Biology Reference
In-Depth Information
FIGURE 6.9
Two
'typical' examples of
trans-membrane
b
-barrel
proteins, (a) a AY2 motif
in OmpF and (b) a YQ2
motif in OmpX. Omp
stands for outer
membrane protein of
which there are several
distinct types.
Reproduced
with permission
[27]
.
[27]
. Shown are side views of two bacterial outer membrane
-
barrels the trans-membrane segments are comprised of only 7 to 9 amino acids
[28]
compared
to the 20 plus amino acids in a trans-membrane
a
-helix. Also, every other amino acid in a
b
-
barrel is hydrophobic, alternating with hydrophilic amino acids. This makes detecting trans-
membrane
b
-barrel segments by hydropathy plots much more difficult than
a
-helix
segments. In a
b
-barrel, hydrophobic amino acids face the acyl chains of the membrane
hydrophobic interior while the hydrophilic (mostly charged) amino acids line the inside of
the aqueous trans-membrane channel. The
b
-barrel strands are arranged in an anti-parallel
fashion. Currently, there are more than 50 known
b
-barrel structures that fall into three cate-
gories; up-and-down, Greek key, and jelly roll. Bacterial porins
[27]
are composed of 16
b
-barrel proteins
[27]
.In
b
18
strands that are connected by beta turns on the cytoplasmic side and long loops of amino
acids on the extracellular side. The porin channel is partially obstructed by an amino acid
loop called the eyelet that gives the channel solute selectivity.
e
TYPE IV. LIPID-ANCHORED PROTEINS
Another classification involves proteins that have lipid anchors. Many of these proteins,
however, are actually trans-membrane proteins that have additional lipid anchors. They
could be classified as either a type of integral protein or as a lipid-anchored protein. For
example, rhodopsin is the prototypical example of a 7
a
-helix membrane spanning protein,
but is also anchored to the membrane through covalently attached myristic acid. The choice
of classification for this protein is arbitrary. Although there are additional examples of lipid
anchors, the most important involve myristic acid (
Figure 6.10
), palmitic acid (
Figure 6.11
),
prenylated hydrophobic acyl chains (
Figure 6.12
) and proteins attached through glycosyl-
phosphatidylinositols (GPI-anchored) (
Figure 6.13
). The GPI-anchored proteins are always
