3.3 A Cryptic Site
Problem: Bcl-xL
Protein
As discussed above, a cryptic site is defined as a hidden binding site
when the protein is in the free/unbound state [20, 21]. Cimer-
mancic et al. used machine learning to predict new cryptic sites
based on the features of available cryptic sites [67]. These features
included their amino acid sequences, structures, and dynamical
attributes. Their major finding was that cryptic sites tend to be as
conserved in evaluation as traditional binding pockets but are also
less hydrophobic and more flexible [67]. Oleinikovas et al. char-
acterized several additional characteristics for cryptic sites. They
concluded that the appearance of a cryptic site does not correspond
to a local minimum in the computed conformational free energy
landscape. They also found that temperature-based enhanced sam-
pling approaches, such as Parallel Tempering, do not improve the
situation, as the entropic term does not help in the opening of these
sites. Interestingly, they found that a conventional MD simulation
can occasionally lead to the opening of a cryptic site [9, 21].
As the Bcl-2 family of proteins, Bcl-xL is a key regulator of
programmed cell death [68]. MD simulations were performed on
the apo-Bcl-xL structure in water and in cosolvent to detect bind-
ing sites on the protein. In water, the binding site of the apo-Bcl-xL
had relatively minor conformational changes. Simulations of three
holo-Bcl-xL structures in water, however, showed that the protein
exhibited significant dynamic transition of conformations, includ-
ing burying of several solvent exposed hydrophobic residues in the
binding groove. In contrast, the apo-Bcl-xL in cosolvent, the
hydrophobic surface tends to exposing itself to the interface,
which is similar to the tendency in the crystal complex of Bcl-xL.
However, the free energy differences of the Bcl-xL conformations
obtained from both solation methods were small, which indicates
the perturbation of cosolvent molecules is acceptable to Bcl-xL
structure in relatively short MD simulations [58]. Furthermore,
the novel binding hot spots that were revealed by cosolvent MD
simulation did not find in the cocrystallized complex [39]. Taken
together, this study suggested that cosolvent is very capable
method in identifying cryptic sites, particularly, for flexible and
hydrophobic targets.4 Conclusion
The surface of a protein target encompasses many hot spots. These
spots are essential in mediating the interactions between the target
protein and other proteins as well as small molecule drugs. A
binding site is formed by the grouping of these hot spots within
the surface of the protein. There are many types of such sites. The
most complicated ones include cryptic and allosteric sites. Both
types do not induce direct effects on the activity of the targetPrediction of Druggable Binding Sites 99