Gene Cloning

294 Gene Cloning
and their function when embedded in the membrane, and so cannot be
studied as totally pure proteins.
Membrane proteins by definition have at least one part of the protein
embedded in the membrane, but in many cases the polypeptide chain of a
membrane protein will cross the membrane several times. These are
referred to as polytopic proteins. Regions of the protein which cross the
membrane often form amphipathic alpha-helices. These are alpha-helices
where residues on one side of the helix tend to have hydrophilic side
chains, and those on the other side, hydrophobic side chains. In a typical
polytopic protein, the alpha-helices will form a bundle where the
hydrophobic side chains point outwards, and interact with the hydrophobic
interior of the membrane, while the hydrophilic residues face inwards
and interact with each other, or form a channel through which charged or
polar substances can pass. Bioinformatic analysis of putative membrane
proteins can be helpful in detecting the regions of the protein which are
likely to form the membrane-spanning segments, but to prove the topology
of a given protein in a membrane requires other methods.
Consider the protein shown in Figure 10.7. This is a purely diagrammatic
representation of the protein showing the regions of the protein which are
crossing the membrane opened out in a straight line for convenience: in
practice, these would be bundled together. Regions between the membrane
spanning helices form domains which are either on the “inside” or
the “outside” of the membrane. How can we determine whether this sort of
model, which could be predicted from a computer analysis of the protein
1
3
C
N
2
4
Figure 10.7 General topology of a membrane spanning protein (shown in blue)
embedded in a lipid bilayer. N and C show the N and C termini of the protein.
Domains 1 and 3 are clearly on the opposite side of the membrane to domains 2
and 4.