Molecular
recognition features (MoRFs) are common in intrinsically
disordered proteins (IDPs) and intrinsically disordered regions (IDRs).
MoRFs are in constant order–disorder structural transitions
and adopt well-defined structures once they are bound to their targets.
Here, we study Escargot (Esg), a transcription factor in
Drosophila melanogaster
that regulates multiple cellular
functions, and consists of a disordered N-terminal domain and a group
of zinc fingers at its C-terminal domain. We analyzed the N-terminal
domain of Esg with disorder predictors and identified a region of
45 amino acids with high probability to form ordered structures, which
we named S2. Through 54 μs of molecular dynamics (MD) simulations
using CHARMM36 and implicit solvent (generalized Born/surface area
(GBSA)), we characterized the conformational landscape of S2 and found
an α-MoRF of ∼16 amino acids stabilized by key contacts
within the helix. To test the importance of these contacts in the
stability of the α-MoRF, we evaluated the effect of point mutations
that would impair these interactions, running 24 μs of MD for
each mutation. The mutations had mild effects on the MoRF, and in
some cases, led to gain of residual structure through long-range contacts
of the α-MoRF and the rest of the S2 region. As this could be
an effect of the force field and solvent model we used, we benchmarked
our simulation protocol by carrying out 32 μs of MD for the
(AAQAA)
3
peptide. The results of the benchmark indicate
that the global amount of helix in shorter peptides like (AAQAA)
3
is reasonably predicted. Careful analysis of the runs of
S2 and its mutants suggests that the mutation to hydrophobic residues
may have nucleated long-range hydrophobic and aromatic interactions
that stabilize the MoRF. Finally, we have identified a set of residues
that stabilize an α-MoRF in a region still without functional
annotations in Esg.