title: Coarse-grained, foldable, physical model of the polypeptide chain.
abstract: Although nonflexible, scaled molecular models like Pauling-Corey's and its descendants have made significant contributions in structural biology research and pedagogy, recent technical advances in 3D printing and electronics make it possible to go one step further in designing physical models of biomacromolecules: to make them conformationally dynamic. We report here the design, construction, and validation of a flexible, scaled, physical model of the polypeptide chain, which accurately reproduces the bond rotational degrees of freedom in the peptide backbone. The coarse-grained backbone model consists of repeating amide and α-carbon units, connected by mechanical bonds (corresponding to ϕ and ψ) that include realistic barriers to rotation that closely approximate those found at the molecular scale. Longer-range hydrogen-bonding interactions are also incorporated, allowing the chain to readily fold into stable secondary structures. The model is easily constructed with readily obtainable parts and promises to be a tremendous educational aid to the intuitive understanding of chain folding as the basis for macromolecular structure. Furthermore, this physical model can serve as the basis for linking tangible biomacromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human-computer interface.
authors.affiliation: The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
authors.forename: Promita
authors.initials: P
authors.lastname: Chakraborty
authors.forename: Ronald N
authors.initials: RN
authors.lastname: Zuckermann
mesh_terms: D000577:Amides / Q000378:metabolism; D040761:Biomimetic Materials / Q000737:chemistry; D002244:Carbon / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D012371:Robotics; D012399:Rotation
chemical_list: D000577:Amides; D010455:Peptides; D002244:Carbon
keywords: biomimetic modular robotics; conformational isomerism; protein folding; rotational energy barrier; self-assembly
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