Nano Biology

01.03.2004
 

 


 

Introduction

 

Illustration: Biologists and miniaturized humans

 


Roaming a molecular-scale kingdom, nanotechologies may change the face of health care

In the future, biologists will use assembler-built nanomachines to probe and modify living cells. - Eric Drexler, Engines of Creation, 1986
 
Having devised nanomachines capable of manipulating single atoms and molecules and begun to apply these technofeats to modify the material world around us, scientists are now shifting their gaze inward, to the human body. They envision nanorobots coursing through our bodies able to fix dangerous mutations on the spot, cleanse blood vessels or secrete insulin to counter an abnormal rise in blood sugar levels.
 
The quest of nanomedicine, however, has had its fair share of controversial enthusiasts, offering grandiose scenarios of future medical therapies. Set in motion by Richard Feynman’s 1959 lecture on miniaturization (see p. 7), it captured popular imagination and picked up speed following Isaac Asimov’s Fantastic Voyage (1966). This science fiction classic describes a crew of miniaturized humans rushing to save Professor Beans, a miniaturization expert who has suffered a life-threatening blood clot deep in his brain. The rescue team navigates through Beans’ circulatory system in an atomic-scale submarine.
 
Eric Drexler addressed the implications of new nano technologies in his classic “Engines of Creations“ (1986). His logic was simple: “Being made of molecules… we will apply molecular machines to biomedical technology… [these] machines will combine sensors, programs and molecular tools to examine and repair the ultimate components of individual cells.”
 
At the time, most of his ideas were deemed far-fetched at best, but now, nearly 20 years later, prototypes of his proposed scenarios are beginning to pop up in research labs around the world. At the Weizmann Institute of Science, researchers have created a tiny computer built of DNA molecules that detects prostate cancer conditions in a test tube. And elsewhere in the nanoscience world, researchers are working to create soap-like films to encapsulate drugs that could deliver their medicinal cargo right on target. The films would protect the drug in the bloodstream, releasing it only under certain chemical or thermal conditions, thus preventing wholesale release of a potentially toxic drug. Other nanotools may identify the presence of bacteria and viruses, which, like many biological particles, have well-defined electrical properties and thus oscillate in characteristic ways when exposed to an electric field.
 
Numerous challenges remain - technical, scientific and even psychological - until nanomedicine will directly influence healthcare. Here’s a look at some of the early steps taken here at the Institute.
 

 

Learning from nature

 
Illustration: Biomimetics

Biological materials and systems are multifunctional, adaptive, nonlinear, complex, and, in general, just "weird and wonderful.” - Biologist Stephen Wainwright, Duke University
 
In the early 1940s, Swiss engineer Georges de Mestral went for a walk in the woods with his dog. Upon his return he noticed they were both covered with seeds of a burdock plant.
 
Removing the burs proved a frustrating task. Taking a closer look, de Mestral observed that the burs had hundreds of tiny little hooks - a clever trick for a plant wishing to disperse its seeds. He thought this might be an ideal means of joining two fabrics together - and the idea of Velcro was born.
 
Today Velcro is found on everything from zippers to sneakers to space suits, and scientists are working on yet another form that rips apart silently - a critical ingredient for military operations.
 
Velcro is a classic example in the story of biomimetics, a field that has scientists turning to nature to examine its countless bioengineering feats, polished over time. The hope is that new ideas for advances in medicine, technology and industry might be hidden in some of the solutions evolved to meet the challenges of life - from bones and teeth, capable of withstanding decades of grinding wear and tear, to the enormous tensile strength and elasticity of spider dragline silk, which ounce for ounce is stronger than steel, enabling a dangling spider to safely dive down and nab its prey.
 
 

Dealing with the daily grind

 
Birds don’t have ‘em, nor do bees; sharks can replace them almost immediately if they break; and we humans have teeth that, excluding sugar junkies and night grinders, can last a lifetime given the right dental care.
 
A team of Institute researchers has now discovered a key factor explaining this hardiness: a spring-like structure that absorbs the mechanical stress incurred as teeth chew, grind or, as circumstance would have it, chatter their way through an arctic freeze. Interestingly, this structural feature constitutes only a tiny percentage of the overall tooth.
 
The team, consisting of Prof. Stephen Weiner of the Structural Biology Department and post-doc Dr. Rhizi Wang, began by scouring the literature in search of a dental component that might fit the bill of mechanical stress absorber. “Drawing on his materials science expertise, Wang put his finger on the core question,” says Weiner. “Given that the two main components of teeth are enamel - a hard, brittle material - and dentin, which is much softer, Wang hypothesized that there must be an intervening layer that allows these two very different materials to work together.”
 
The researchers knew that studies dating back to the 1960s had uncovered a certain structural zone positioned directly between enamel and dentin, but they found no follow-up studies exploring its significance. They decided to determine whether teeth actually compress preferentially in this unexplored area when subjected to mechanical stress.
 
As published in the Journal of Biomechanics, the team found that the structure in question, which they dubbed the “soft zone,” is where almost all compression takes place. The study showed that the zone - which is merely 200 microns thick, compared to enamel’s 1,000 microns and dentin’s 5,000 - is in fact the “working part” of the tooth. When we chew, the enamel part of our teeth is pushed back while the soft zone compresses. It then functions like a spring, bouncing back after the compression.
 
Together with Prof. Asher Friesem and dentist Paul Zaslansky, now a Ph.D. student at the Institute, the team is currently using a new technique known as speckle interferometry to map the deformation of objects in response to an applied force, at a resolution of tens of nanometers. An enhanced understanding of dental stress absorption mechanisms should prove valuable in tooth reconstruction.
 
 

Biological computer diagnoses cancer - in a test tube

 
Trillions of microscopic computers vigilantly patrolling your body in search of disease? Institute researchers have recently made a pioneering step in this direction, developing a biological computer able to identify - in a test tube - molecular changes indicative of certain cancers, to diagnose the type of cancer, and to react by producing an appropriate drug.
 
The study, recently published in Nature, was performed by Prof. Ehud Shapiro of the Departments of Computer Sciences and Applied Mathematics and Biological Chemistry, his research students Yaakov Benenson, Binyamin Gil and Uri Ben-Dor, and Dr. Rivka Adar.
 
The team programmed their computer to detect prostate cancer and one form of lung cancer. The computer evaluates four genes that become either under-or overactive once the disease sets in. The genes chosen control the expression of messenger-RNA (which carries information from the nucleus to the ribosome, the cell’s protein factory). The scientists introduced different levels of these RNA molecules into the test tube to simulate the presence or absence of cancer.
 
Made entirely of biological molecules, the computer has three components - input, computation and output. The first consists of short strands of DNA, called transition molecules, which check for the presence of the messenger RNA produced by each of the four cancerous genes.
 
The second component is a computation (diagnostic) module, consisting of a hairpin-shaped long DNA strand. As the computer’s input component checks for the presence or absence of the four cancerous markers, this diagnostic unit checks each input in turn, producing a positive diagnosis of malignancy only if all four markers point to cancer.
 
This diagnostic module also contains the computer’s third component: a single-stranded DNA that is known to interfere with the cancer cell’s activities. In the case of a positive diagnosis, the unit releases its hold on the therapeutic unit, activating its cancer-fighting potential.
 
Shapiro’s team first went on record in 2001, when it created the first autonomous biological nanocomputer. Made entirely of biological molecules, the computer's input, output, and “software” were made up of DNA molecules. The device was so small that as many as a trillion such computing devices could work in parallel in one drop of water, collectively performing a billion operations per second with greater than 99.8 percent accuracy per operation. It was recently awarded the Guinness World Record for the “smallest biological computing device.”
 
Shapiro: “Our study offers a vision of the future of medicine. It is clear however, that it may take decades before such a system operating inside the human body becomes a reality.”
 
 

Computers in the dust

 
In 1954 researchers at the Weizmann Institute built the first electronic computer in Israel, and one of the first computers worldwide, which they fondly named WEIZAC. Thirty years later, silicon chip computers routinely functioned at a rate that was thousands and millions of times faster than WEIZAC.
 
Today, research at the Institute targets the development of ever-faster, more compact chips designed according to the emerging principles of quantum electronics. These will inevitably leave silicon chips in the dust, much as the silicon chips once turned WEIZAC into a museum exhibit.
 
Yet even before these quantum electronic chips have become a reality, they already have a potential successor - the tiny biological computer developed by Prof. Shapiro’s team.
 

 

The slick joint

 
Body joints are superbly lubricated. They have to be. As the meeting point between every two bones in our body, they are what makes our every movement possible - from walking, bending and maneuvering our fingers to playing ball and dancing. And they’re supposed to last a lifetime.
 
Mimicking key design elements of this biolubrication system, physicist Prof. Jacob Klein of the Weizmann Institute of Science, has recently created a synthetic lubricant that cuts friction by a thousand-fold or more. The study, published in Nature, could lead to a range of applications - from longer-lasting micromachines and higher-density hard disks to biomedical devices, including improved hip transplants and treatment for dry eye syndrome.
 
Previous studies had suggested that biolubrication systems, including those in our joints and eyes, may contain hyaluronan, a molecule that coats the rubbing surfaces of our joints, shielding them from mechanical damage. Hyaluronan was also known to be strongly attracted to water. But how these two factors combined to create the most effective lubricatory system anywhere, remained a mystery.
 
Klein and colleagues suspected that in joints, hyaluronan may be attached to a thin cartilage layer covering the bone, while parts of this long, chain-like molecule stick out into the synovial fluid between the bones, similar to bristles on a hairbrush. These bristles or others playing a similar role, they believed, function as the body’s lubricants.
 
To test their theory, the team developed a synthetic model that mimicked a double-brush system, anchoring two charged molecules (polyelectrolytes) to opposite-facing ceramic surfaces. The resulting system showed extremely effective friction resistance, particularly when exposed to a water-based solution. “The brushes strongly try to avoid each other, resisting penetration even when an external force is applied that presses them closer. This enables them to easily slide past one another,” says Klein.
 
The superior lubrication may largely be explained by electrical charges. The synthetic brushes were designed to imitate the electrically-charged nature of biolubricants. Similar to the negative charge characterizing the hyaluronan molecule, for instance, the end of the synthetic brushes stretching away from the ceramic surface was designed to be negatively charged. This negative charge then attracted water molecules - which in fact explains why the brushes performed most effectively in a water-based solution. “The water molecules are tightly bound to charges on the brushes, causing them to act like molecular ball bearings to reduce friction,” says Klein.
 
Other players in this charge cast are the small mobile ions trapped in the space between the bristles. According to Klein, when the brushes approach one another, their respective clouds of positive ions are mutually repellant, increasing the brushes “distaste” of penetrating one another.
 
“Our general idea was to draw on nature, says Klein. “It made sense to try out the design principles evolved and optimized over millions of years.”
 
 

Humpty-Dumpty mechanics

 
Two hundred and six - this is the number of bones in the adult human skeleton. Over the years of your life, as you walk, play basketball, dance through the night or bungee jump from a steep cliff, these bones will see you through, supporting your weight when you stand upright and protecting your brain and internal organs.
 
How bones withstand the immense array of mechanical stresses imposed upon them has long fascinated scientists, who have set about probing their chemical and biological properties and even crushing them to determine the relationship between their structure and their outstanding performance. Yet despite several decades of research, a full understanding of this complex biological material remains elusive.
 
The beauty of bone stems from two key properties - it is a composite material and it is highly hierarchical in structure. The principle of forming a composite is to take two materials, often highly different from each other - say, a soft and an extremely hard material - weave them together somehow, and, presto, a new material is born that is generally far superior to either of its individual components.
 
In bone, this partnership comes in the form of a ceramic-like, brittle mineral salt called hydroxyapatite, which is bolstered by collagen (a protein) that adds elasticity and strength. The tissue has several levels of organization, ranging in scale from nanometers to centimeters, each with a different structure and function. Adding to this complexity is the fact that bone changes over time, with specialized bone cells actively replacing older bone tissue in a process that has adults renewing their entire skeleton roughly every 7-10 years.
 
In the 1990s Prof. Stephen Weiner of the Institute’s Structural Biology Department and Prof. Daniel Wagner of the Materials and Interfaces Department collected data on the micro-mechanical properties of bone and developed a mathematical model explaining how bone’s various components affect its mechanical function, including bone elasticity. The model made it possible to predict the mechanical properties of bone with unprecedented accuracy.
 
Weiner is currently working to further understand the contribution to mechanical strength made by the individual cylinders within bone. Each of these cylinders changes over time, altering its mineral content and thus its mechanical properties. “While past studies succeeded in determining the average mechanical properties of bones, what we really need to know is how each of these individual cylinders responds to stress,” says Weiner. Insights at this structural level may yield new treatments for osteoporosis and other bone diseases.
 
 

When bones become porous

 
Osteoporosis, or porous bones, is a disease characterized by structural deterioration of thebone tissue, leading to low bone mass, fragility and increased vulnerability to fractures of the hip, spine, and wrists.
 
Generally appearing at age 50 or above, osteoporosis is caused by unbalanced bone “remodeling,” as cells responsible for breaking down old bone tissue (osteoclasts) become more active than those laying down new tissue (osteoblasts), causing bone loss.
 
The disease affects more than 44 million people in America alone, 68 percent of whom are women, causing an estimated annual national expenditure of $17 billion.
 
 

Fine spine choices

 
Back when marine animals first began trying on mineralized, exoskeleton armor, over 550 million years ago, sea urchins had a crucial “choice” to make. The odds pointed to calcite, an abundant calcium carbonate mineral, as a natural candidate for their skeletal and spine construction. But while clearly the “cheapest” material available, calcite seemed a fragile choice at best - it’s an extremely brittle material, easily shattered by mechanical stress. Some of their contemporaries opted for silica, magnetite or calcium phosphate. Yet sea urchins stuck with calcite. They then proceeded to evolve unique biological adaptations to dramatically enhance its material strength.
 
At the Institute, Profs. Stephen Weiner and Lia Addadi have discovered key features that explain the surprising strength of sea urchins, as well as of mollusks and bones - all natural composites.
 
Scientists had long been unable to explain the durability of sea urchin spines, which they believed consisted entirely of a single calcite (and thus highly fragile) crystal. The Weizmann scientists revealed that while calcite indeed constitutes 99.9 percent of the urchin spine, the remaining 0.1 percent consists of proteins entrapped within the crystalline matrix. And amazingly, that is what makes all the difference.
 
Working with researchers from the Brookhaven National Laboratory in New York, the Weizmann team discovered how the entrapped proteins act to reinforce urchin calcite against fracture, preventing cracks from spreading through the crystal. The scientists grew pure calcite crystals in solutions containing proteins extracted from urchin spines. They found that the proteins integrated into the crystal, altering its structure and making it far less brittle. The question remained, however, how a component present in such minuscule proportions could have such far-reaching effects on material quality.
 
Follow-up studies showed that the proteins had integrated into the pure crystals preferentially, along planes that are oblique to the crystal cleavage plane, thus disrupting fracture propagation. “The crystal's ability to withstand mechanical stress is enhanced because resulting cracks do not rip catastrophically along the cleavage planes but are diverted along the protein-induced planes, which absorb the force of impact,” explains Weiner.
 
These findings might lead to the development of new crystal-polymer composites for building lightweight, tougher ceramics and improved electrooptic materials.
 
 

Composite cornucopia

 
You shall no longer give the people straw to make brick as before (Exodus 5:6-7).
 
This is the first recorded account of a man-made composite, describing bricks used in ancient Egypt, which were made of mud mixed with straw. The straw increased the bricks’ thermal stability, preventing them from cracking. Modern studies show that these bricks were three times stronger than those lacking straw. Thousands of years later, the Egyptian landscape is still dotted with monuments made of such bricks.
 
Composites are everywhere. Though often referring to the fiber-reinforced metals, polymers and ceramic materials originally developed for use in the 1950s, composite superstars include those found in nature - from human bone, to tree trunks, sea shells and spider dragline silk, which ounce for ounce is stronger than steel and tougher than kevlar.
 
 

“Sightless” marine creature found to be all eyes

 
A team of scientists has found that the brittlestar, a marine invertebrate long thought to be sightless, is in fact covered with calcite crystals that function as optical receptors for a compound eye. A better understanding of how to build such high-quality microlenses may lead to improved computer circuits.
 
Profs. Lia Addadi and Stephen Weiner of the Weizmann Institute’s Structural Biology Department had long been interested in the ways in which animals build their skeletal structures. When they met Dr. Gordon Hendler of the Natural History Museum of Los Angeles County, Hendler brought to their attention one particular species of brittlestar that appeared to be particularly sensitive to changes in light, quickly escaping into dark crevices at the first sign of danger. He suspected that spherical crystal structures on the brittlestar’s outer skeleton serve as lenses, transmitting light to its nervous system.
 
By analyzing the geometry of the crystal lenses Addadi and Weiner, together with their then graduate student Joanna Aizenberg, were able to pinpoint the expected focal point on the nerve bundles below, but they lacked the means of proving that these lenses indeed transmit light to the nervous system within.
 
This is where things stood for almost ten years, until the team came up with the idea of examining the lenses using lithography, a semiconductor technology.
 
Placing one of the crystals above a layer of photosensitive material, Aizenberg exposed the system to light and found that it reached the photosensitive tissue in spots directly underneath the crystals. Her findings also demonstrated that the crystalline lenses act as “corrective glasses,” filtering and focusing light on photoreceptors within the nerves. But unlike man’s ability to see in virtually only one direction, this complex visual system enables the brittlestar to detect approaching danger from many directions. The lenses expertly compensate for common optical distortion effects. This unique visual architecture has prompted hopes for new materials that would mimic the brittlestar model. Knowing how to build such microlenses of high optical quality could lead to improved microlithography tools used in etching the integrated circuits found in computers.
 

 

Peering into nature’s secrets

 

Peering into nature’s secrets

 


Cells vary in length. Bacteria are about 1 micron long, while plant and animal cells vary from about 50 microns to meters in the case of certain neurons.
 
The cell - the elementary unit of life - is rich in engineering know-how. The ultimate self-assembler, it applies its molecular machinery to convert readily available materials from food and water into a wonderland of materials - from over 100,000 proteins, lipids and sugars, to the materials they build: wood, bones, horns, scales and skin. It performs these feats in a tiny setting. Cells are generally only a few micrometers long, and their functional units, the organelles, are only a few nanometers. Scientists around the world are hard at work applying a range of tools to chip away at the cell’s secrets by viewing and manipulating nanoscale objects within and around the cell.
 
Lessons from the cell, they believe, might prove vital in understanding the basic mechanisms of life - the key to unprecedented medical advances. The cell might also help in shaping our material world, with its varied nanostructures serving up solutions to central challenges in material design.
 
 

Connect the dots

 
Cell adhesion, in which cells bind to adjacent cells or to the matrix between them, is an essential first step in many fundamental life processes, including the formation of tissues and organs, wound healing and the exchange of information between cells, known as signaling. But how are these contacts formed and regulated? What cues within a living organism influence adhesion properties, instructing a cell to stick, move, proliferate or die?
 
Until recently, scientists studying the forces influencing cell adhesion faced a major difficulty: they lacked the tools to effectively identify and measure the minuscule forces applied between cells and their environment. Heading a multidisciplinary team, Prof. Benjamin Geiger of the Institute’s Molecular Cell Biology Department developed a powerful new tool for studying cellular adhesion, which allows the measurement of forces in the Lilliputian range of nanonewtons (one nanonewton is roughly equivalent to the weight of one thousand red blood cells).
 
The method involves creating a transparent elastic template imprinted with a grid of dots or lines spaced at fixed intervals. When a cell sticks to the patterned template and applies a force, it distorts the grid. By measuring these distortions, the scientists are able to infer the magnitude and direction of the forces applied by the cell to the contact area. This approach is proving vital in revealing the interplay between adhesion and internal cellular processes.
 
In related research, Geiger and Prof. Alexander Bershadsky of the Molecular Cell Biology Department have shown that cells constantly “probe” their surrounding by touching and pulling at it. New research questions include the nature of the forces occurring between two cells as they anchor on the same substrate, a topic that plays a role in how cells aggregate to make a tissue and may thus have relevance to tissue engineering.
 
 

Simulating life

 
In related research, Prof. Benjamin Geiger is working to construct models that simulate the conditions experienced by cells as they move around the body. In their travels, cells encounter continuously changing “terrains” determined by the type of tissue they meet. They are able to sense the chemistry, geometry and mechanical properties of these environments and to modify their behavior accordingly - for instance, applying extra adhesive force in settings lacking sufficient anchorage.
 
Collaborating with Prof. Lia Addadi of the Institute’s Structural Biology Department, Ph.D. student Baruch Zimmerman and Prof. Yoachim Spatz of Germany’s Heidelberg University, Geiger is creating artificial micro- and nanoscale models that simulate the body’s varying tissue matrices (collagen, fibers etc.) to obtain a better understanding of the interactions between a cell and its environment - specifically, how a cell’s behavior and motility are affected by the chemistry and mechanical properties of its environment. Insights into these questions may have implications in cancer research aimed at preventing the migration of cancerous cells to form metastases. The artificial models tested at the WIS may also advance tissue engineering research, yielding knowledge of the type of scaffolds needed to create specific tissues.
 
 

Soft matter science

 
When physicist Sam Safran started work in the 1980s at the Exxon petrochemical company, he had little idea this job would end up changing the course of his career, sparking an interest in the science of soft matter. Today, this field has relevance for diverse applications, from the management of oil spills to pharmaceuticals.
Also known as complex fluids, soft matter often deals with the dispersion of a solid or liquid in another liquid. In his work at Exxon, Safran, today a professor in the Institute’s Department of Materials and Interfaces, focused on unique “split-personality-like” molecules used in oil extraction and recovery. Known as amphiphiles, these molecules have both polar (charged) and nonpolar regions. While one end is attracted to polar molecules such as water, the other end is generally a nonpolar hydrocarbon chain, attracted to oils or lipids. This enables amphiphilic molecules to break up oil slicks into small droplets, which might then be further degraded by oil-eating microbes.
 
The unique polar/nonpolar duality of amphiphiles makes them key players in the body, where they self- assemble into an extremely rich assortment of soft matter structures that perform regulatory and housekeeping chores. For instance, the membranes of all cells in the body contain a nonpolar region facing the inside of the cell and a polar region on its surface, which is vital to the cell’s interaction with nearby molecules. Another example is that of micelles - a cluster of molecules critical to efficient digestion, which break up otherwise insoluble fat molecules.
 
A better understanding of the body’s self-assembling systems may help in creating vesicles for use as potent drug delivery systems.
 
 

Soft materials and cancer diagnosis

 
As a red blood cell rushes through the arteries it is repeatedly pounded, stretched and deformed as it passes small capillaries, yet it rarely breaks apart. This feat is made possible by the fact that, like all soft materials, cell membranes are relatively durable in their response to external forces.
 
Hoping to explore the relationship between cell function and the cytoskeleton (a structure just below the cell membrane that affects cell shape, division and adhesion) Prof. Safran and colleagues demonstrated that exposing live cells to a drug called latrunculin weakens the cytoskeleton, impairing its incorporation of the actin protein.
This finding may lead to new tools for cancer diagnosis and drug development. When exposed to actin-impairing drugs, cancerous cells are strongly affected since their cytoskeleton is weak to begin with, whereas healthy cells are generally better able to maintain the integrity of their cytoskeleton.
 
 

Opening the gates

 
In biblical times, the gate was the most vulnerable point of a walled city. Judges were placed there to interview travelers, verifying that their presence was welcome. The same is true of the gates to the cell’s inner sanctum - the nucleus.
 
These gates (called nuclear pore complexes) lead to and from the cell’s genetic material, safeguarding the essential codes of life. Only “desirable” molecules can pass through. Molecules that succeed in entering the nucleus from other parts of the cell activate genes, causing the information these genes encode to be dispatched to the cell’s “protein factory” by another molecule - messenger RNA - which exits the nucleus through the same gates.
 
Understanding the mechanism by which molecules pass the nucleus’ gates is crucial to controlling such traffic. These methods may be applicable in barring the entry of viruses into the cell’s nucleus, or in gene therapy, in which a beneficial gene is introduced into the patient’s DNA to replace a damaged counterpart gene.
 
Dr. Michael Elbaum of the Weizmann Institute’s Material and Interfaces Department is studying the passage of DNA molecules through these gates using optical and electron microscopy. His team applies a tool based on tiny tweezers composed of laser beams focused in a microscope.
 
In collaborative research with Prof. Alexander Bershadsky of the Molecular Cell Biology department, Elbaum and his team applied similar optical tweezers to probe cell adhesion and its relation to cell movement in the body - phenomena playing a key role in embryonic development, wound healing and other fundamental life processes.
The team designed small beads coated with proteins involved in adhesion. They then used the optical tweezers to hold the beads over the cell surface and map their resulting interaction with the cell. In the study, published in Biophysical Journal, they showed striking differences in the way different regions of the cell surface respond to the stimuli generated by the adhesion proteins, making it possible to pinpoint specific regions where adhesion takes place.
 
 

Skeletal surveying tool

 
In more materials-oriented research, Elbaum and his team are currently studying a central ingredient of the cell’s internal skeleton, known as microtubules, which might hold clues to longstanding questions in physics and biology.
 
Twenty-five nanometers in diameter and up to a hundred microns in length, microtubules are shaped as hollow, rigid, chimney-like structures. The cell uses microtubules for communication and delivery, sending “packages” running along them, driven by specialized motor proteins.
 
Studies of this system are shedding light on molecular traffic in the cell. Since microtubules are elastic polymers, such studies may also yield a better understanding of the dynamics of both natural and synthetic polymers, revealing properties important to a range of applications, from food packaging to industrial glues.
 
 

Metal ‘a day to keep diseases away

 
Every time we breathe, the oxygen drawn into our lungs binds to iron atoms present in hemoglobin molecules in the blood. The hemoglobin transports the oxygen to cells throughout the body, where it is released and used to produce energy. Iron’s ability to bind, release and activate oxygen stems from its capacity to “give” and “receive” electrons. In this respect, it is similar to other metals such as copper, cobalt and nickel. These metals underlie the actions of numerous enzymes - “molecular machines” essential for nearly all cellular processes.
 
Prof. Daniella Goldfarb, of Institute’s Chemical Physics Department, is studying metalloenzymes (enzymes containing iron and other metals) with the aim of mapping the precise structure of their metal-containing active sites. Insights in this field will help advance the construction of molecular machines - 10 to 50 nanometers large - that, equipped with these metal-containing active sites, would be capable of performing diverse industrial functions, some dramatically improved from existing technologies.
 
A good example is that of ammonia production - a reaction that calls for extreme temperatures and pressure when performed industrially, yet is synthesized in bacteria in a series of elegant biochemical reactions, at ambient temperatures and without the production of harmful byproducts.
 
Mapping the metal-containing sites may also lead to methods for repairing damaged enzymes, offering an invaluable medical tool since damaged or faulty enzymes lie at the root of many diseases.
 
 

First sightings of individual proteins as they fold

 
Proteins, the fundamental components of all living cells, start out as randomly shaped chains and twist into a well-defined structure that determines their function. A botched job of protein folding has been linked to a growing list of diseases, including Alzheimer's and certain cancers.
 
Until recently, scientists studying protein folding had to rely on information gathered from a huge number of molecules. The experimental results represented an average of the different processes these molecules underwent and could not pick up individual differences. This shortcoming highlighted the need for a new technology that would make possible the study of individual proteins as they fold - a huge challenge since proteins are generally only a few nanometers in size and are constantly on the go.
 
Applying a new optical technology designed in his lab, Dr. Gilad Haran of the Institute’s Chemical Physics Department has made the first glimpses ever of single proteins in the process of folding. The technology’s success lies in striking the right balance. Since proteins are continuously active, one must limit their motion to get a clear understanding of their folding process. However, a fully immobilized protein defeats the purpose. It won’t fold. Earlier attempts to gain a steady look at proteins sought to pin them down to a surface; but this could be achieved only by binding the protein to a surface, thus changing its properties.
 
To skirt this obstacle, Haran’s team designed novel vesicles that envelop the proteins in question. Each vesicle is 100 nanometers wide and designed to envelop a single protein molecule, generally only 3-4 nanometers long. Unaware of their scientist-made borders, the proteins can move about freely, yet not so actively as to impair the scientists’ ability to observe their behavior.
 
The results verify what theoretical scientists have suspected for nearly a decade - that proteins may vary in their folding process. Even identical proteins ending up with the same shape may take different routes to reach it. The new WIS technology might help clarify the reasons for protein misfolding and ensuing disease.
 
 

DNA? Proteins? Fish ‘em out with a nanoprobe

 
Coupling the delicate touch of a nanotube probe with atomic force microscopy (AFM), Dr. Ernesto Joselevich is able to produce today’s highest-resolution images of live, moving DNA.
 
AFM works like a record player “reading” surfaces with a needle-fine tip; it rises and descends as it meets “bumps” or “valleys” in the target surface. These motions are translated via a computer to create an atomic-scale image. But while AFM provides detailed topographical information, it offers only limited information about an object’s surface chemistry. “It’s like being able to determine where a cake is without knowing whether it’s a chocolate swirl or blueberry with cream,” says Joselevich, of the Institute’s Materials and Interfaces Department.
 
Seeking to enhance the tool’s sensitivity, Joselevich, at the time completing a post-doc at Harvard under Prof. Charles Leiber, decided to link it up with nano-tubes that were one to a few nanometers in diameter. The idea was to replace the conventional AFM probe with nanotubes fitted with different chemical tips, such as molecules that might interact with those on the target surface. By detecting binding forces between these chemical tips and the target surface, he reasoned, one might gain new information about the surface chemistry.
 
Another motivation was the nanotube’s tiny diameter. The team hypothesized that they could significantly increase AFM resolution by replacing its standard tip, which has a radius of curvature of 5 to 20 nanometers, with that of a carbon nanotube 0.5 nanometers in radius. “A blunt tip makes it difficult to detect fine objects. It’s like trying to feel or pick up a grain of rice with a boxing glove,” explains Joselevich.
 
The study, published in Nature, showed that he was on the mark. The new approach successfully detects the presence of specific molecules on the target surface. Likewise, having added a temporal resolution system that photographed the interaction every 30 seconds, Joselevich is able to view live, moving DNA as it undergoes various biochemical processes. This real-time view offers an important advantage over electron microscopy, which can be applied only to dead samples, since the high flow of electrons intrinsic to that technology destroys the sample.
 
Potential future applications of chemical force microscopy range from basic research aimed at a better understanding of gene expression, to the ability to detect a person’s susceptibility to disease, to industrial applications, including the detection of chemical impurities on semiconductor chips.
 
 

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