Leu & Ile in class A GPCRs
We compared Leu and Ile residues based on how densely packed their side
chains are and how strongly these side chains are exposed on the protein
surface. Since GPCRs are membrane proteins, protein-surface exposure
captures contact with the lipid bilayer or solvent, depending on the
location of the side chain. Further, side-chain packing density and
protein-surface exposure measure overlapping properties of residues
within protein structures, i.e. a high level of protein-surface exposure
will lead to a small packing density for a given residue. A sample of
216 experimental structures from 95 unique GPCRs indicates that Ile
tends to occur in more densely packed regions than Leu (Fig. 1A) and
that Leu tends to be more protein-surface exposed than Ile (Fig. 1B).
This is true for the majority of receptor structures, with a total of
88.4 % of them displaying more densely packed Ile residues and 81.0 %
more protein-surface exposed Leu. This general difference between the
two amino acids suggests that Leu and Ile residues tend to occur within
different structural contexts within class A GPCRs, with Leu being more
prone to interact with the lipids in the membrane bilayer.
Interestingly, significant differences in side-chain packing between
active- and inactive-state GPCRs are present for Leu and Ile (Fig. 1C).
In both cases, packing density is smaller in active- than in
inactive-state structures (Ile: − 8.6 %, Leu: − 4.9 %). This is
further accompanied by a less pronounced and non-significant increase in
protein-surface exposure of the two amino acids (Ile: + 4.6 %, Leu: +
2.8 %) (SI Fig. S1). GPCR activation leads to conformational changes
that allow G proteins to bind. These conformational changes include the
outward movement of TM6 and the subsequent opening of a cytosolic
crevice that accommodates the C-terminal helix of a G
protein.5,19 Active-state GPCR structures are
generally solved in presence of G proteins or G protein-alike
substitutions20,21, which were not included in the
calculation of packing densities. It is therefore likely that the
decrease in packing density upon activation reflects the opening-up of
the G protein binding pocket. This further matches the more pronounced
decrease in packing density for Ile than Leu since this conformational
change can be expected to have a stronger impact on buried residues.