Peptoid structure prediction

Guest post from Dr. Greg Bowman, UC Berkeley

Prof. Vince Voelz’s lab has published an exciting paper on
their recent successes with predicting the structures of protein-like molecules
called peptoids (here).  Peptoids are
similar to proteins but with a rearrangement in their chemistry (see example below).  Their similarity to proteins allows peptoids
to function like proteins.  However, the
alteration in peptoid chemistry relative to proteins effectively makes them
invisible to parts of the immune system designed to recognize foreign
proteins.  Therefore, peptoids are an
attractive option for drug design.  To
fully realize this potential, we need to be able to predict the structures of
peptoids and design them to perform specific functions.  The Voelz lab’s work demonstrates that
computer simulations can provide this sort of information by presented
predicted structures of a number of peptoids along with experimental structures
confirming the accuracy of their predictions (see example below).


Peptide vs. peptoid chemistry.  In peptoids, a group of atoms (called R) is moved from a carbon to an adjacent nitrogen (N).


An example of one of the Voelz lab's predicted structures (in green) overlaid with the experimental structure (in white).