New algorithm helps engineers choose self-assembling proteins

June 1, 2011
Bio Design

The researchers’ designed structure, left, was inspired by natural viruses, such as the tobacco mosaic virus, right (credit: University of Pennsylvania)

A method of computationally selecting the best blocks of molecules and individual atoms for designing proteins has been developed by researchers at the University of Pennsylvania.

The algorithm draws inspiration from the behavior of proteins in making biological structures, such as viruses.

The researchers’ algorithm works in three steps that successively eliminate proteins that will not produce the right shape. The elimination criteria are based on traits like symmetry, periodicity of binding sites, and similarity to protein “motifs” found in nature.

The result is a list of thousands of candidate proteins. While still a daunting number, the algorithm makes the protein selection process merely difficult, rather than impossible, the researchers said.

The research team tested their algorithm by designing a protein that stably wrapped around a nanotube in a helix, and also provided a regular pattern on its exterior to which gold particles could be attached.

G. Grigoryan, Y. H. Kim, et al., Computational Design of Virus-Like Protein Assemblies on Carbon Nanotube Surfaces, Science, 2011; 332 (6033): 1071 [DOI:10.1126/science.1198841]