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Peppytides: An Interactive, Scaled, Physical Model of the Polypeptide Chain


For a video demonstration hosted by the researchers, go here.




Promita Chakraborty and Ronald Zuckermann of Berkeley Lab have developed Peppytides, the first mechanically flexible, interactive, scaled physical model of the polypeptide chain that accurately simulates the folding mechanisms of functional proteins. Peppytides can be used to probe the mechanics of protein structure or to demonstrate protein-folding pathways.

Berkeley Lab Peppytides accurately demonstrates the molecular dynamics behind protein folding such as degrees of freedom of rotatable bonds, bond lengths and angles, and short- and long-range (nonbonding) interactions between amino acids. The technology achieves its unique mechanical flexibility by breaking down the amino acids into coarse-grained components linked by rotatable bonds. Unlike most 3-D printed protein models, the Berkeley Lab invention features a backbone chain that can be folded or unfolded to model at scale all of the common protein secondary structure elements, such as alpha helices, beta sheets, and turns.

Available nonflexible scaled physical models of organic small molecules and biomolecules are important educational aids and research tools for illustrating the scale and complexity of polypeptide chains, but their inflexible design cannot accurately demonstrate the dynamics of the protein-folding process as Peppytides can. In addition, the Berkeley Lab invention represents a key step towards a sophisticated computer input device that can manipulate and intuitively interact with existing computer-visualization tools.

DEVELOPMENT STAGE:  Proven principle.

STATUS:  Patent pending.  Available for licensing or collaborative research.

Chakraborty, P., Zuckermann, R.N., “Coarse-grained, foldable, physical model of the polypeptide chain,” Proc. Natl. Acad. Sci. U.S.A., 2013, 110(33), 13368–13373.   


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