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Structure Prediction of CPPs and Iterative Development of Novel CPPs 193
FIGURE 9.2 Structures of Phe and Asn used to optimize the atomic transfer energy scale.
energy of glycine from those of all other residues in order to obtain the transfer
energies of the lateral side chains. Thus the error between experimental and calculated
data for an amino acid x is
( ) − exp
δ = H −H
H
( x) theo( x) theo( gly) ( x)
The total error between the calculated and experimental H was minimized by a
Monte Carlo procedure applied to the atomic transfer energy errors.
9.2.3 LIPID PERTURBATION (SECOND RESTRAINT)
To build restraints of the lipid perturbation, one must define the general structural
features of IMPs. 31 The observation of bacteriorhodopsin and photosynthetic reaction
center 48 shows that IMPs are similar to soluble proteins with respect to surface area,
interior hydrophobicity and packing, conservation of buried residues, and stability.
The major difference between IMPs and soluble proteins is the nature of surface
residues, which are more hydrophobic in IMPs than in globular proteins. 31 This
feature has been used in many methods aimed at determining the transmembrane
segments of IMPs. This striking segregation of hydrophobic and hydrophilic parts
of the molecule imposed by the membrane properties is the hydrophobic effect. To
simulate it, we calculate the hydrophobic restraint as