De Novo Design of Proteins - Peptide and Protein Design for Biopharmaceutical Applications - page 218

There are only relatively few examples of parallel triple helical
structures. However, the de novo sequence CoilV a L d , b-branched
and with Val in position a forms a parallel trimeric coiled
coil (VEALEKKVAALESK-VQALEKKVEALEHG, 28AA, helix-helix
design, V a L d ) [67,68]. In solution, a monomer-trimer equilibrium was
observed.

6.3.3 a-helical Bundles

Among the most frequently used structural motifs for de novo design is
the 4-a-helix bundle. Its folding is driven by the hydrophobic collapse of
amphiphilic helices and is guided by the position and nature of loop
regions, by electrostatic effects and by shape complementarity in side-
chain packing (Figure 6.6). Several artificial, de novo -designed 3-, 4- and
5-helix structures have been reported (for a review, see [69]). They rely on
a-helical, amphipathic peptide sequences either (i) by linear connection in
a helix-loop-helix pattern, or (ii) by assembled on a template to provide
artificial TASP structures. Here we focus on 3- vs. 4-helix structures. It is
important to restrict the side-chain mobility of the hydrophobic core, i.e.
to avoid a dynamic or fluid character, which can be achieved by incor-
poration of b-branched and aromatic residues in the core [70].
DeGrado and coworkers have since the mid 1980s been on a long quest
toward de novo design of proteins, especially 4-helix bundles, which has
culminated in the design of proteins and metalloproteins with native-like
properties [2,3]. They started out with single-helix sequences and then
moved on to longer helix1-loop-helix2 sequences (see Table 6.1). It has
been concluded that helices of four or more turns pack preferably in
elongated bundles, while shorter helices can pack into a number of
other geometries [4,71]. Also, it has been concluded that conformational
specificity requires a correct balance of hydrophobic and hydrophilic
interactions, as too few hydrophobic residues leads to inadequate stabi-
lity, while too many leads to highly stable but dynamic structures [4,72].

6.3.3.1 3-helix bundles

DeGrado and coworkers have concluded that the way helices interact is less
regular in a 3-helix bundle than in a three-stranded coiled coil [38]. Starting
from coil-Ser, DeGrado and coworkers developed the uniquely folded 73-
residue 3-helix bundle proteins a 3 C nda 3 D [73,74]. The