The Shape of Pathogenic Proteins

New details about structure and size of prion proteins reveal insights into infectivity.

Sep 1, 2007
Kelly Rae Chi
<figcaption>The prion consists of spiraling alpha helices (orange) and straight beta sheets (green). Credit: © Alfred Pasieka / Photo Researchers, Inc.</figcaption>
The prion consists of spiraling alpha helices (orange) and straight beta sheets (green). Credit: © Alfred Pasieka / Photo Researchers, Inc.

Prions infect cells and turn good proteins bad by inducing structural overhaul. How these proteins replicate is not known, but what is it about their structural elements and sizes that make them infectious?

Structure and infectivity of these proteins has been difficult to analyze using conventional methods, because the proteins are sticky and insoluble, says Claudio Soto of the University of Texas Medical Branch in Galveston, who was not an author on the studies featured here. These three Hot Papers each use different techniques to give detailed looks into the size, structure, and infectivity of different prion proteins. Though the papers are quite different from each other, they are "exemplary" in that they offer "new ways of looking at infectivity," says Andy Hill at the University of Melbourne in Australia, who was also not involved in the studies.

Secondary structure findings

In a June 2005 issue of Nature, David Eisenberg and his group at the University of California, Los Angeles, provided detailed structural data on the smallest cross-β spines of amyloid-like fibrils of yeast prion protein Sup35.1 The group used X-ray microcrystallography to find stacked β-sheets bonded by tightly interlocking side chains. According to the authors, the study offered a picture of stability of amyloid fibrils, whose formation is a necessary event for prion infectivity.

In the same issue of Nature, Roland Riek's group from the Salk Institute in La Jolla, Calif., looked at the importance of such formation in infection. Using quenched hydrogen-exchange NMR and solid-state NMR, the authors interrupted the secondary structure of the HET-s yeast prion protein by making mutants with proline residues (a common β-strand breaker).2 Without β-sheet structural elements, the prion was not infectious, as measured by its involvement in a program cell death phenomenon called heterokaryon incompatibility. "The basis [of infectivity] goes back to the structure, which is why the structural studies are important," says Riek, who is now at the Swiss Federal Institute of Technology.

Hill says it's "nice that, using two different methods and two different proteins," the two papers came out with similar structures for the amyloid fibrils. Eisenberg and colleagues have since found that amyloid fibrils from different proteins involved in other neurodegenerative diseases, such as Alzheimer and Parkinson diseases, also contain this cross-β spine, "suggesting that common structural features are shared by amyloid diseases at the molecular level," the authors note in a follow-up study.3

Size matters

In the third Hot Paper, using flow field-flow fractionation to tease apart mammalian prion protein particles of different sizes, Byron Caughey and his group at NIH's Rocky Mountain Laboratories in Hamilton, Mont., found that intermediate-sized aggregates were the most infectious.4 Caughey says that when his group first looked at the results, they found it "quite striking" that infectivity was not associated with extremely small oligomers or monomers of prion protein. That was important, Caughey says, "because it had long been argued that the infectious unit could even be a prion protein monomer."

Hill says the findings have implications for protein misfolding diseases such as Alzheimer disease, because they suggest "that strategies aimed at breaking up the fibrils could unleash these smaller, toxic oligomers."

Caughey and colleagues have initiated cell culture studies to identify the most neurotoxic particle sizes, with the ultimate goal of doing this study in vivo. They are trying to better visualize and determine the chemical composition of the most infectious protein units. "It's been tough to see them," he says. "They're small and not uniform in size and shape." Also, the particles with the most infectivity make up only a tiny fraction of total protein content, so the challenges of getting enough material to work with "has impeded subsequent progress," Caughey adds.

Soto and colleagues came up with a way to make more mammalian prion protein material in vitro using brain homogenates. Called protein misfolding cyclic amplification (PMCA), the method will aid prion structure studies.5 With more prion proteins to work with, "we can really go down to the molecular level and study the basis of infectivity in vitro," Riek says.

Soto's group has since amplified misfolded prion protein from even more minute starting quantities of misfolded prion protein from hamster brain, supporting the long-held view that these proteins are infectious without the help of nucleic acids or other materials.6 After two years, an independent group, led by Surachai Supattapone at Dartmouth Medical School in Hanover, NH, was able to reproduce the PMCA technique.7

Riek says more structural data are on the horizon, while others are working to carry this work into physiologically relevant conditions. "We're interested in how we can prevent the growth of these fibrils and how can we break them up," Eisenberg says.

References

1. R. Nelson et al., "Structure of the cross-β spine of amyloid-like fibrils," Nature, 435:773-8, 2005. (Cited in 170 papers) 2. C. Ritter et al., "Correlation of structural elements and infectivity of the HET-s prion," Nature, 435:844-8, 2005. (Cited in 82 papers) 3. M.R. Sawaya et al., "Atomic structures of amyloid cross-beta spines reveal varied steric zippers," Nature, 447:453-7, 2007. 4. J.R. Silveira et al., "The most infectious prion protein particles," Nature, 437:257-61, 2005. (Cited in 82 papers) 5. J. Castilla et al., "In vitro generation of infectious scrapie prions," Cell, 121:195-206, 2006. 6. P. Saá et al., "Ultra-efficient replication of infectious prions by automated protein misfolding cyclic amplification," J Biol Chem, 281:35245-52, 2006. 7. N.R. Deleault et al., "Formation of native prions from minimal components in vitro," Proc Nat Acad Sci, 104:974-6, 2007.

Data derived from the Science Watch/Hot Papers database and the Web of Science (Thomson ISI) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age.

R. Nelson et al., "Structure of the cross-β spine of amyloid-like fibrils," Nature, 435:773-8, 2005. (Cited in 170 papers) C. Ritter et al., "Correlation of structural elements and infectivity of the HET-s prion," Nature, 435:844-8, 2005. (Cited in 82 papers) J.R. Silveira et al., "The most infectious prion protein particles," Nature, 437:257-61, 2005. (Cited in 82 papers)