Nature's masonry: The first steps in howthin protein sheets form polyhedral shells22 December 2015

This illustration shows how hexagonal bacterial proteins(shown as ribbon-like structures at right and upper right)self-assemble into a honeycomb-like tiled pattern (centerand background). This tiling activity, seen with an atomic-resolution microscope (upper left), represents the earlyformation of polyhedral, soccer-ball-like structuresknown as bacterial microcompartments or BCMs thatserve as tiny factories for a range of specializedactivities. Credit: Berkeley Lab

Scientists have for the first time viewed howbacterial proteins self-assemble into thin sheetsand begin to form the walls of the outer shell fornano-sized polyhedral compartments that functionas specialized factories.

The research, led by researchers at the U.S.Department of Energy's Lawrence BerkeleyNational Laboratory (Berkeley Lab) and MichiganState University in collaboration with the Universityof Liverpool, provides new clues for scientistsseeking to use these 3-D structures as

"nanoreactors" to selectively suck in toxins or churnout desired products.

The new insight may aid scientists who seek to tapthis natural origami by designing novelcompartments or using them as scaffolding for newtypes of nanoscale architectures, such as drug-delivery systems.

"We have a new clue in understanding nature'sinner-cell architecture," said Cheryl Kerfeld, aBerkeley Lab structural biologist who is co-corresponding author on the study. Her researchgroup at Berkeley Lab specializes in the structureand inner workings of these tiny compartments,known as bacterial microcompartments or BMCs.Kerfeld holds joint appointments with BerkeleyLab's Molecular Biophysics and IntegratedBioimaging (MBIB) Division and Michigan StateUniversity.

"We usually only get to see these structures afterthey form, but in this case we're watching themassemble and answering some questions abouthow they form," Kerfeld said. "This is the first timeanyone has visualized the self-assembly of thefacets, or sides, of the microcompartments. It's likeseeing walls, made up of hexagonally shaped tiles,being built by unseen hands."

The study was published online Nov. 30 in NanoLetters.

Several models had been proposed for how thesecompartments are built from scratch inside bacteriaby proteins, and there were many open questionsabout the construction process.

Researchers combined X-ray studies of the 3-Dstructure of a protein that resembles a hexagonwith imaging by an atomic-force microscope toreveal how the hexagons arrange in a honeycombpattern in the microcompartment's walls.

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Markus Sutter, a Berkeley Lab scientist who is thestudy's lead author, determined the 3-D structure ofthe basic building block protein at the AdvancedLight Source at Berkeley Lab using crystallizedsamples. Patterns produced when X-rays struck theprotein crystals provided key details about theprotein's shape, at the scale of individual atoms."That gave us some exact dimensions," Sutter said,which helped to interpret the microscope images. "Italso showed us that hexagons had distinctsidedness: One side is concave, the other side isconvex."

Liverpool's atomic-force microscope, BioAFM,showed that individual hexagon-shaped proteinpieces naturally join to form ever-larger proteinsheets in a liquid solution. The hexagons onlyassembled with each other if they had the sameorientation—convex with convex or concave withconcave.

"Somehow they selectively make sure they end upfacing the same way," Kerfeld added.

The study also found that individual hexagon-shaped pieces of the protein sheet can dislodgeand move from one protein sheet to another. Suchdynamics may allow fully formed compartments torepair individual sides.

Markus Sutter, a Berkeley Lab scientist, determined the3-D atomic structure of a bacterial protein that self-assembles into honeycomb-patterned sheets using X-rays at beamline 5.0.1 (pictured here) at Berkeley Lab's

Advanced Light Source. Credit: Roy Kaltschmidt/BerkeleyLab

The protein sheets studied were not viewed insideliving bacteria, though the conditions of themicroscope experiment were designed to mimicthose of the natural bacterial environment. "Wethink this is what goes on when thesecompartments assemble inside the microbe,"Kerfeld said.

Some studies have proposed that the protein shellof microcompartments might be several layersthick. However, this study suggests that the shellfacets are composed of a single protein layer.Sutter said this makes sense: The compartmentsare known to selectively allow some chemicalexchanges between their contents and their outsideenvironment, and a thicker shell could complicatethese exchanges.

The exact mechanism for this chemical exchange isnot yet well-understood. This and other mysteriesof the microcompartments can hopefully beresolved with follow-up studies that seek tochronicle the complete assembly process, theresearchers said.

Fully-formed 3-D microcompartments have asoccer-ball-like geometry that incorporatespentagon-shaped protein structures known aspentamers, for example, that were not included inthe latest study.

"The holy grail is to see the structure and dynamicsof an intact shell, composed of several differenttypes of hexagonal proteins and with the pentagonsthat cap its corners," Kerfeld said.

It's possible that simply adding these pentamers tothe protein sheets from the latest experiment couldstimulate the growth of a complete 3-D structure,but Kerfeld added, "I wouldn't be surprised if there'smore to the story."

Once more is learned about themicrocompartments, it's conceivable they could beused to concentrate the production of beneficial

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enzymes, organize them to produce an orderedsequence of chemical reactions, or to removeparticular toxins from the surrounding environment,she said.

More information: Markus Sutter et al.Visualization of Bacterial Microcompartment FacetAssembly Using High-Speed Atomic ForceMicroscopy, Nano Letters (2015). DOI:10.1021/acs.nanolett.5b04259

Provided by Lawrence Berkeley NationalLaboratoryAPA citation: Nature's masonry: The first steps in how thin protein sheets form polyhedral shells (2015,December 22) retrieved 13 October 2021 from https://phys.org/news/2015-12-nature-masonry-thin-protein-sheets.html

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