Biophysical studies of membrane proteins/peptides. Interaction with ...

Figure I.11 – Experimentally obtained hydrophobicity scales for whole residues (including the peptide
bond). Results obtained for the transfer from water to the polar interface of POPC bilayers and from water
to octanol are presented (Wimley and White, 1996; Wimley et al., 1996).
It is clear from Figure 1.11 that residues like Trp (W), Phe (F), Tyr (Y), Leu (L), Ile
(I), Met (M) or Val (V) favour incorporation in hydrocarbon environments, while
charged residues are particularly averse to this. From this information and from the
primary sequence of a protein it is possible to make previsions for possible alpha helical
TM segments inside the protein sequence. A calculation is made through summation of
the free energy required to insert (from water into the bilayer hydrocarbon core)
successive segments of the polypeptide chain. Segments tested have a finite size, around
20 aminoacids, as this is just about sufficient to spam the hydrocarbon core of a typical
bilayer (this aminoacid length corresponds to 30 Å if the helix is oriented along the
bilayer normal). This procedure allows the creation of hydropathy plots that signal the
polypeptide segments which are the most likely candidates for a TM configuration
inside the protein.
Aminoacids also exhibit preferential localization in certain positions along the
bilayer normal. This fact is of utmost importance to the final position of an alpha-helix
in membranes and will be discussed in more detail in section 2 of this chapter.
1.9. Lateral dynamics in biomembranes
The Singer-Nicolson fluid mosaic model for biomembranes (1972) (Figure I.12)
described the lipid membrane as a two dimensional liquid where both lipids and
membrane proteins moved freely. In fact, in pure lipid bilayers in the fluid phase, lipids
experience fast lateral diffusion, as well as rotational diffusion, wobbling, and
movements in the axis of the bilayer. Crossing from one monolayer to the other is
20