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

Figure I.9 – Depiction of the several possibilities for association of proteins with biomembranes. Protein
domains in the exoplasmic side of the membrane are frequently glycosilated and can interact with the
extracellular matrix. Protein domains on the cytoplasmic side on the other hand are responsible for the
coupling of the cytoskeleton network with the lipid membrane (From Lodish et al., 2000).
Membrane proteins on the extracellular side of the plasma membrane generally bind
other molecules, including external signalling proteins, ions, small metabolites, and
adhesion molecules in other cells. Protein domains within the plasma membrane, mainly
those that are part of channels and pores, are generally responsible for transport of
molecules across the bilayer, while peripheral protein membranes in the cytosolic side
of the plasma membrane are responsible for many different functions (Lodish et al.,
2000).
The possibilities of secondary structure available for membrane spanning protein
domains are very limited. Only two structures are available, the alpha-helix and the
beta-barrel (Figure I.10). These structures have a common characteristic. In both, the
peptide bonds of the aminoacids are hydrogen bonded. In fact, if this were not the case,
insertion in the highly apolar environment would be energetically unfavourable, even
for the most hydrophobic amino acids. The energetic cost of partitioning a peptide bond
into a highly apolar phase, is significantly larger than the free energy reduction
associated with insertion of the Trp side chain in the same environment (White and
Wimley, 1999). Therefore, only a polypeptide segment with complete backbonebackbone
hydrogen bonding can insert in the highly hydrophobic core of the bilayer,
and the alpha-helix and the beta-barrel are the two structures that satisfy this condition.
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