteins
6. Peripheral membrane proteins
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Integral or intrinsic membrane proteins
Integral membrane proteins are associated with membranes and interact strongly with the
hydrophobic part of the phospholipid bilayer. Presence of one or more apolar regions accounts
for the span of lipid bilayer (α-helix and β-sheet as well). They interact mainly through van der
Waals interaction with the hydrophobic core of the lipid bilayer. Thus they can be extracted from
the membrane only through membrane disruption by detergents. Examples: GPCRs, rhodposins
proteins etc.
Peripheral or extrinsic membrane proteins
Peripheral or extrinsic membrane proteins are known to interact either non covalently with the
membrane surface through electrostatic or hydrogen bonds or with covalent bonds through lipids
or GPI (glycosylphosphatidylinositol) anchors [Fig. 2 (d)]. They interact with the hydrophilic
surfaces of the bilayer through electrostatic interaction. They can be isolated from the membrane
using strong salt or change in pH. Examples: Cytochrome C protein.
Type I membrane proteins
This is a single-pass transmembrane protein. The N-terminus of this protein is extracellular
(luminal) and C-terminus remains in the cytoplasmic region for a cell (or organelle) membrane.
[Fig. 1 (a)]
Type II membrane proteins
This is a single-pass transmembrane protein. The C-terminus of this protein is extracellular
(luminal) and N-terminus remains in the cytoplasmic region for a cell (or organelle) membrane.
[Fig. 1 (b)]
Multipass transmembrane proteins
Multipass transmembrane proteins [Fig. 2 (a)] are able to cross the lipid bilayer multiple times
compared to Type I and Type II single pass membrane proteins [Fig. 1 (a) and (b)] which can
cross the lipid bilayer only once. Membrane straddling region of polypeptide chains possess
mostly α-helical conformation as in the lipid environment hydrogen bonding between
polypeptide chains would be maximum if it form helical conformation.
Lipid chain anchored-membrane proteins
Lipid chain anchored-membrane proteins [Fig. 2 (b)] are related with lipid bilayer via one or
greater than one covalently attached fatty acid chains or prenyl groups (other type of lipid
chains).
GPI-anchored-membrane proteins
GPI-anchored-membrane proteins [Fig. 2 (c)] are associated with lipid bilayer via
glycosylphosphatidylinositol (GPI) anchor.
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Structure of membrane proteins
Biological membranes
Before going into the details of the membrane proteins we need to look at the structural aspect of
the biological membranes. Biological membranes were considered to be two dimensional fluids
consist of two ‘leaflets’ which comprised of mainly lipid molecules. According to the fluid
mosaic model, the outer part is made up of hydrophilic (ionic and polar head groups) groups
which interact with the aqueous solvents. The inner part is comprised of hydrocarbon chains of
the lipid. The fluid mosaic model considers membrane as a dynamic system where both proteins
and lipids can move and interact.
Role of length and magnitude of dielectric gradient of membrane bilayer thickness
The variation in the dielectric constant between the ionic part and the hydrophobic part (~80 to 2
Debye) is significant which occurs over a comparatively short distance and thus cover up of
charge or leaving a hydrogen bond unsatisfied is unfavored. Peptide backbone of a protein is
comprised of polar amino and carbonyl groups and thus covering of a peptide backbone in the
membrane interior leaving the hydrogen bonding unsatisfied is energetically unfavorable.
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Thickness of the bilayer governs the length of low dielectric well which in turn determines
interior, exterior and interfacial regions of proteins. Only specific conformations of proteins get
stabilized according to the bilayer thickness. There should be comparable length factor between
the hydrophobic thickness of the bilayer and the hydrophobic length of membrane protein. It
further regulates self aggregation of protein to minimize the unfavorable interactions if the
comparable relationship is absent.
Hydrophobic chain packing plays an important role in stabilizing protein structure. The favored
arrangement of the hydrophobic chains of bilayer is when they are aligned to each other
maximizing van der Waals interactions. Thus, cylindrical shape of the protein will be able to
minimize number of lipid chains disordered by their presence and also area of the proteins
exposed to the bilayer.
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Structural Classifications: Primary, Secondary, Tertiary and Quaternary
Primary Structure:
The interior of the membrane is nonpolar in nature. Therefore, surface residues of
transmembrane proteins are expected to be nonpolar in nature so that they can reside in the
interior part of the membrane. A hydrophobicity scale was formulated to assign numerical values
to the hydrophobic nature of amino acid side chains for the prediction purpose. Numerous scale
such as Kyte-Doolittle scale, GES scale, etc have been introduced to postulate which part of the
proteins will reside in the inner part of the membrane.
Secondary Structure
The inner part of the membrane is devoid of water. Thus the only possibility of the atoms of the
peptide backbone to undergo hydrogen bonding is either side chain atoms or other atoms on the
peptide backbone. The most favored arrangements are α-helical or β-sheet arrangement as
regular arrays of hydrogen bonding occurs between amide nitrogen and carbonyl oxygen atoms.
Most of the membrane proteins are found to be helical in nature. This preference for helical
structure over β-sheet arrangement might be due to the following reasons:
1. Helix length is sufficient to accommodate any little changes in bilayer thickness
2. Individual insertion of helices is possible whereas before insertion β-strands have to be aligned
or zipper up to form sheets
Tertiary Structure
Folding of integral membrane proteins occurs via a two step process. This picture is clear from
the structure of transmembrane helical protein glycophorin. In the first step insertion and
formation of helices followed by association of transmembrane helices in the second step. In
case β-sheet proteins, first formation of β-sheet occurs followed by insertion in the membrane.
Similar type of packing is observed in the packing of membrane proteins, hydrogen bonding
between the helices is less in number and salt bridges are absent.
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Mechanism of association of transmembrane helices in the membrane interior
Two proposed mechanisms are there:
1. Arrangement of nonpolar side chains of proteins takes place resulting maximum packing of
helices
2. Polar and hydrogen bonding side chains of proteins arrange such that they will stabilize
interaction between the helices
As rise/residue is ~3.6 for a helix, thus atleast one residue should be polar for interaction
between two helices and two or more residues for multiple helix interaction. To explore which
side of the helix interact with the membrane interior and which side interacts with other helix a
term hydrophobic moment has been introduced by Eisenberg and co-workers. The hydrophobic
moment is a vector of the sum of the hydrophobicity of the particular residues on the helix times
the unit vector from the nucleus of the α-carbon to the center of the side chain.
3. Helical moment which arises due to the particular configuration of peptide bonds in helix
structure that favors association of helices. Peptide bonds have weak dipole which arises due to
their resonance structure. Alignment of these moments within helix results in an overall moment.
Antiparallel structure of helix is preferred over parallel structure. More the length of the helix
more will be the moment. It has been observed that transmembrane helices have mostly
antiparallel configuration.
4. Optimal packing of the helices also governs association of the helices in the bilayer. Angle
between membrane spanning proteins and bilayer plane is ~21 ° which is 20 ° for the angle
between two membrane spanning proteins. A knob-into-hole packing arrangement of helices
results left-handed coiled-coil arrangement of proteins.
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Quaternary structure
Membrane protein oligomerization has been explored by measuring the dimerization of the
single transmembrane protein glycophorin with the association of bacteriorhodopsin helices in
bilayers. The significance of packing interactions between the helices was recognized. Our
knowledge about the thermodynamics, kinetics and several other physical properties that direct
the oligomerization of integral membrane proteins is inadequate due to the lack of methods to
monitor protein-protein interaction in the membrane.
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