Mathematical Modeling and Optimization Methods for De Novo Protein Design - Systems Biology: Networks, Models, and Applications - page 52

In addition to identifying the global minimum energy conformation,
the global optimization algorithm provides the means for identifying
a consistent ensemble of low-energy conformations [66,68,69]. Such
ensembles are useful in deriving quantitative comparisons between
the free folding and template-constrained simulations. In this way, the
complications inherent to the specification of an appropriate reference
state are avoided because a relative probability is calculated for each
sequence studied during this stage of the approach.
The relative probability for template stability, p temp , can be found by
summing the statistical weights for those conformers from the free fold-
ing simulation that resemble the template structure (denoted as set temp),
and dividing this sum by the summation of statistical weights for all con-
formers from the free folding simulation (denoted as set total):

∑ exp[ − β

β

E
E

]

i ∈ temp i

p =

temp

∑ exp[ − ]

i ∈ total i

where exp[ − b E i ] is the statistical weight for conformer i .

COMPUTATIONAL AND EXPERIMENTAL FINDINGS

Compstatin
The target chosen to test the novel protein design framework proposed
by Klepeis et al. [24,25] is compstatin. Compstatin is a 13-residue cyclic
peptide that has the ability to inhibit the cleavage of C3 to C3a and C3b.
The effect of targeting the C3 cleavage is triple and results to hindrance
in (i) the generation of the proinflammatory peptide C3a, (ii) the
generation of opsonin C3b (or its fragment C3d), and (iii) further com-
plement activation of the common pathway (beyond C3) with
end result the generation of the membrane attack complex (MAC). A
C3-binding complement inhibitor was identified as a 27-residue pep-
tide using a phage-displayed random peptide library [70]. This peptide
was truncated to an equally active 13-residue peptide named comp-
statin with sequence I[CVVQDWGHHRC]T-NH 2 , where the brackets
denote cyclization through a disulfide bridge formed by Cys 2 -Cys 12
[70,71]. Acetylation of the N-terminus of compstatin (Ac-compstatin)
resulted in a 3-fold increase in activity [72-74].
Compstatin blocked the cleavage of C3 to the proinflammatory pep-
tide C3a and the opsonin C3b in both hemolytic assays, and in human
normal serum [70,72]; prevented heparin/protamine-induced comple-
ment activation in baboons in a situation resembling heart surgery [75];
inhibited complement activation during the contact of blood with bio-
material in a model of extracorporeal circulation [76]; increased the
lifetime of survival of porcine kidneys perfused with human blood in