While all the information required for the folding of a protein is contained in its amino
acid sequence, one has not yet learned how to extract this information in order
to predict the three-dimensional, biologically active, native conformation of a
protein whose sequence is known. Using insights obtained from simple model
simulations of the folding of proteins, in particular the fact that this phenomenon is
essentially controlled by conserved (native) contacts among (few) strongly
interacting ('hot'), as a rule hydrophobic, amino acids, which also stabilize local
elementary structures (LES, hidden, incipient secondary structures such as
α-helices
and β-sheets) formed early in the folding process and leading to the postcritical folding nucleus
(i.e. the minimum set of native contacts which brings the system beyond the highest
free-energy barrier found in the whole folding process) it is possible to work out a successful
strategy for reading the native structure of designed proteins from a knowledge of only
their amino acid sequence and of the contact energies among the amino acids. Because LES
have undergone millions of years of evolution to selectively dock to their complementary
structures, small peptides made out of the same amino acids as the LES are expected
to selectively attach to the newly expressed (unfolded) protein and inhibit its
folding, or to the native (fluctuating) native conformation and denature it. These
peptides, or their mimetic molecules, can thus be used as effective non-conventional
drugs to those already existing (and directed at neutralizing the active site of
enzymes), displaying the advantage of not suffering from the increase in resistance.