Rational Design Of Complementary Peptides To The Beta Amyloid 29-42 Fusion Peptide: An Application Of Pepdesign

Peptides in solution currently exist under several conformations; an equilibrium
which varies with solvent polarity. Despite or because of this structure
versatility, peptides can be selective biological tools: they can adapt to a
target, vary conformation with solvents and so on. These capacities are crucial
for cargo carriers. One promising way of using peptides in biotechnologies is to
decipher their medium-sequence-structure-function relationships and one approach
is molecular modelling. Only few "in silico" methods of peptide design are
described in the literature. Most are used in support of experimental screening
of peptide libraries. However, the way they are made does not teach us much for
future researches. In this paper, we describe an "in silico" method (PepDesign)
which starts by analysing the native interaction of a peptide with a target
molecule in order to define which points are important. From there, a modelling
protocol for the design of 'better' peptides is set. The PepDesign procedure
calculates new peptides fulfilling the hypothesis, tests the conformational space
of these peptides in interaction with the target by angular dynamics and goes up
to the selection of the best peptide based on the analysis of complex structure
properties. Experimental biological assays are finally used to test the selected
peptides, hence to validate the approach. Applications of PepDesign are wide
because the procedure will remain similar irrespective of the target which can be
a protein, a drug or a nucleic acid. In this paper, we describe the design of
peptides which binds to the fusogenic helical form of the C-terminal domain of
the Abeta peptide (Abeta29-42).