crc press - E-Lib FK UWKS

Structure Prediction of CPPs and Iterative Development of Novel CPPs 191
1
0
core core
Water Interface Interface Water
-18
-13.5
q 2 (-15.75Å)
FIGURE 9.1 Model membrane of IMPALA.
1
13.5 18
Monolayer 2 Monolayer 1
q 1 (15.75Å)
generally these interactions do not seem crucial for folding membrane proteins, as
the proteins may refold in vitro under nonbiological conditions. 42 This assumption
is also made for the crystallization of integrated membrane proteins (IMPs) in which
lipids are replaced by detergents. Moreover, the description is so simple that it could
be easily adapted to other interfaces (e.g., monolayer, spherical, or discoidal).
9.2.2 ATOMIC SURFACE HYDROPHOBICITY (FIRST RESTRAINT)
Z ( Å)
To calculate the hydrophobic and hydrophilic restraints, we use atomic surface
transfer energies, a concept relying on the assumption that the overall transfer energy
of a molecule, H, can be calculated as
N
= ∑ i tr() i
i=
1
H SE
(9.2)
where i is an index for the N atoms of the molecule, S (Å 2 ) the solvent-accessible
surface calculated with Shrake and Rupley’s algorithm with 192 points, 43,44 and E tr
(kJ/·mol·Å 2 ) is the transfer energy by surface of individual atoms (Table 9.1). A
similar approach was successfully used on small molecules 45 by considering that
N
= ∑ ()
i=
1
H E atr i
(9.3)