(360b) Multiscale Models for Peptoid Simulations

Peptoids (poly-n-substituted glycines) are peptide-like macromolecules composed of modified glycine units with side chains attached to their nitrogen atoms [1]. Peptoids are biocompatible, resistant to protease degradation[2], and they can be synthesized using more than 300 commercially available amines [1,3]  making peptoids versatile and appealing compounds for combinatorial materials design. Applications for peptoids include antimicrobial coatings and lung surfactants.

We present multiscale simulation studies of peptoids using newly developed atomistic and coarse-grained force field parameters. Atomistic simulations are performed to investigate the relationship between peptoid side-chains and the peptoid backbone secondary structure. We use a variation of the CHARMM all atom force field with newly developed peptoid-specific parameters. Simulations are performed for several peptoid sides-chains and the simulation results are compared to experimental peptoid structures. We also present a simple, coarse-grained peptoid model where each peptoid monomer is represented by a single coarse-grained bead. This one-site model is used to predict the equilibrium phase behavior of peptoid-water systems. In future work, these peptoid force fields will be used combinatorial design of more complex peptoid sequences.

References:

[1]      J. Seo, B. Lee, Z. R. N. P. Synthesis, N. I. P. Ducheyne, K. E. Healy, D. W. Hutmacher, D. W. Grainger, C. J. Kirkpatrick, and C. Biomaterials, “Peptoids: Synthesis, Characterization, and Nanostructures,” Comprehensive Biomaterials, vol. 2, pp. 53–76, 2011.

[2]      K. T. Nam, S. a Shelby, P. H. Choi, A. B. Marciel, R. Chen, L. Tan, T. K. Chu, R. a Mesch, B.-C. Lee, M. D. Connolly, C. Kisielowski, and R. N. Zuckermann, “Free-floating ultrathin two-dimensional crystals from sequence-specific peptoid polymers.,” Nature materials, vol. 9, no. 5, pp. 454–60, May 2010.

[3]      R. N. Zuckerman, S. B. H. Kent, and W. H. Moost, “Efficient Method for the Preparation of Peptoids [Oligo(N-substituted glycines)],” no. 6, pp. 10646–10647, 1992.