The folding of linear polymer chains is fundamental to the nanoarchitecture of biopolymer-based materials. The complexity of protein folding makes the process difficult to understand, and yet this understanding is crucial to the design of next-generation bio-inspired materials. Interacting with a conformationally dynamic physical model is an intuitive and informative way to develop new insights into molecular structure. As a first step towards building a computer-augmented physical polypeptide model that may have applications in structural biology and drug design, we have designed, fabricated and validated a dimensionally accurate, physical model of the polypeptide chain, that has a flexible backbone where the dihedral bonds are rotationally constrained to match their molecular counterparts. We have reproduced all the backbone degrees-of-freedom to better understand folding dynamics of the chain. The model can be folded with accuracy into alpha helices, beta sheets, beta turns and protein tertiary structures, which are stabilized by multiple weak short-range and long-range interactions within the model. Figure 1 shows a comparison of the Ramachandran landscape from native state protein structures from Protein Data Bank (left) with that of the physical model resulting from the magnet-array implemented rotational barriers of f and ? bonds (right).

Coarse-grained, foldable, physical model of the polypeptide chain

248th National Meeting (2014)

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