Dynamic polyhedral models of globular proteins

Abstract

We have devised several mechanical models of globular proteins by approximating them to various polyhedra (dodecahedron, truncated octahedron, icosahedron, truncated icosahedron). The models comprise hollow blocks linked together in a flexible chain. Between blocks there is a set of several reversible, weak magnetic interactions such that when the chain is agitated, it will fold into a stable polyhedral structure about the size of a hand. Folding may be followed in real time with a video camera. Key to the success of the folding process is the lightness of the chain. Several side chains may also be added to the blocks such that they come together to create a polyhedral core when the chain folds. The models have a number of similarities to globular proteins: each chain folds into a unique, but dynamic, three-dimensional structure; the instructions that determine this structure are built into the configuration of blocks; and it is difficult to predict this structure given the unfolded block configuration. Furthermore, the chains fold quickly, generally in less than a minute, several pathways are involved, and these pathways progress through elements of “native” structure. In particular, the models emphasize the importance of restricted conformational mobility in assisting the chain to fold, and also in eliminating undesirable interactions. Because of these similarities to globular proteins, we believe that the polyhedral models will, with continued development, be helpful in understanding the protein folding process, while at the same time acting as valuable educational visual aids. They might also inspire the construction of new types of microscopic, self-assembling devices.