RESOLUTION OF ARTIFICIAL PROTEIN-PROTEIN INTERACTIONS FROM STATISTICALLY OPTIMIZED SEQUENCE LANDSCAPES

Coevolutionary theories describe the probability distribution of interacting proteins in
terms of a Boltzmann statistical model. As a result of selective pressures, that
distribution is expected to sharply deviate from uniformity by featuring a relatively
small number of highly probable sequences across the entire sequence space.
While that statement must be true for interacting protein systems in general, their
sequence distributions may have not been fully shaped by selective pressures
opening the possibility that novel protein-protein interactions could be selected from
artificially generated lower entropy distributions. The aim of this work was to
investigate the physical meaning of protein-protein interactions selected from
artificial fitness landscapes, optimized with statistical criteria. For that, we explore a
Genetic Algorithm, which solves the optimized distributions by maximizing the
statistical coupling, starting from the native multi-sequence alignments and exploring
the space of scrambled multi-sequence alignments. We also solve a distribution by
minimizing statistical couplings through random shuffling of multiple sequence
alignment. Once likely artificial sequences are selected from maximized and
minimized distributions, their binding free-energies at a fixed native bound state are
evaluated according to free energy calculations based on the MM/PBSA method. To
evaluate the physical meaning of native and artificial sequences, we calculated the
selection temperature in relation to random sequences of the same composition. Our
results indicate that it is possible to select new non-similar artificial sequences at
colder or warmer selection temperatures than the native selection temperature, and
that the selected artificial sequences show no differences in binding affinity, in
relation to the native interactions. It is suggested that the molecular evolution of the
dimers can be restricted only by sequence design, since the affinity must only be a
consequence of the amino acid composition determined by the folding restrictions.