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