BioCAT Science


Conformational states and recognition of amyloidogenic peptides of human Insulin-degrading enzyme
Proteins in living organisms face acute and chronic challenges to their integrity, which require proteostatic processes to protect their functions. Proper protein function is ensured through protein turnover through a balance between synthesis and proteolysis. Amyloidogenic peptides, such as amyloid β (Aβ) and amylin, present a major challenge to proteostasis, because they can form toxic aggregates that impair diverse physiological functions and contribute to human diseases. Insulin-degrading enzyme (IDE), a Zn2+-metalloprotease, prefers to degrade amyloidogenic peptides to prevent the formation of amyloid fibrils. Thus, IDE retards the progression of Alzheimer's disease.

Molecular packing and fibrillar structure of type II collagen
Type II collagen is the principal extracellular matrix (ECM) component of mammalian cartilage. It has been shown that lamprey (a cartilagenus fish) notochord collagen fibrils are indistinguishable from human cartilage fibrils, their differences being minor amino acid sequences and in the specific arrangement of the fibrils to build their respective ECM's. Recently, the Orgel group demonstrated that a human anti-biglycan antibody had the capacity to 'deconstruct' lamprey notochord type II collagen fibril bundles to give a pure source of 'thin-fibril' collagen fibrils that are primarily composed of type II collagen. This procedure provides both a possible explanation for the initiation of Rheumatoid arthritis and a means of studying the structural arrangement of tissue.


Non-enzymatic decomposition of collagen fibers by a biglycan antibody and a plausible mechanism for rheumatoid arthritis
Rheumatoid arthritis (RA) is a systemic autoimmune inflammatory and destructive joint disorder that affects tens of millions of people worldwide. Normal healthy joints maintain a balance between the synthesis of extracellular matrix (ECM) molecules and the proteolytic degradation of damaged ones. In the case of RA, this balance is shifted toward matrix destruction due to increased production of cleavage enzymes and the presence of (autoimmune) immunoglobulins resulting from an inflammation induced immune response.

The cross-bridge spring: cool muscles store elastic energy
The Hawkmoth Manduca sexta is an emerging model system for a wide range of studies in integrative biology. The flight muscles are particularly interesting in that, unlike most insect flight muscle, but like vertebrate skeletal and cardiac muscles, they are a synchronous muscle where each stimulus generates one muscle twitch. The length tension curve also shows intriguing similarities to mammalian cardiac muscle even though the sarcomere structure is known to be quite different. Another property of the muscle is that the dorsal-most region of the flight muscle is ca. 5 degrees C cooler than the ventral muscle closer to the midline to the body. (Such spatial temperature gradients are also likely to occur in large muscles in mammals but this has not been well investigated). In Manduca flight muscle these spatial gradients lead to a spatial variation in power production spanning from positive to negative values across the predicted temperature range. Warm ventral subunits produce positive power at their in vivo operating temperatures, and therefore act as motors producing force. Concurrently, as muscle temperature decreases dorsally, the subunits produce approximately zero mechanical power output. These muscles, therefore, not only generate force, but also may act as springs, providing energy storage to drive locomotion.

A New Phase in Cellular Communication
In many biological processes, various substances undergo phase transitions, where they are transformed from one state (solid, liquid, or gas) to another. Wiskott-Aldrich Syndrome Proteins (WASP) function as intracellular signaling molecules, and one member of the family, N-WASP, interacts with two other proteins, forming a complex that plays an integral role in the regulation of the cell's internal scaffold. This interaction provides a system for investigation of phase transitions that result from multivalent interactions. Using dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS) techniques at the APS, researchers investigated interactions between engineered multivalent substances. They described the occurrence of sharp liquid-liquid-demixing phase separations corresponding to transformation between small complexes and large polymers at the molecular level, leading to the production of micrometer-diameter liquid droplets in aqueous solution. They also examined the phase transition that occurs in relation to N-WASP activity, and found that phosphorylation of one of its interactive proteins by a kinase enzyme plays an integral role in the transformation.

RNA Folding - How A Little Cooperation Goes A Long Way
The nucleic acid RNA plays an important role in protein synthesis in cells. However, noncoding RNAs also exist that are not converted into proteins, but still play important roles in many biological processes. RNA molecules aggregate into complex tertiary structures, producing globular forms stabilized by various interactions. Proteins, ligands, and other RNA molecules recognize tertiary folded RNAs and result in the biochemical pathways that affect all aspects of cellular metabolism. Using small-angle X-ray scattering (SAXS) at the APS, and other techniques, researchers investigated the unique folding behavior of RNA. They described how this occurs with the cooperation of folding intermediates of an RNA enzyme, ribozyme.


The Molecular Mechanism of Stretch Activation in Insect Muscle
Flying insects are among the most successful species on our planet. Flight is very metabolically demanding and many insects have found a clever way to reduce energy costs in their flight muscles by employing a process called "stretch activation, which has been recognized since the 1960s as an interesting and physiologically important phenomenon, but a mechanistic explanation has been elusive. Now, research at the Biophysics Collaborative Access Team x-ray facility at the U.S. Department of Energy's Advanced Photon Source provides another, important step toward a full explanation of stretch activation, which also plays an important role in mammalian cardiac expansion and contraction.

An Understanding of Elastin's Properties Springs Forth
It's not stretching the truth to say that flexibility is an important and desirable human physiological trait. We owe our flexibility to a protein called elastin, and elastin derives its properties from a building-block molecule called tropoelastin. Tropoelastin behaves as an ideal elastomer because it loses no energy between stretch and relaxation. Understanding the structure and function of tropoelastin is already helping to pave the way for the development of synthetic materials that can reproduce nature's elastic properties. Researchers using high-brightness x-rays at the U.S. Department of Energy Office of Science's Advanced Photon Source at Argonne National Laboratory have identified how tropoelastin molecules form a "head-to-tail" assembly, which helps explain how these molecules work together to confer elastic properties in tissues throughout the body.

How Dinosaurs Put Proteins into Long-Term Storage
How does one prove that the protein isolated from a 68-million-year-old dinosaur bone is not a contamination from the intervening millenia or from the lab? This is the task of a research team who say they have isolated peptides of the common structural protein, collagen, from bones of Tyrannosaurus rex and Brachylophosauraus canadensis.

Increased brain iron coincides with early plaque formation in a mouse model of Alzheimer's disease
Elevated brain iron content, which has been observed in late-stage human Alzheimer's disease, is a potential target for early diagnosis. However, the time course for iron accumulation is currently unclear. Using the PSAPP mouse model of amyloid plaque formation, researchers from Stony Brook University, University of Chicago, Illinois Institute of Technology, BNL, and the APS conducted a time course study of metal ion content and distribution [iron (Fe), copper (Cu), and zinc (Zn)] in the cortex and hippocampus using X-ray fluorescence microscopy (XFM). They found that iron in the cortex was 34% higher than age-matched controls at an early stage, corresponding to the commencement of plaque formation. The elevated iron was not associated with the amyloid plaques. Interestingly, none of the metal ions were elevated in the amyloid plaques until the latest time point (56 weeks), where only the Zn content was significantly elevated by 38%. Since neuropathological changes in human Alzheimer's disease are presumed to occur years before the first cognitive symptoms appear, quantification of brain iron content could be a powerful marker for early diagnosis of Alzheimer's disease.


The Molecular Mechanism of Stretch Activation in Insect Muscle
Stretch activation is important in the mechanical properties of vertebrate cardiac muscle and essential to the flight muscles of most insects. Despite decades of investigation, the underlying molecular mechanism of stretch activation is unknown. Researchers from Duke University investigated the role of recently observed connections between myosin and troponin by analyzing real-time X-ray diffraction "movies" from sinusoidally stretch-activated Lethocerus muscles. Observed changes in X-ray reflections arising from myosin heads, actin filaments, troponin, and tropomyosin were consistent with the hypothesis that troponin bridges are the key agent of mechanical signal transduction.

At the Crossroads of Chromosomes
On average, one hundred billion cells in the human body divide over the course of a day. Most of the time the body gets it right but sometimes problems in cell replication can lead to abnormalities in chromosomes---resulting in many types of disorders from cancer to Down syndrome. Now, researchers from the University of Pennsylvania School of Medicine (UPSM) have defined the structure of a key molecule that plays a central role in how DNA is duplicated and then moved correctly and equally into two daughter cells to produce two exact copies of the mother cell. Without this molecule, entire chromosomes could be lost during cell division, so this work is a major advance in understanding the molecules driving human genetic inheritance.

Packing it in: A New Look at Collagen Fibers
Nature uses collagen everywhere in constructing multicellular animals. There are at least 20 types of collagen, but 80-90% of the collagen in the body consists of types I, II, and III. Collagen type I is used to form skin, tendon, vascular, ligature, organs, bone, dentin, and interstitial tissues. Collagen type II makes up 50% of all cartilage protein and is essential in normal formation of such structures as cartilage, the vitreous humor of the eye, bones, and teeth. To create these structures, collagen molecules are positioned in arrays called fibrils, producing what are known as the D-periodic fibrillar collagens. Though previous work has given some idea of what the D-periodic structure looks like, technical limitations prevented accurate structural studies of collagen type II packing. A research team aided by the BioCAT and BioCARS beam-lines at the APS has determined the molecular structure of collagen type II in living tissues. These results mark significant progress in understanding the architectural differences between collagen type I and type II.

The Push and Pull of Plant Viruses
New insights into the way a simple-seeming plant virus, the turnip crinkle virus (TCV), goes about replicating in infected cells have been obtained using solution nuclear magnetic resonance spectroscopy (NMR) and small/wide angle x-ray scattering (SAXS/WAXS) studies with a novel methodology at two APS x-ray beamlines. The findings build on earlier work but provide a clearer understanding of RNA genetics and can even explain the paradox of how RNA translation and protein synthesis operate in parallel even though they pull the machinery---the enzymes and ribosome---of the host cell in different directions. The work may have implications for coping with crop plant viral diseases.


Protein Assembly and Disease
Proteins known as amyloids have been implicated in the onset and advance of diseases such as Alzheimer's disease and type 2 diabetes. It would seem that it is the unusual folding properties of these protiens which lead to disease. In the case of Alzheimer's and cerebral amyloid angiopathy, mutations such as the Iowa mutant are associated with familial inheritance and early onset of the disease. Patients carrying the mutation develop neuritic plaques and large deposits of the nutant protein in cerebreal blood vessels. Exactly how the protein does so much damage has been the subject of intense research. With the help of the BioCAT beam-line, a research team used x-ray diffraction in conjunction with electron microscopy and nuclear magnetic resonance spectroscopy to show how the mutant and normal proteins differ with respect to folding and assembly. What the research group found goes a long way toward explaining how the mutant protein is able to create so much havoc in tissues.

Getting to Know Cellulose
As humans continue to deplete the Earth's supply of fossil fuels, finding new sources of energy becomes a priority. Biomass, such as cornhusks left after a harvest, is one such alternative energy source. Before efficient use can be made of such materials, understanding how to break down cellulose---the fiber in human nutrition and the main component of much biomass waste---is crucial. With the help of the NE-CAT and BioCAT beam-lines at the APS and beamline BL38B1 at SPring-8 in Japan, an international research team has identified important new features of cellulose structure. Their work provides important new details that could be used in designing more efficient treatments for cellulosic biomass.

The Power of Proteins: Prion Diseases Demystified
It is hard to believe that a single protein can be responsible for the damage inflicted by diseases such as human Creutzfeldt-Jakob and bovine spongiform encephalopathy (Mad Cow Disease). Yet the implicated protein, known as a prion and only about 200 amino acids long, can initiate and propagate a disease cycle just by changing its shape. Prions are amyloids, which are misfolded proteins now implicated in numerous diseases. Studying the prion diseases has required patience and fortitude because of disorder and insolubility of the prion samples. Aided by four U.S. Department of Energy x-ray beamlines, a collaborative research team have achieved a significant advance in our understanding of the infectious power of the prion protein.


A Closer Look at Protein Breathing
To take a static view of proteins and regard them as simple strings of amino acids that do grunt work in cells would be a mistake. Decades of biomedical research have proven that proteins are often large, complex in structure, and undergo sophisticated changes in space and time in order to keep cells functioning properly. Some proteins, when in solution, exhibit dramatic fluctuations in their three-dimensional structures, movement that looks like breathing. Because this movement has usually been studied in relatively dilute solutions, and not in the crowded interior of a cell, it has been difficult to know how much of the motion would actually occur in living systems. Researchers used the BioCAT beam-line to study the breathing motions of a diverse group of five animal proteins.

Revealing the Structural Secrets of Plant Viruses
Viruses are extremely successful at finding ways to circumvent just about every host defense system. The secrets to this success seem to lie in their simplicity and in their elegant, often breathtakingly beautiful, and highly functional structures. Viral architecture, especially the coat protein structure, is intricately intertwined with successful invasion and infection of the host. Yet detailed structure information for many viruses have remained elusive. Researchers using the BioCAT x-ray beamline at the APS have obtained important details about the structures of a soybean and a potato virus. This is good news for crop scientists concerned with finding ways to combat viral infestations.

Shedding Light on Protein Drug Interactions
Proteins, the biological molecules that are involved in virtually every action of every organism, may themselves move in surprising ways. This may shed new light on how proteins interact with drugs and other small molecules. For more than a century, the standard model of protein behavior depicted them as inflexible “locks” that could interact only with a small set of equally rigid molecular “keys.” “Proteins are not static, they're dynamic,” said Argonne biochemist Lee Makowski, who headed the project. “Part of the common conception of proteins as rigid bodies comes from the fact that we know huge amounts about protein structures but much less about how they move.”


Mechanisms of a Molecular Trash Disposal
The ubiquitin proteasome system (UPS) is part of the waste management system of a cell. Proteins that are destined to have limited life spans in the cell are identified by labeling the proteins with the molecule ubiquitin---present in all eukaryotes. Once tagged, the proteins are degraded by a complex machine known as the proteasome. The UPS performs its function with specificity that is provided by the class of ubiquitination enzymes called E3 ligases. The E3 ligases identify proteins to be degraded through domains called F-boxes, but the mechanism of enzymatic transfer of ubiquitin to the doomed protein is still not completely understood and may be facilitated by the dimerization of another domain, known as the D-domain. In studies carried out at four APS beam-lines, researchers solved the structures of two of these D-domains. This work provides new insights into the mechanism of the E3 ligases by revealing that D-domain dimerization plays a role in positioning different substrates for ubiquitination.

Muscle-Fiber Research Expands
It is well known that muscle fibers shorten slowly under heavier loads and faster under lighter loads. Now, researchers from the Università degli Studi di Firenze, Università di Roma, Dexela Ltd., the Illinois institute of Technology, and King’s College London, using the Bio-CAT 18-ID-D beamline at the APS, have discovered the molecular basis of this fundamental property of muscle function. Their work was the cover article for the issue of Cell magazine. Understanding exactly how muscle fibers work helps lay the groundwork for the development of new treatments for muscle disorders as well as enhancing the understanding of athletic performance.

Deconstructing Heart Muscle
The stars of muscle contraction---be it the flex of a bicep or the throb of a heart---are microscopic fibres spun from the proteins actin and myosin. To play their parts properly, these proteins need help from an additional, less well-understood molecule known as Myosin-Binding Protein-C. Thanks to data collected at the BioCAT beam-line, researchers from the University of Wisconsin Medical School and the Illinois Institute of Technology have gleaned insights into this protein's contribution to a smoothly beating heart.

A “Copper Bullet” to Kill Cancer
A drug normally used to treat Alzheimer's disease may act as a “copper bullet,” killing tumor cells by coating itself in copper ions. Using the BioCAT beam-line at the APS, researchers from Wayne State University, the Henry Ford Hospital, the Illinois Institute of Technology, and Shandong University found that the drug clioquinol, when mixed with copper, killed two types of prostate cancer cell in Petri dishes. The drug without copper also slowed the growth of prostate tumors implanted in mice by up to two-thirds, apparently by soaking up copper ions present in the implanted tumor cells.


Filling the Gaps in Collagen Structure
Collagens---we might take them for granted, but without them there wold be no way to build the tissues which comprise the heart, skin, cornea, or bones. In much the same way that two-by-fours are used to frame and provide the structure for a house, the protiens called collagens are used as the framework of mammalian tissues. Knowing more about the structure of collagens could help biochemists improve their understanding of heart disease and cancer. But gaining an accurate picture of their three-dimensional structure in vivo has proven difficult. Work performed by a research group at the Illinois Institute of Technology using the BioCAT beam-line has elucidated a complete structure for the collagen molecule as it actually appears in the extracellular matrix.

Sarcomere Synchrony
The mechanical details of muscle contraction have been known for a long time---deduced from experiments with frogs' legs, reconstruction of the proteins involved in crystallographic studies, and other techniques. But no one has ever taken such detailed time-lapse molecular pictures of the proteins at work within a living muscle until researchers from Brandeis University, the University of Florence, and Illinois Institute of Technology wanted to learn if muscle-contracting proteins work the same way inside muscles as they do inside laboratories.

The Correct Signals to Regulate Assembly in Bacteria
“You are what you eat” is just another way of saying that input determines output, after some metabolic messing around in between. It's the “in between” that interests biologists, because that is where the difference between healthy and diseased cells can originate. Disrupting the normal sequence of steps of a biochemical pathway can lead to major changes in cell functioning. Using the BioCAT 18 ID beam-line at the APS, researchers were able to describe---in stunning detail---a novel two-component mechanism for assembling a protein associated with bacterial transcription.

Reaching for answers to questions about the heart
Can studying the mechanisms of stretch activation in insect flight muscle help us learn more about the way our hearts function? Researchers using the BioCAT beam-line at the U.S. Department of Energy's Advanced Photon Source think so.

What Connects Rat Tails to Cancer and Heart Disease?
Innovative synchrotron x-ray research techniques used at APS beamlines have yielded new information on the molecular structure of collagen. Because this ubiquitous protein is involved in the progression of cancer and heart disease, the structural information obtained in this study may help in the fight against these deadly ailments.


Storing the Power to Fly
Fruit flies beat their wings faster than their cellular powerplants can generate the energy needed for flapping them. To study the mechanism which allows fruit flies to fly, researchers from the California Institute of Technology, IIT, and the University of Vermont used the BioCAT beam-line to obtain a series of x-ray diffraction images which reveals the fruit fly's secret.

Atomic Models of Plant Viruses
An “Around the Experiment Hall” interview with Amy Kendall from the Gerald Stubbs Lab in the Department of Biological Sciences at Vanderbilt University.


Measuring the Efficiency of the Myosin Motor at High Load
The sliding filament model of muscle contraction is more than 50 years old, yet theories about the precise mechanisms of the motor funciton still generate controversy. Researchers from Universita di Firenze, Instituto Nazionale di Fisica della Materia, Brandeis University, King's College London, the ESRF, IIT, and ANL used the BioCAT beam-line to take a closer look at the molecular structure of myosin II---the molecular motor in muscle---as it works under various loads.

Finding Active Proteins
When combinatorial chemistry produces new varieties of reagents, the tricky step is figuring out whether those moleucules will be biochemically active. While there are several methods for finding active molecules, they all have limitations. Researchers at ANL employed wide-angle x-ray scattering (WAXS) at the BioCAT beam-line to develop a method for identifying drug candidates.

How Water Molecules are Connected
Water may be the most important molecule on Earth, but our understanding of its properties is embarrassingly limited. In ice, water takes on numerous phases and structures that can be studied by means of diffraction techniques. As a liquid, however, water poses a frustrating structural puzzle. Recently, researchers from SSRL, BESSY, Stockholm University, Linkoeping Unversity, and Ultrecht University used the BioCAT beam-line to obtain detailed information about water.


Grasping the Structure of Insect Muscle Poised to Contract
Researchers at BioCAT have achieved the first detailed view of resting muscle filaments poised to contract---a long sought-after window into the biochemical cycle that causes muscle contraction. The group determined the overall structure of insect muscle fibers from x-ray diffraction patterns and performed computer modelling to analyze the data.


The Role of Interfilament Spacing in Muscle Fliament Calcium Sensitivity
The heart regulates ventricular output in response to changes in ventricular filling, a mechanism known as Frank-Starling's law of the heart. Part of the cellular basis for the law is an increase in myofilament Ca2+ responsiveness upon an increase in sarcomere length. This study investigates how information on sarcomere length is transmitted to myofiliments.

The “Second Stalk” of ATP Synthase: Dimerization Domain Structure
Hydrolysis of adenosine triphosphate (ATP) drives many of the vast range of energy-consuming processes within a cell. The ATP synthase enzyme is a molecular motor that couples proton movement to ATP synthesis. This study focuses on a model for the isolated dimerization domain of the b subunit of Escherichia coli, derived from solution small-angle x-ray scattering (SAXS) of the dimeric domain and x-ray crystallography of the monomer carried out at BioCAT.