May 22, 2014: News coverage in Berkeley Lab's Materials Sciences Division (MSD) website. MSD news May 22, 2014: News coverage in Today at Berkeley Lab (TABL). TABL news May 17-18, 2014: We exhibited at Maker Faire Bay Area. Download flier.        Apr 26, 2014: Talk and hands-on with students in grade 7-10 (to students from Johns Hopkins Center for Talented Youth).   Apr 12, 2014: We exhibited at Lawrence Hall of Science. Featured Makers in NanoDays.   Jan, 2014: Make Magazine article. Steps on how to make Peppytides Promita Chakraborty and Ronald N. Zuckermann, Peppytides, MAKE Projects, Jan 2014 Aug 26, 2013: Work on Peppytides featured in Berkeley Science Review blog. Check out this nice post here. Jun 25, 2013: Our first paper on Peppytides has been accepted in PNAS (www.pnas.org/cgi/doi/10.1073/pnas.1305741110) Coarse-grained, foldable, physical model of the polypeptide chain Promita Chakraborty and Ronald N. Zuckermann The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 Proceedings of the National Academy of Sciences 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 advan- ces 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 bio- macromolecular models directly to the vast array of existing computational tools to provide an enhanced and interactive human– computer interface. |
