Peptoids (N-substituted glycine oligomers) are synthetic foldamers.  Peptoids are similar to peptides, except the side chain normally found on the alpha carbon is bonded to the nitrogen. Because they are easily synthesized, peptoids have been used in a variety of biomimetic applications, including antimicrobials and surrogate antibodies.  Can current forcefield models be used to predict peptoid solution structure?  To answer this, we used UCSF Chimera to build a model of a small peptoid pentamer shown to have a stable folded conformation in solution (Armand et al. PNAS 1998).  We then applied the GAFF forcefield with partial charges computed by the AM1-BCC method, along with a Generalized Born implicit solvent model (GBSA).  Using this model, we simulated replica-exchange molecular dynamics (REMD) using the OpenMM package.  In this investigation, we assess the accuracy of the model by comparing the simulation results to experimental distance restraints obtained by NMR.

Can current forcefield models accurately simulate peptoids

244th National Meeting (2012)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.