To pack a strand tight, make it a helix

Physicists in Italy and the United States have demonstrated that the best strategy for packing a string into the least space is to coil it into a helix. What’s more, the helices that fill space most efficiently in the team’s computer simulations closely resemble those that form naturally in proteins, report Amos Maritan of the International School for Advanced Studies (SISSA) in Trieste, Italy, and his colleagues. Their study appears in the July 20 Nature.

Reasoning based on chemistry and thermodynamics predicts that proteins will form helices. But the newfound, space-saving advantage of these geometries “might be one reason underlying the particular selection of the helices found in nature,” says Jayanth R. Banavar of Pennsylvania State University in University Park, a member of the research team.

Maritan, Banavar, and SISSA colleagues Cristian Micheletti and Antonio Trovato simulated molecular strands as beads connected by short tubes. The scientists’ computers then confined the faux molecules within the boundaries of a small cube or within more abstract, mathematically defined constraints.

Because a fatter thread might fill a space more thoroughly than a skinny one, the stringpacking algorithm inflated each tube as much as possible within the imposed limits. The computer program then made the plumped-up strands slither, wiggle, and gyrate into myriad configurations, tallying how efficiently each arrangement filled the allowed space. A comparison showed that the optimally packed computer-generated helices closely matched the specific twists and diameters of helices in proteins.

Might this packing advantage have anything to do with the shape of DNA’s double helix? Data from another study indicates it does, argue Andrzej Stasiak of the University of Lausanne in Switzerland and John H. Maddocks of the Swiss Federal Institute of Technology Lausanne in a commentary in the same journal.