Clinging for Dear Life

English
 
Xeroderma pigmentosum is a rare hereditary disease in which sun-damaged skin is unable to mend itself. Its sufferers run a risk of skin cancer that is 5,000 times higher than normal.
 
Ten years ago, scientists discovered that the genetic defect behind one form of this disease, known as xeroderma pigmentosum variant (XPV), is a mutant version of an enzyme called DNA polymerase eta, which allows the cell to tolerate sun-induced DNA damage without removing this damage from the DNA molecule. In new research published in the Proceedings of the National Academy of Sciences (PNAS), USA, Prof. Zvi Livneh and research student Omer Ziv of the Biological Chemistry Department reveal how XPV cells manage to survive despite having this mutated enzyme – and at what cost.
 
With help from Nicholas Geacintov of New York University, and Satoshi Nakajima and Akira Yasui of Tohoku University, Japan, the researchers found that at least three other repair enzymes fill in when the mutated version cannot function. Yet even this combined effort of the three substitutes – DNA polymerases iota, kappa and zeta – only manages to do part of the job, increasing the risk of DNA errors 10- to 20-fold. “What’s fascinating about these findings,” says Livneh, “is that they represent an extreme example of the biological drive to preserve life, even when the price is a heavy load of genetic mutation and a high risk of cancer.”
 
Prof. Zvi Livneh’s research is supported by the Helen and Martin Kimmel Institute for Stem Cell Research; the estate of Lore F. Leder; and Esther Smidof, Switzerland. Prof. Livneh is the incumbent of the Maxwell Ellis Professorial Chair in Biomedical Research.
Life Sciences
English

Turning to Bone

English

Profs. Stephen Weiner and Lia Addadi and Julia Mahamid. Bone formation

 

 

 

 

 

 

 

 

 

 

 

In the search for new and better materials, many a scientist has turned to the study of living organisms. Generally these studies have focused on such tissues as bone or shell – complex mixtures of minerals, proteins and sugars that result in hard, strong, fracture-resistant materials. Recent research in the Institute's Structural Biology Department has shown that bones and shells share similar formation processes.

Bone and shell are composite materials in which the mineral component forms within a framework of soft macromolecules such as proteins. The framework is essentially a "mold" that directs the mineral formation. Bone grows continuously, layer by layer; but, unlike shell, it also undergoes constant remodeling. This makes it hard for scientists studying bone to distinguish new material from old, much less to trace the process by which bone is formed. Because of this difficulty, conflicting theories have arisen as to the mechanisms of bone formation. Many scientists thought that the minerals precipitate directly from a solution in the way that stalactites and stalagmites grow from elements dissolved in water. But findings published in the 1960s already hinted at the possibility that a different process was at work.

Ten years ago, research in a group headed by Profs. Lia Addadi and Stephen Weiner of the Institute's Structural Biology Department confirmed these earlier observations for shells. They showed that organisms first produce packets of amorphous material (unorganized material, as opposed to the ordered organization of crystal). These packets are transferred from the inside of cells to the building site – the spot where the mineralized tissue eventually forms. There, the packets undergo structural changes that turn them into a hard crystal. This observation triggered widespread interest in amorphous precursor mineral phases, and many different invertebrate mineralization processes were investigated.

Addadi and Weiner revealed this process in sea urchin spines, and their findings have been joined by a body of global research confirming that this method of construction is common to many different invertebrates that have shells, spines or other hard body structures. Addadi: "The original idea of precipitation from solution would require huge quantities of liquid to flow from inside the mollusk to the outside of its body. Transferring the materials in solid form – 'bricks and cement' – is a much more energy-efficient way of doing things."

While the issue has been more or less settled for the shells of invertebrates, the question of how vertebrate bones are formed remained unresolved. This is partly because of the difficulty inherent in attempting to observe a substance with no fixed location that exists for only a fleeting stage of growth. Recently, however, research student Julia Mahamid, together with Addadi and Weiner, found a biological system that enabled them to follow bone formation step by step and identify the processes taking place at each stage. This system is the fin of a small aquarium denizen called a zebrafish. The zebrafish fin bones, which continue to grow throughout the fish's lifetime, form a sort of fan. Each bony rib of the fan is composed of segments, and the segments nearest the fin's edge are always the newest. Thus the segments can be studied as a sort of timeline of bone formation. In addition, zebrafish, which live in relatively cold water, grow slowly, and the leisurely pace of their bone development enabled the scientists to get a good look at each stage.

Using both light microscopy and scanning electron microscopy, the scientists succeeded in observing abundant spherical parcels of amorphous mineral material in the newly formed fin bone. Their findings, which appeared in the Proceedings of the National Academy of Sciences (PNAS), USA, showed that about half the mineral makeup of the newer bone segments is amorphous – a fraction that dwindles in the segments farther away from the fin edge. Their observations suggest that the amorphous material does, indeed, turn to crystal over time.

These findings are shedding light on a number of scientific mysteries, giving scientists a unique perspective on how the hard substances in our body – bones and teeth – are formed. The scientists hope that a deeper understanding of these biological processes may, in the future, help researchers find cures for diseases involving faulty bone development or repair.

Prof. Lia Addadi's research is supported by the Clore Center for Biological Physics; the Ilse Katz Institute for Material Sciences and Magnetic Resonance Research; the Helen and Martin Kimmel Center for Nanoscale Science; the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; and the Carolito Stiftung. Prof. Lia Addadi is the incumbent of the Dorothy and Patrick Gorman Professorial Chair.

Prof. Stephen Weiner's research is supported by the Kekst Family Center for Medical Genetics; the Helen and Martin Kimmel Center for Archaeological Science; the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; and George Schwartzman, Sarasota, FL. Prof. Weiner is the incumbent of the Dr. Walter and Dr. Trude Borchardt Professorial Chair in Structural Biology.

 

Scanning electron microscope images of bone crystalizing: Bone development in zebra fish.

 

 

 

 

 

 

 

 

 

(l-r) Profs. Stephen Weiner and Lia Addadi and Julia Mahamid. Like shell, like bone
Chemistry
English

Winning Design

English
 

 

Tawfik and Khersonsky. Evolutionary design

 

 

 

 

 

 

 

 

 

 

 

 

Have humans beaten nature at its own game? The attempt required a team of scientists using some of the most advanced computer-aided design and biological engineering techniques available, as well as one very ancient technique – evolution. Recently scientists created a new enzyme that performs a function unknown in nature. Compared to the millions of years nature takes to come up with a new enzyme, the scientists managed this feat in hardly any time at all.

 
Enzymes are biological catalysts – dynamic molecular machines that initiate chemical reactions in the body and speed them up millions of times. Each of the tens of thousands of enzymes in the human body is constructed of a long string of amino acids (the building blocks of proteins), and their sequence determines the intricate three-dimensional shape they assume as the string folds in and around itself. Whereas nature fashions enzymes to fit different functions by adapting basic designs over millions of years, the scientists started from scratch with a problem: How to speed up a common chemical reaction in which a proton (a positively-charged hydrogen atom) is removed from carbon, breaking the tough carbon-hydrogen bond. No existing natural enzyme performs this task with the particular substrate the team applied.
 
Two designs for a synthetic enzyme

 

The team began with the design of the active site – a string of amino acids responsible for the chemical reactions that take place. They then turned their attention to the rest of the enzyme – its backbone. This entailed generating a sequence for the 200 amino acids in its protein structure. While in theory there are a nearly infinite number of ways to arrange the 20 types of amino acid into strings of 200, in practice only a limited number can yield a structure, and thus a mode of action, capable of performing the task.
 
To identify possible sequences for their enzyme, Prof. David Baker of the University of Washington, Seattle, used novel computational methods to scan tens of thousands of computer-designed sequences. Eventually he and his team identified 60 that could potentially facilitate the chemical reaction, and these he tested further to see if they would work in biological systems.
 
Real enzyme matches its computer design

 

Of the 60 sequences tested, eight showed signs of biological function and only three made it to a “final round” of the scientists’ challenge by showing a detectable level of activity. At this stage, the enzymes had moved from the computer “drawing board” to the bioengineering lab. Drs. Orly Dym and Shira Albeck of the Weizmann Institute’s Structural Biology Department solved the structure of one of the final contenders, confirming that the structure of the enzymes created was essentially identical to the predicted computational design.
 
Yet even with the benefit of the most advanced computer and bioengineering technologies, the winning enzymes could not compete with the speed and efficiency of their naturally evolved counterparts. At this point, Prof. Dan Tawfik and research student Olga Khersonsky of the Biological Chemistry Department entered the picture. In a twist on natural evolution, they have found that the principles of random mutation and natural selection can be applied in the lab. Test-tube grown enzymes are mutated, and the most efficient ones are selected to undergo further rounds of mutation and selection.
 
At the end of only seven rounds of test-tube evolution, the enzymes’ efficiency had increased 200-fold over those created from the computer design template, and the new enzyme-assisted chemical reaction rates were a million times those taking place with no enzyme at all. While the designed/evolved enzymes are still much slower than their natural counterparts, a comparison of the evolved enzymes to their computer-designed ancestors showed how adjustments to the enzyme structure can increase its efficiency: One near the active site improved the reaction rate, while others increased the molecules’ flexibility, allowing the enzyme to detach faster upon completing a step in the reaction.
 
“The combination of computational design and molecular in vitro evolution opens up new horizons in the creation of synthetic enzymes,” says Tawfik. “Reproducing the breathtaking performance of natural enzymes is a daunting task; but thanks to this research, we have gained a better understanding of the structure of enzymes as well as their mode of action. This, in turn, will allow us to design and create enzymes that nature itself has not ‘thought’ of. The possibilities are nearly endless: neutralizing poisons, developing medicines and future applications that we ourselves have not yet imagined.”  
 
Prof. Dan Tawfik’s research is supported by the J&R Center for Scientific Research; the Wolfson Family Charitable Trust; the Jack Wolgin Prize for Scientific Excellence; Mr. and Mrs. Yossie Hollander, Israel; Rowland Schaefer, New York, NY; and the estate of Fannie Sherr, New York, NY.

 

 
 

 

 

 

The enzyme’s structure (blue), revealed via X-ray crystallography, closely matches its computer design (gray). The yellow structure in the center is the substrate molecule the enzyme acts upon
Life Sciences
English

The Other Half

English

Barkai, Shilo and Ben-Zvi. Regeneration in proportion

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

More than 80 years ago, the German scientist Hans Spemann conducted a famous experiment that laid the foundations for the field of embryonic development – research that would later earn him a Nobel Prize. After dividing a salamander embryo in half, Spemann noticed that one half – the ventral half that gives rise to the salamander’s “belly” – starts to wither away. However, the “back” (dorsal) half, from which the head, brain and spinal cord arise, continues to grow, regenerating the missing belly and developing into a complete – though small – embryo. Spemann then conducted another experiment. This time, he removed a few cells from the back half of one embryo and transplanted them into the belly half of a different embryo. To his surprise, the result was a Siamese twin embryo with an extra head generated from the transplanted cells. Although the resulting embryo was smaller than normal, all its tissues and organs developed in the right proportions, and they functioned properly.

 
How does this happen? How exactly is half an embryo able to maintain its tissues and organs in the correct proportions even though it’s smaller than normal? Despite the attention this question has received in the ensuing years, it has remained unanswered – until now. Four scientists – Prof.  Naama Barkai and research student Danny Ben-Zvi of the Molecular Genetics Department, and Prof. Ben-Zion Shilo, Dean of the Faculty of Biochemistry, together with Prof. Abraham Fainsod of the Hebrew University-Hadassah School of Medicine, Jerusalem – have finally discovered the mechanisms involved.
 
The scientists knew that the growth and development of cells and organs within the embryo are linked to a unique group of substances called morphogens. Morphogens are produced in one particular area of the embryo, and from there they spread throughout the entire embryo in varying concentrations. Scientists have begun to realize that the different morphogen levels themselves contain information, and that the fate of embryo cells – the specific type of tissue and organ they are eventually going to develop into – is determined by the amount of the morphogen they come into contact with. But how those concentrations are determined in a way that maintains organ proportions is a question that remained unanswered.

 

 

 

Tadpole with two heads
 
The idea for the present research came about when Barkai and her colleagues developed a mathematical model to describe the interactions that occur within an embryo’s gene networks. In this model, the dorsal side contains all the morphogens needed for organ development, while the ventral side has none.
 
The data suggest that morphogens become unevenly distributed in the embryo in a different way than previously thought. The team predicted that an inhibitor molecule secreted from a localized source on one side of the embryo binds the morphogen and acts as a type of ferry for “shuttling” it over to the other side. According to the model, the interactions between the two substances determine the morphogen concentration in any location, enabling the embryo to preserve the relative proportion of its organs. Barkai and her team then tested and validated their predictions in experiments conducted on frog embryos.
 
The importance of the role of these morphogenic substances, as well as their mechanism of action, is evidenced by the fact that they have been conserved throughout evolution: Variants can be found in species ranging from worms to fruit flies to higher species, including humans. Understanding the processes that govern embryonic cell development, therefore, could have many implications. For example, it could lead, in the future, to the development of new ways to repair injured tissue.
 

A Piece of Work

 

When Hamlet said “What a piece of work is man,” he had no idea how right he was: The human body has trillions of living cells that make up several hundred tissues and organs. Each one of these cells is more sophisticated than the most powerful computer; the transportation and communications systems in a single cell are more complex than those of a mid-sized city. And all of this is run by 30,000 genes that manage everything from embryonic development to aging and death.
 
How is this colossal undertaking coordinated? What are the basic rules governing life? Life scientists have struggled with these questions for decades, but they have recently been joined by physicists who, until a few years ago, were mainly investigating phenomena in non-living materials. Physicists such as Prof. Naama Barkai bring to this effort a new set of research tools and new approaches, many of them particularly well adapted to sorting out complex systems. No less importantly, they come with new ways of thinking that lead them to ask novel questions and follow fresh paths of inquiry.
 
Much of this work involves mapping such large, tangled, multi-scale gene networks as those that manage embryonic development, intercellular communication or the processes within cells that are involved in diseases such as cancer. As the models of these networks become ever more precise, they provide scientists with ever better methods for approaching those basic questions about the nature of life, as well as practical tools for biomedical applications.
 
 Prof. Naama Barkai’s research is supported by the Kahn Family Foundation for Humanitarian Support; the Helen and Martin Kimmel Award for Innovative Investigation; the Carolito Stiftung; the Minna James Heineman Stiftung; the PW-Iris Foundation; and the PW-Jani. M Research Fund.
 
Prof. Ben-Zion Shilo’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the J&R Center for Scientific Research; the Jeanne and Joseph Nissim Foundation for Life Sciences Research; and the Mary Ralph Designated Philanthropic Fund. Prof. Shilo is the incumbent of the Hilda and Cecil Lewis Professorial Chair of Molecular Genetics.

 

(l-r) Prof. Naama Barkai, Prof. Ben-Zion Shilo and Danny Ben-Zvi. All in proportion
Life Sciences
English

Right On Target

English
 

Dr. Avraham Yaron. biological GPS for growing axons

 
 
 
 
 
 
 
 
 
 
 
 

It’s an electrical engineer’s nightmare: a complex “wiring system” of nerve fibers that connects more than 100 billion nerve cells in the brain to one another and to the rest of the nervous system. These nerve fibers, called axons, are often up to several feet in length, and they must grow out to their targets bit by bit, making their way through surrounding tissues and around a myriad of obstacles. How do the growing axons find their intended connection without getting lost along the way?

Dr. Avraham Yaron of the Biological Chemistry Department is trying to elucidate the mechanisms that guarantee the proper wiring of these billions of nerve cells during the development of the fetal nervous system. Such discoveries could one day lead to ways of alleviating or curing ailments tied to nerve fiber injury or wiring defects.

Over the past decade, it’s become clear that growing axons are guided by a sort of biological “GPS system.” It’s not satellite signals that help the axons navigate their way around the nervous system, however, but chemical guidance cues. These cues can work in two ways to ensure that the axons “take the right road”: Their signals can be attractive – like neon lights luring the axons toward the right target; or they can be repellent – acting as “roadblocks” to prevent axons from making a wrong turn. Scientists have already described several major families of guidance molecules, each of which seems to work in a different way. But little is known about the way this elaborate chemical guidance system actually operates.

Yaron mainly researches the guidance of sensory axons – those nerve extensions that transmit sensations of pain, heat and touch from the skin to the brain. These axons are guided in their development by an important family of guidance cues, the semaphorins. However, just as in GPS systems, it appears that axons need a “receiver” to detect the guidance signals. The axons’ receivers are protein receptors located on their outer surface.



During his postdoctoral studies, Yaron had identified two members of the family of sensory axon receptors – the plexin family – which are essential for receiving the signals from the semaphorins. Now, in his lab in the Weizmann Institute, he seeks to further clarify how signals are transmitted through these receptors. He also aims to identify new guidance cues and investigate how all the different cues are integrated.



To do this, Yaron and his team employ two complementary approaches. In the first, conducted in lab cultures, they can manipulate and expose the axons to different guidance cues, observing their effects at a basic level. They also use mouse models, in which they try to validate their in vitro results, as well as controlling various additional factors to analyze the behavior of axons in a more complex, real-life setting. So far, preliminary results suggest that the semaphorin guidance cues and plexin receptors work together to transmit repelling signals. This is evident from the scientists’ observations that in the presence of the receptor, the axons grow in stereotypical fashion toward their correct targets, but when the scientists knock out the receptor genes, effectively removing the roadblock, the axons lose their way and grow in all different directions.



One particular project in Yaron’s lab has clinical relevance: It focuses on diabetes neuropathy. In people with diabetes, as well as some cancer patients treated with chemotherapy, sensing axons may become disconnected from their targets, leading to severe pain in the extremities. Yaron is trying to discover whether the developmental guidance molecules might play a role in these pathological conditions. If this is indeed the case, understanding how they work could provide a novel solution to these conditions, for which there is currently no effective treatment.



Recent evidence suggests that chemical guidance cues play a role in many additional processes – for example, in the growth of new blood vessels, cell migration in the immune system and cancer. Thus, in addition to addressing significant basic research questions on axon guidance, Yaron’s discoveries could also yield insights in many other fields of biology.   

 
Sensory axons in a transgeneic mouse
 
 

 

 

 

 

 

 

 

 

 

On Track

 

 

Born in Jerusalem, Dr. Avraham Yaron earned a B.Sc. in biology from the Hebrew University of Jerusalem in 1993. He then went on directly to a Ph.D. program in the Hebrew University-Hadassah School of Medicine Department of Immunology and received his degree in 1999. “Ever since childhood, I have always been interested in science, yet it was only during my Ph.D. that it became absolutely clear to me that I wanted to pursue science as a career and have my own lab,” says Yaron. His Ph.D. thesis earned him the 2000 Amersham/Pharmacia Biotech prize for young scientists awarded by Science magazine. Yaron then conducted postdoctoral studies in the laboratory of Prof. Marc Tessier-Lavigne at the University of California, San Francisco, where he was first introduced to research on the mechanisms of axon guidance and made his discovery of the plexin receptors. Yaron joined the Weizmann Institute as a senior scientist in 2006.

 

Dr. Avraham Yaron’s research is supported by the Nella and Leon Benoziyo Center for Neurosciences; the Estelle Funk Foundation President’s Fund for Biomedical Research; the Dr. Ernst Nathan Fund for Biomedical Research; the Robert Rees Applied Research Fund; and the Henry S. and Anne S. Reich Research Fund for Mental Health.

 
Dr. Avraham Yaron. sensory neuron guidance system
Life Sciences
English

Safety Catch

English
 

Gradus, Fainzilber and Yudin. Nerve signals by rail

 
 
 
 
 
 
 
 
 
 
 
 

 

Sensations like pain or heat travel in a fraction of a second along the extensions – the axons – of nerve cells, an impressive feat considering that axons such as those that run from the base of the spine all the way down the leg can reach over a meter in length – 40,000 times longer than their width. But when a nerve cell is injured somewhere along its length, a different kind of signal must be sent – one that more closely resembles a mechanical railway car than an electrical impulse. Thus getting the call for help back to the remote cell nucleus is something like sending a message by boxcar to headquarters halfway across the state.



Prof. Michael Fainzilber of the Weizmann Institute’s Biological Chemistry Department has been investigating emergency transportation systems in nerve cells. His previous research had shown that this information is packaged in a molecular “railcar” complex: A motor protein called dynein works together with importins to move the complex along microtubule “tracks.” The importins are nuclear import proteins that ferry various molecules in and out of the nucleus, thus delivering the message straight to the command center of the cell.



Fainzilber and research students Dmitry Yudin and Shlomit Hanz, working in collaboration with the group of Dr. Jeffrey Twiss (Nemours Institute, Wilmington, DE) wanted to know what controls the triggering of this system right after injury, as it gears up for the long journey. Using rat sciatic nerves as their model, the scientists looked for changes in the molecular makeup up of the nerve cell material around the injury site. Their findings recently appeared in Neuron.



To their surprise, they found molecules that until now were believed to exist only around the cell nucleus. These molecules, known collectively as the Ran system, are found in two main configurations, one inside the nucleus and one outside, and they help to control the importins’ molecule-ferrying activities through gates in the walls surrounding the nucleus. The research team found that the nuclear form of Ran sits on the axonal complex, preventing importins from coupling with the rest of the transport machinery. When damage occurs, Ran is switched to the second configuration, which causes it to disengage. The waiting importin can then plug into the machinery, and the expedition gets under way.



The researchers believe the Ran system works like a safety catch – preventing unwanted activation of the alarm machinery until an actual emergency occurs, and then switching quickly to allow efficient triggering of the system. Understanding this mechanism may help devise ways by which nerve cells can be induced to repair damage and may aid in developing treatments for nerve injury in the future.




Prof. Michael Fainzilber’s research is supported by the M.D. Moross Institute for Cancer Research; the Nella and Leon Benoziyo Center for Neurological Diseases; the Dr. Miriam and Sheldon G. Adelson Medical Research Foundation; the PW-Bes Foundation; the European Union FP6 NEST Axon Support project; the J&R Center for Scientific Research; the Minerva Foundation; and the USA-Israel Binational Science Foundation. Prof. Fainzilber is the incumbent of the Chaya Professorial Chair for Molecular Neuroscience.

 

 

 

(l-r) Tal Gradus, Prof. Michael Fainzilber and Dmitry Yudin. Gearing up
Life Sciences
English

Watch for Flying Elephants

English
 

Dr. Michal Sharon. Scientist and mother

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Dumbo may have been ridiculed by his fellow elephants, but his flying skills have been evoked to describe a revolutionary advance in protein science. John Fenn, who received the 2002 Nobel Prize in Chemistry for inventing a technique that makes it possible to study the structure of large, bulky proteins by flying them in the air, said in his prize acceptance speech that his approach provided “wings for molecular elephants.”
 
Dr. Michal Sharon of the Weizmann Institute’s Biological Chemistry Department is taking this technique a step further: She is providing wings for entire “herds” of molecular elephants. She launches not just individual proteins but entire protein complexes into the air in order to clarify their structure.
 
The major protein complex that takes flight in her lab is a large molecular machine called the proteasome, whose job in the cell is to break down unwanted proteins. Such recycling is central to a multitude of cellular events, from DNA repair to programmed cell death, while disruptions in proteasome functioning can lead to a host of diseases: Clumps of proteins that have not been properly taken apart can lead to Alzheimer’s and other neurodegenerative diseases. Failure to break down molecules that stimulate cell division can lead to the uncontrolled cell proliferation and growth that occurs in cancer. The improper breakdown of proteins might even trigger a mistaken response from the immune system – for example, in the form of autoimmune disease. Establishing how the proteasome works, then, is essential for understanding and treating numerous diseases.
 
Sharon’s lab at Weizmann is the first in Israel – and one of only a handful in the world – to study large protein complexes by mass spectroscopy, which provides unique insights into protein structure (see box). Elucidating the proteasome’s structure is an enormous challenge: At least 33 different proteins – a huge assembly of “molecular elephants” – along with additional short-lived protein molecules, interact to create each proteasome.
 
Sharon is pursuing three major projects. One concerns a proteasome particle called 19S, known as the “brain” because it identifies the proteins to be broken down. During her postdoctoral studies at the University of Cambridge, she already determined part of its structure; now she plans to determine the architecture of the entire “brain,” which includes 18 different subunits. In another project, conducted in collaboration with Profs. Chaim Kahana and Yosef Shaul of Weizmann’s Molecular Genetics Department, Sharon focuses on a second proteasome molecule, called 20S. The scientists are testing the hypothesis that this particle serves as the cell’s “vacuum cleaner,” removing all proteins that are naturally unfolded. In the third project, Sharon investigates the structure of yet another protein complex, the signalosome, whose job is to regulate the placement of special tags on proteins that need to be broken down so that the proteasome’s “brain” can identify them.
 
These studies are aimed at determining the structure of the proteasome and other biological complexes in minutest detail, a feat that was unthinkable before the advent of the latest technologies. Knowing the structure, in turn, provides valuable information about the way these complexes function in both health and disease.
 
Flying elephants in the lab
 

 

 

 

 

 

 

 

 

 

 

 

 

Mass Spectroscopy in Biology

 

Mass spectroscopy, whose foundations were laid in 1898, has various uses, from identifying substances to defining their structure. A substance is vaporized into a gas consisting of charged particles, and the properties of these particles are analyzed on the basis of their mass-to-charge ratio. Initially, large biological molecules could not be studied in this manner because they didn’t survive the “bombardment” needed to turn them into a gas. Biologists started using mass spectroscopy to study protein structure only in the 1980s, with the invention of techniques for gently flying proteins in the air, such as John Fenn’s electrospray. Equipment for exploring entire protein complexes, which became available in the late 1990s, is found in only few laboratories around the world, including Sharon’s lab at Weizmann.
 
In Sharon’s mass spectroscopy machines, microscopic amounts of a protein complex are passed through a thin gold-plated tube and dispersed within a chamber as a spray of charged drops. The technique, referred to as nano-electrospray, allows scientists to study minute quantities of material and analyze non-uniform and asymmetric complexes, which is particularly important for investigating such biological complexes as the proteasome.
 

Scientist and Mother


Born in Jerusalem, Dr. Michal Sharon earned her Ph.D. from the Weizmann Institute under the guidance of Prof. Jacob Anglister. Her doctoral research focused on the structure of HIV, the virus that causes AIDS. After spending four years as a postdoctoral fellow at the University of Cambridge, she joined the Weizmann staff in the fall of 2007. She is the mother of three: a 9-year-old boy and two girls, aged 7 and 1. Her secret for successfully combining scientific work with motherhood: a strong drive, effective time management and a supportive husband – Alon, whom she met during her army service, when they were both field school instructors in the Negev.


 Dr. Michal Sharon’s research is supported by the Y. Leon Benoziyo Institute for Molecular Medicine; the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly; the Chais Family Fellows Program for New Scientists; the Wolfson Family Charitable Trust; Karen Siem, UK; and the estate of Shlomo (Stanislav) and Sabine Bierzwinsky. Dr. Sharon is the incumbent of the Elaine Blond Career Development Chair in Perpetuity.

 
Illustration: Flying elephants in the lab
Life Sciences
English

Breaking Down is Hard

English

Klein, Luxenburg, Geiger, Geblinger and Addadi. Forming a tight circle

 

 

Breaking down bone is a tough job. Yet our bones undergo remodeling every day of our lives, and old material must be cleared away so that new bone can form. The heavyweights of the breakdown team are cells called osteoclasts that specialize in digesting bone. In diseases such as osteoporosis, an imbalance in this process is responsible for the characteristic bone loss.
 
Osteoclasts have some unique features. They move around the bone until they sense that their services are required, at which point they undergo a transformation called polarization. The polarized osteoclast sticks itself tightly to the bone, while an impermeable ring forms around the cell perimeter. This ring functions to keep the bone-eating acids and enzymes produced between the cell and the bone confined to the demolition site. New research at the Weizmann Institute of Science, which recently appeared in the on-line journal PLoS ONE, has revealed, in unprecedented detail, how these roving, bone-dissolving cells seal off their work area as they get down to business.
 
Prof. Benjamin Geiger, Dean of Biology, and Prof. Lia Addadi of the Structural Biology Department, together with doctoral students Chen Luxenburg and Dafna Geblinger, and with the assistance of Dr. Eugenia Klein of the Electron Microscopy Unit, and Prof. Dorit Hanein and Karen Anderson of the Burnham Institute, San Diego, applied two different observation methods to samples of stripped-down, polarized osteoclasts: electron microscope imaging that allowed them to see fine details of the ring structure, and a light microscope method in which specific features were induced to glow. Because each method captures a different type of information and on a different scale, combining them was tricky, but the two together gave them a uniquely extensive picture. 
 
The team found that the ring is composed of dot-like structures called podosomes anchored to the cell membrane. When the osteoclast is on the move, these little dots amble randomly around the cell, but when the cell prepares to dissolve bone, they make a beeline for the edge. Scientists had been unsure of the podosomes’ role in ring formation. The research team’s findings showed clearly that the ring is made up of individual podosomes held together by interconnecting protein filaments they throw out to each other. “The podosomes are like folk-dancers,” says Geiger. “As soon as the music starts, they join hands and form a tight circle. From afar, a circle of dancers looks like a blur, but now we have managed to make out the individual dancers.”
 
Addadi points out that isolated podosomes look, from above, like big-top tents with “ropes” radiating out from a central pole. She says: “The podosomes may be more than just seals. They appear to act as highly connected nodes of communication between the inside and outside of the cell, enabling the cell to adjust its activity according to the condition of the bone underneath.”
 
Prof. Lia Addadi’s research is supported by the M. D. Moross Institute for Cancer Research; the Clore Center for Biological Physics; the Ilse Katz Institute for Material Sciences and Magnetic Resonance Research; the Helen and Martin Kimmel Center for Nanoscale Science; and the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly. Prof. Addadi is the incumbent of the Dorothy and Patrick Gorman Professorial Chair.
 
Prof. Benjamin Geiger’s research is supported by the Clore Center for Biological Physics; the Leo and Julia Forchheimer Center for Molecular Genetics; the Mario Negri Institute for Pharmacological Research - Weizmann Institute of Science Exchange Program; the Edith C. Blum Foundation Inc.; and the estate of Lore. F. Leder, Manchester, VT. Prof. Geiger is the incumbent of the Professor Erwin Neter Professorial Chair of Cell and Tumor Biology.
(l-r) Dr. Eugenia Klein, Chen Luxenburg, Prof. Benjamin Geiger, Dafna Geblinger and Prof. Lia Addadi. All join hands
Life Sciences
English

An Enzyme out of Water

English
 

Profs. Eitan Bibi and Deborah Fass. Surprise in the cell membrane

 

 

 
 
 
 
 
 
 
 
 
 
 
 

 

 

 

Even in the most thoroughly researched fields, surprises can still turn up. Once in a while these surprises challenge the accepted wisdom, even when that wisdom is well founded in fact. For instance, scientists studying the family of enzymes known as proteases recently found a new type of protease that seemed to stand the body of knowledge about these enzymes’ actions on its head. 

 
Proteases (literally: protein cutters) are a large collection of enzymes responsible for clipping proteins. Because they are found in every life form and play key roles in numerous basic life processes, proteases are some of the best-studied enzymes around. But recent research turned up evidence of another long-lost branch of the family. While their well-known cousins are to be found floating in fluids inside or around the cell, these proteases are hidden away, embedded in the cell membrane. It was the enzymes’ location inside the membrane that created a paradox for the researchers: The proteases they had studied require water molecules to help them cleave proteins. The interior of the cell is hydrophilic – water-loving – and the enzymes have no trouble finding water molecules to use there. By contrast, the cell’s outer wall – the cell membrane – is made of fatty molecules that are water-repellent. How, then, could a protease function in this environment?
 
At first, scientists, steeped in the common wisdom, doubted the evidence hinting at the existence of membrane-bound proteases. Findings, however, continued to mount showing that they not only exist, but are involved in a range of important activities in the cell. These activities include intercellular communication, signaling inside the cell, regulating programmed cell suicide and preventing invasion by parasites. Membrane proteases also play a role in the formation of beta-amyloid protein segments such as those that accumulate in the brain in Alzheimer’s disease.
 
Yet the central question re-mained: How does protease activity, dependent as it is on water, take place in a water-repellent environment such as the cell membrane? To answer this question, Prof. Eitan Bibi and postdoctoral fellow Dr. Adam Ben-Shem of the Biological Chemistry Department, together with Prof. Deborah Fass of the Structural Biology Department, succeeded in solving the three-dimensional structure of a protease found in the cell membrane of the bacterium E. coli. The study, which recently appeared in the Proceedings of the National Academy of Sciences (PNAS), points to a possible mode of action for this enzyme – one that suggests an answer to the paradox.
 
The enzyme is made up of six coils joined together by loops. Five of the six coils form a sort of cylinder that transverses the membrane, extending out past the membrane surface on either side. Inside this tube, the sixth coil, shorter than the others, harbors the protease’s active site – where the actual cutting is performed. Situated right above the active site, supported by the ring of coils, is a sac-like structure that’s padded with amino acids. These amino acids carry electrical charges on their ends that attract water, and the sac’s position implies that the water molecules are then funneled down to the active site to create a hydrophilic mini-environment in which the enzyme can work.
 
protease structure and position

 

In solving one mystery, however, the scientists stumbled on another: How does the protein that’s cut by the protease gain access to the active site, which is set deep within the enzyme structure and surrounded by closely packed protein coils? The research team’s findings suggest a number of possibilities. In one place, the structure showed evidence that one of the loops binding two of the outer coils together might act as a gate that opens to let in the protein molecule. Alternately, a V-shaped opening that showed up between another two coils might give the protein access. But both openings are far from the active site, and the scientists believe that protein, protease or both probably need to undergo a change in shape for cleavage to take place. “A change in the structure of the substrate protein might allow it to access the enzyme’s active site and also expose the spot that needs cutting,” says Bibi.
 
The next stage of inquiry poses a challenge to the researchers. The enzyme’s location makes it hard to study, and they are currently searching for ways to observe the changes it undergoes as it cuts proteins deep inside the cell membrane. Because membrane proteases are so widespread and are vital to so many of the cell’s functions, this research is likely to have an impact on a wide range of biological and medical research.  
 
Prof. Eitan Bibi’s research is supported by La Fondation Raphael et Regina Levy.
 
Prof. Deborah Fass’s research is supported by the Clore Center for Biological Physics; and the Helen and Milton A. Kimmelman Center for Biomolecular Structure and Assembly.
 

Dr. Adam Ben-Shem. Location

 

 
Profs. Eitan Bibi and Deborah Fass. Working in the wet
Chemistry
English

Changing the Plan of Attack

English

Prof. Jacob Anglister and Osnat Rosen. Two forms of HIV

 

 

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
About 3 million people die every year as a result of infection with HIV, the virus that causes AIDS. Efforts to develop a vaccine against the virus are up against a particularly clever enemy: HIV assumes different guises even after entering the human body, going through rapid genetic changes that allow it to escape the immune system. In fact, HIV undergoes more changes while residing in the body of a single person than the flu virus has undergone since it was first discovered.
 
HIV-1, the type of HIV responsible for 90% of all infections, comes in two principal forms, called R5 and X4. These differ from each other significantly, both in the type of immune cells they attack and in the progression of the disease. R5 binds to proteins on the surface of the immune cells known as macrophages, weakening the immune system in the latent stage of the disease, when the person is a carrier of the virus but has not yet developed full-blown AIDS. By contrast, X4 attaches to the membranes of different immune system cells called T cells, causing these cells to die rapidly and bringing on the fatal stage of the syndrome, in which the immune system collapses completely. Yet for all the functional disparity between these two versions of the virus, when it comes to their constitutional sequence of amino acids – the building blocks of proteins – they differ in only one or two amino acids found in a certain protein on the viral envelope.
 
How does a change in a single amino acid affect the virus’s attack mechanisms to such an extent? In a study reported in the Proceedings of the National Academy of Sciences (PNAS), Prof. Jacob Anglister and research students Osnat Rosen and Michal Sharon of the Weizmann Institute’s Structural Biology Department used nuclear magnetic resonance (NMR) to closely examine the two versions of the virus. They focused on that segment of the envelope protein called V3 which is involved in the protein’s binding to target cell membranes – a critical stage in viral infection.
 
The scientists synthesized the sequence of amino acids making up the V3 protein segment in both versions and examined the structure produced when they bind to two different antibodies. They reasoned that in binding to an antibody, V3 would assume its natural spatial shape – the one that exists in the free virus and allows it to bind to various human cells. At first glance, the experiment seemed to produce two identical V3 structures, both shaped like a hairpin. However, a closer examination revealed a difference: Whereas the line-up of amino acids on one side of the hairpin was identical in both versions, on the other side, the orientation of X4 differed from that of R5. Consequently, the position of certain bonds between the amino acids on the two sides of the hairpin also changed. In addition, in X4, the amino acid side chains on one of the hairpin’s sides were pointed in the opposite direction to those of R5, resulting in significant differences in the protein’s shape and in the spatial organization of its binding site. Because of these variations in the shape of one crucial protein, the different versions of the virus latch on to different cells – macrophages in the case of R5, T cells in the case of X4 – and attack the immune system in different ways.
 
But what is it about the changes in the chemical sequence of the viral envelope protein that brings about the structural changes? And what makes this change so dramatic? To answer these questions, the scientists created a more complete picture of the spatial structure of V3, including the amino acid responsible for the differences between the two types of HIV. The picture revealed that this amino acid has a negative electric charge in R5, which allows it to interact with a positively charged amino acid on the opposite side of the hairpin, thereby stabilizing this structure. In contrast, a mutation in the X4 version causes the negatively charged amino acid to be replaced with a positively charged one, resulting in repulsion between the two parts of the hairpin: Here, the amino acids’ side chains, which carry the electric charge, turn on their axes and distance themselves from each other. Another mutation that can result in the transition of the virus from the R5 to the X4 form creates a sequence of three positively charged amino acids, which interacts with the electron clouds of another set of amino acids located diagonally across on the other side of the hairpin. The resulting structure is stable but different from the one characterizing the viral envelope protein in R5.
 
Two forms of HIV
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
These findings reveal how a single mutation causes the virus to progress rapidly from one version of HIV to another. Moreover, they explain how mutations taking place in the virus inside the human body significantly affect the development of the disease and allow the virus to branch out in its attack strategy.    
 
Prof. Jacob Anglister’s research is supported by the Joseph and Ceil Mazer Center for Structural Biology; Mr. Samy Cohn, Rio de Janeiro, Brazil; and Mr. Joe Gurwin, New York, NY. Prof. Anglister is the incumbent of the Joseph and Ruth Owades Professorial Chair in Chemistry.
 
Prof. Jacob Anglister and Osnat Rosen. Two forms of HIV
Life Sciences
English

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