Coarse-grained models have revealed the mechanisms for canonical secondary structure formation (α-helices, β-sheets) in wide-ranging biological polymers. However, coarse grained-models are less frequently applied to model non-canonical secondary structures. The development of coarse-grained models which are: a) extensible to the investigation of non-canonical secondary structures, and b) reliable for polymers built from monomers with varying physico-chemical properties, is a considerable challenge in the field of molecular modeling. We will discuss a new software package, foldamers, which addresses this challenge by providing a flexible framework for building coarse-grained models, performing simulations with these models in OpenMM, and rapidly evaluating their thermodynamic properties with the Multistate Bennett Acceptance Ratio (MBAR) estimator. We will demonstrate how this software can be used to explore the physico-chemical properties of biologically-inspired polymers (built from monomers with two coarse-grained beads, corresponding to backbone and sidechain units) that exhibit non-canonical, helical secondary structures. Finally, we will discuss the strengths and limitations of this framework for the design and investigation of heteropolymers with previously-unknown secondary structures.

Leveraging coarse-grained models to design heteropolymers with novel secondary structure

Macromolecular Chemistry: The Second Century

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ACS Spring 2020 National Meeting & Expo

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