Snakes on a plane: This atomic-resolution simulation of a two-dimensional peptoid nanosheet
reveals a snake-like structure never seen before. The nanosheet’s layers include a water-repelling
core (yellow), peptoid backbones (white), and charged sidechains (magenta and cyan). The right
corner of the top layer of the nanosheet has been “removed” to show how the backbone’s alternating
rotational states give the backbones a snake-like appearance (red and blue ribbons). Surrounding
water molecules are red and white. (Credit: Ranjan Mannige, Berkeley Lab)
Computer sims and microscopy research at Berkeley Lab yield first atomic-resolution structure of a peptoid nanosheet
(October 7, 2015) Scientists aspire to build nanostructures that mimic the complexity and function of nature’s proteins, but are made of durable and synthetic materials. These microscopic widgets could be customized into incredibly sensitive chemical detectors or long-lasting catalysts, to name a few possible applications.
But as with any craft that requires extreme precision, researchers must first learn how to finesse the materials they’ll use to build these structures. A discovery by scientists from the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab), and reported Oct. 7 in the advance online publication of the journal Nature, is a big step in this direction.
The Molecular Foundry scientists who helped discover a new nano design rule.
From left, Ellen Robertson, Alessia Battigelli, Ron Zuckermann, Caroline Proulx,
Stephen Whitelam, and Ranjan Mannige. (Credit: Roy Kaltschmidt, Berkeley Lab)
The scientists discovered a design rule that enables a recently created material to exist. The material is a peptoid nanosheet. It’s a flat structure only two molecules thick, and it’s composed of peptoids, which are synthetic polymers closely related to protein-forming peptides.
The design rule controls the way in which polymers adjoin to form the backbones that run the length of nanosheets. Surprisingly, these molecules link together in a counter-rotating pattern not seen in nature. This pattern allows the backbones to remain linear and untwisted, a trait that makes peptoid nanosheets larger and flatter than any biological structure.
The Berkeley Lab scientists say this never-before-seen design rule could be used to piece together complex nanosheet structures and other peptoid assemblies such as nanotubes and crystalline solids.
A simulation of a peptoid nanosheet, shown first from a top-down view with the peptoid
backbones colored to highlight their snake-like structure. The view then rotates to the side,
and finally transitions to an all-atom representation. (Credit: Ron Zuckermann and
Ranjan Mannige, Berkeley Lab)
What’s more, they discovered it by combining computer simulations with x-ray scattering and imaging methods to determine, for the first time, the atomic-resolution structure of peptoid nanosheets.
“This research suggests new ways to design biomimetic structures,” says Steve Whitelam, a co-corresponding author of the Nature paper. “We can begin thinking about using design principles other than those nature offers.”
Whitelam is a staff scientist in the Theory Facility at the Molecular Foundry, a DOE Office of Science user facility located at Berkeley Lab. He led the research with co-corresponding author Ranjan Mannige, a postdoctoral researcher at the Molecular Foundry; and Ron Zuckermann, who directs the Molecular Foundry’s Biological Nanostructures Facility. They used the high-performance computing resources of the National Energy Research Scientific Computing Center (NERSC), another DOE Office of Science user facility located at Berkeley Lab.