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204 Cell-Penetrating Peptides: Processes and Applications
conformation, the peptide hydrophobicity splits up in an asymmetric gradient: a
more hydrophobic extremity at one side decreasing towards the other extremity of
the helix. 45 These peptides insert in a tilted way with respect to the membrane
interface and are able, in vitro, to destabilize the liposomal membranes and lead to
their fusion. 58 The 3D envelope of the SIV fusion peptide shows that the surface of
minimal energy is large, which means that the peptides may adopt an insertion angle
which varies around 50°. In our calculations, the mass center penetration varies from
(±) 8 to (±) 10 Å and the peptide inserts with an angle of about 50 to 60° with
different local minima. Their tilted orientation, due to the hydrophobicity gradient,
allows destabilizing the regular organization of the acyl chains of membrane lipids.
9.3.1.2 Membrane Proteins
Following validation of the method with peptides whose orientation is experimentally
known, and since there was a good concordance between predictions and
experimental observations, membrane proteins of known structure were processed.
The formation of the dimer of Glycophorin A has been studied; the restraint terms
increase the efficiency of the Monte Carlo algorithm to reach the dimer structure
from monomers; this analysis was the first step to evaluate interactions between
transmembrane parts of polytopic proteins. 59
Bacteriorhodopsin was the first structurally described IMP. 60 It is found as a 2D
crystal in the internal membrane of archaebacteria Halobacterium salinarium. Each
monomer of the bacteriorhodopsin contains seven transmembrane α-helices and
covalently binds a retinal chromophore by a lysine of the seventh transmembrane
helix. In response to illumination, the geometry of the retinal is modified from a
trans to a 13-cis configuration. This transconformation initiates a set of steps including
a large conformational change of the protein and leads to translocation of a
proton from the interior to exterior of the cell, which in turn puts the retinal and the
protein back to their initial state. The transmembrane gradient of protons provides
a way to capture and use light energy in order to allow ATP synthesis in the cell.
Three of the helices are almost normal to the surface of the membrane, while four
are tilted to 70°. 61,62 The reference vector for the insertion angle is localized into the
first helix (Trp7-Phe22).
In Figure 9.6A, the 3D envelope shows a position of the protein mass center
around –2 Å and an orientation of about –70°, which is in agreement with experimental
observations. In the case of the β-Barrel proteins, the first IMP described
was a porin of the external membrane of a gram-negative bacteria. Proteins with
similar structures were further suspected in the external membranes of mitochondria
and chloroplasts. 63
Porins have a molecular weight between 28 and 48 kDa. They are made of 8 to
22 antiparallel strands organized in β-sheets making a barrel that delimits a channel.
They are able to transfer small hydrophilic molecules, but no macromolecules, from
outside to inside the cell and are associated with the peptidoglycan as well as the
lipopolysacharides of the bacterial cell wall. 64
Maltoporin, a homotrimer of β-barrel found in the external membrane of Escherichia
coli, has been tested with our model of lipid bilayer. The function of this