Science Tips: Three Updates from the Weizmann Institute of Science
LEGO PROTEINS REVEALED
Self-assembling protein complexes based on a single mutation could provide scaffolding for nanostructures
When hemoglobin undergoes just one mutation, the protein complexes stick to one another, stacking like LEGO® blocks to form long, stiff filaments. These filaments, in turn, elongate the red blood cells found in sickle-cell disease. For over 50 years, this has been the only known textbook example in which a mutation causes such filaments to form. According to Dr. Emmanuel Levy and his group in the Weizmann Institute of Science’s Department of Structural Biology, LEGO-like assemblies should have formed relatively frequently during evolution. Could this assembly method be common, or even easy to reproduce? Their answer, which was recently published in Nature, may have implications for both biological research and nanoscience.
Hemoglobin and a fair number of other protein complexes are symmetrical: made of identical units. And since identical units are produced from the same gene, each genetic mutation is repeated multiple times in the complex. Mutations that create sticky patches and are repeated on opposite sides of the complex can induce the proteins to stack into long protein fibers. Unlike amyloid-like protein fibers, the complexes in these stacks do not change shape or unfold in order to assemble.
The stickiness occurs because the mutation substitutes an amino acid that is normally hydrophilic – “water-loving” – with one that is hydrophobic – “water-hating.” In the watery environment in which proteins move, the hydrophobic regions on those proteins prefer to interact with one another, like foam bubbles in water.
In their experiments, Dr. Levy and his group, including Hector Garcia-Seisdedos, Charly Empereur-Mot (who is now at Conservatoire National des Arts et Métiers in Paris), and Nadav Elad of the Weizmann Institute’s Chemical Research Support Department, began with an ultra-symmetric protein complex made up of eight identical units. They followed just one rule for mutating the proteins: switch a hydrophilic amino acid with a hydrophobic “sticky” one.
The team initially created proteins with three mutations to two different sticky amino acids and observed LEGO-like self-assembly in both cases. Investigating further, the team experimented with each mutation individually and found that one was capable of producing the long filaments all on its own.
So, are mutations that only do one thing – increase the stickiness of the protein’s surface – likely to induce LEGO-like self-assembly? The researchers mutated 11 additional proteins known to form symmetrical complexes – creating 73 different mutations in all – and produced them in Baker’s yeast cells, adding a fluorescent-protein label to enable their visualization. In 30 of these variations, the researchers observed behavior that suggested self-assembly: around half had stacked into long filaments, while the other half were bunched together in a more amorphous way, forming “foci.”
If the researchers reproduced the phenomenon of sickle-cell filaments so easily in the lab, why is it not seen more in biomedical research? Dr. Levy proposes two answers: firstly, the team revealed that naturally symmetric proteins evolved to have extra hydrophilic amino acids on their surfaces, thus minimizing the risk of self-assembly. Secondly, he says, researchers probably see more LEGO assemblies than they think: “Now that researchers know they can evolve so readily, they may look at foci more carefully and see many more biologically relevant LEGO-like assemblies.”
“Also,” Dr. Levy adds, “the filaments are produced so easily in the yeast, they could be good candidates for the scaffolding of nanostructures. Our study was unique in that it did not require complex computational design, nor did we have to scan thousands of mutations to find the one we wanted. We simply started with an existing structure and found a simple strategy to induce the assembly of filaments.”
Dr. Emmanuel Levy’s research is supported by the David and Fela Shapell Family Foundation INCPM Fund for Preclinical Studies; the Henry Chanoch Krenter Institute for Biomedical Imaging and Genomics; the Louis and Fannie Tolz Collaborative Research Project; the Richard Bar Laboratory; and Anne-Marie Boucher, Canada. Dr. Levy is the incumbent of the Recanati Career Development Chair of Cancer Research in Perpetuity.
THE BREAKING POINT
What happens at the moving edge of a crack?
It is said that a weak link determines the strength of the entire chain. Likewise, defects or small cracks in a solid material may ultimately determine the strength of that material – how well it will withstand various forces. For example, if force is exerted on a material containing a crack, large internal stresses will concentrate on a small region near the crack’s edge. When this happens, a failure process is initiated, and the material might begin to fail around the edge of the crack, which could then propagate, leading to the ultimate failure of the material.
What, exactly, happens right around the edge of the crack, in the area in which those large stresses are concentrated? Prof. Eran Bouchbinder of the Weizmann Institute of Science’s Department of Chemical Physics, who conducted research into this question with Dr. Chih-Hung Chen and Prof. Alain Karma of Northeastern University, Boston, explains that the processes that take place in this region are universal – they occur in the same way in different materials and under different conditions. “The most outstanding characteristic we discovered,” says Prof. Bouchbinder, “is the nonlinear relationship between the strength of the forces and the response taking place in the material adjacent to the crack. This nonlinear region, which most studies overlook, is actually fundamentally important for understanding how cracks propagate. Most notably, it is intimately related to instabilities that can cause cracks to propagate along wavy trajectories or to split, when one would expect them to simply continue in a straight line.”
By investigating the forces at play near the crack’s edge, Prof. Bouchbinder and his colleagues developed a new theory – published recently in Nature Physics – that will enable researchers to understand, calculate, and predict the dynamics of cracks under various physical conditions. This theory may have significant implications for materials physics research and for understanding the ways in which materials fail.
Islands of Softness
Exploring a different topic, in a paper that recently appeared in the Proceedings of the National Academy of Sciences of the United States of America (PNAS), Prof. Bouchbinder and a group of colleagues investigated the fundamental properties of the “glassy state” of matter.
The glassy state can exist in a broad range of materials if their liquid state is cooled quickly enough to prevent them taking on an ordered, crystalline state. Glasses are thus disordered, or amorphous, solids and include, for example, window glass, plastics, rubbery materials, and amorphous metals. Even though these materials are all around us and find an enormous range of applications, understanding their physical properties has been extremely challenging, owing, in large part, to the lack of tools for characterizing their intrinsically disordered structures and characterizing how these structures affect the materials’ properties.
Dr. Jacques Zylberg of Prof. Bouchbinder’s group, Dr. Edan Lerner of the University of Amsterdam, Dr. Yohai Bar-Sinai of Harvard University (a former PhD student of Prof. Bouchbinder’s), and Prof. Bouchbinder found a way to identify particularly soft regions inside glassy materials. These “soft spots,” which are identified by measuring the local thermal energy across the material, were shown to be highly susceptible to structural changes when force is applied. In other words, these soft spots play a central role when glassy materials deform and irreversibly flow under the action of external forces. The theory developed by the researchers thus brings us a step closer to understanding the mysteries of the glassy state of matter.
Prof. Eran Bouchbinder’s research is supported by the Rothschild Caesarea Foundation and Paul and Tina Gardner, Austin, TX.
NEW YEAR’S FOR RESEARCHERS
For one night, the Weizmann Institute of Science opens its doors to the public
Ever wanted to know how to fix a broken heart? What a scratch, pneumonia, and soil pollution have in common? Why insects could be the food of the future? Researchers’ Night at the Weizmann Institute of Science is an evening dedicated to science for everyone – to answering any and all questions about science.
Researchers’ Night has been taking place annually at the Weizmann Institute of Science since 2006, as part of the European Union Researchers’ Night event that takes place in hundreds of sites all over Europe. In Israel, it occurs within a nationwide framework of activities at academic research institutes and science museums and is supported by the Israeli Ministry of Science, Technology and Space. Researchers’ Night at the Weizmann Institute is organized by the Davidson Institute of Science Education, the Weizmann Institute’s educational arm.
This year’s Researchers’ Night theme is [email protected], and it will take place just one night before the eve of Rosh Hashana, the Jewish New Year. By opening its doors to the public, the Weizmann Institute of Science is hoping to help answer a big question: just what do all of its scientists do in their labs?
The public is invited to partake of lectures and hands-on sessions, exhibits and demonstrations, tours of labs, and a visit to the Clore Garden of Science. Nobel Laureate Prof. Ada Yonath will explain why some of the most amazing discoveries in medicine have been snatched from the brink of “bankruptcy;” Prof. Tzachi Pilpel will talk about evolution as you’ve never heard it before; Dr. Ulyana Shimanovich will speak about worms and mice and what they teach us; Prof. Dan Yakir will ask whether planting forests is the best way to alleviate global warming; Prof. Varda Rotter will give us a peek into the cancer genome; Prof. Eli Arama will talk about cells that commit suicide; and many other scientists will be present to speak about their latest forays into the forefront of global science.
The activities will commence at 17:00 (5:00 p.m.) on September 19, 2017, and continue until late in the evening in the auditoria, halls, and open spaces of the campus. The activities are suitable for children, youth, and adults. All the events and activities are free of charge, but some may require registration on the Davidson Institute’s website.