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

size corresponding to the hydrophobicity of each amino acid drawn from the centre of
the putative helix. Through calculation of the hydrophobic moment of an appropriate
residue window (typically 11 – three turns in the alpha-helix) for each position in the
protein sequence, it is possible to draw an “amphipatic profile” of the protein (Fig.
I.14), and by comparison with values obtained from known amphipatic helices it is
possible to predict which protein domains are likely to correspond to amphipatic helices
(Auger, 1993).
Figure I.14 – Amphipatic profile of gp41 from envelope protein of HIV variant bh10 (taken from
Auger, 1993).
2.4. Peptide partitioning to the membrane
Several approaches have been used to study peptide binding to lipid membranes.
The most important are fluorescence spectroscopy (Santos et al., 2003), circular
dichroism, surface plasmon resonance and isothermal titration calorimetry. The binding
of a peptide to the lipid bilayer is not a conventional reaction with a defined
stoichiometry. In reality, the process is better described as a water/bilayer partition
problem. Although stable complex formation between proteins and specific lipids have
been proved and bound lipid molecules have been observed in the crystal structures of
some proteins (see Section 2.8) (Lee, 2003), this type of interaction is not generally
found for most membrane proteins.
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