Imagine an alien species sees a
single photo of a human. They would have no idea how our arms and legs move, or
that our mouths can open and close. So it is with protein crystal structures: even
multiple static images often fail to show possible conformations. Pockets open
and close in unexpected places, and these can be critical for drug discovery.
But how do you find these “cryptic” pockets? Harsh Bansia, Suryanarayanarao
Ramakumar, and collaborators at Indian Institute of Science, Bengaluru and
Pennsylvania State University provide a new approach in J. Chem. Inf. Mod.
The researchers were studying a
bacterial xylanase called RBSX and had mutated a tryptophan residue to an
alanine. When they solved the crystal structure, they found that the mutation
had created a surface pocket that was filled with a molecule of 1,2-ethanediol
(EDO). EDO is an ingredient in antifreeze because of its ability to prevent ice
formation, and this property also makes it a common cryoprotectant in
crystallography. The EDO molecule was making both van der Waals contacts as
well as a hydrogen bond with the protein. The researchers found similar results when they used
propylene glycol. (See here for a related discussion of MiniFrags, the smallest of which are the
size of propylene glycol.)
To see whether water could make
these same interactions, the researchers determined another crystal structure in
the absence of EDO. Surprisingly, a phenylalanine side chain rotated and closed
the pocket. Had this been the only structure solved, the possibility of pocket formation
would not have been suspected.
Next, the researchers conducted
molecular dynamics simulations. Starting from the closed state, the pocket
remained occluded by the phenylalanine, giving no hint of its potential presence. Starting
from the open state and removing EDO, the pocket also rapidly closed. In other
words, in the absence of a ligand, the pocket appears to collapse in upon itself.
Importantly, these observations are not limited to a mutant bacterial protein. The researchers looked at published
crystal structures of four unrelated proteins with known cryptic
pockets and found that EDO could bind in all of them. They also ran molecular dynamic
simulations on two proteins in which EDO was included as a virtual cosolvent.
For both NPC-2 and IL-2, addition of EDO was able to open up cryptic pockets
that had been previously found using other molecules; we’ve discussed earlier computational
work on IL-2 here.
This is a nice example of following
up on an unexpected observation, and is well-suited for further study. For example,
it would be interesting to do a systematic study of EDO and propylene glycol binding sites throughout the
entire protein data bank. For those of you doing molecular dynamics or crystallography,
it may be worth adding EDO – virtually or experimentally – to see if it reveals
any surprises in your favorite proteins.
No comments:
Post a Comment