Stanford Synchrotron Radiation Lightsource

Cells bind each other using specialized cell surface adhesion complexes called adherens junctions. These complexes direct the formation of tight, Velcro-like contacts that are essential for the development, architecture, maintenance, and function of tissues in all higher organisms. Exactly how this cell to cell binding is accomplished has not been fully understood.  Researchers from the Florida campus of The Scripps Research Institute (TSRI) have now solved a piece of this puzzle by determining the structure of α-catenin using SSRL’s Beam Line 11-1.

Understanding the physical underpinnings of how proteins interact specifically with one another and not with the myriad other molecules that coexist in every cellular compartment is a major goal of molecular biology. The broad outlines of an answer were suggested by Linus Pauling in the 1940’s: the aggregate effect of numerous weak and nonspecific van der Waals, hydrogen-bonding, and electrostatic interactions underlie high specificity and affinity. Since Pauling’s days thousands of co-crystal structures have provided concrete examples for how molecular recognition is achieved in different biological contexts. Yet, the ultimate proof for understanding a natural phenomenon lies in recapitulating it; in the words of Thomas Edison, ‘until man duplicates a single blade of grass, Nature laughs at his so-called scientific knowledge’.

Researchers have for the first time obtained a high-resolution structure of a three-molecule receptor-ligand complex that could help shed light on neurodegenerative diseases such as Parkinson's. The complex includes two receptor molecules, called GFRα3, bound with its ligand, artemin, which fit together like a lock and key. These molecules play a key role in chemical signal transmission and in the development and health of neurons.

Manganese oxides form in the oceanic water column as a result of the bacterially catalyzed oxidation of a relatively abundant form of dissolved manganese. As they settle through the water column, manganese oxides participate in myriad chemical reactions important to sea life and to maintaining the trace-metal composition of sea water. These reactions profoundly impact the geochemical cycling of carbon, nitrogen, sulfur, nutrients and containments.

Researchers have literally unearthed clues as to why the 1918 influenza pandemic was so deadly. The 1918 influenza pandemic ranks as the largest and most destructive outbreak of an infectious disease, killing 20 to 40 million people worldwide. Using fragments of the flu genome from Alaskan victims preserved by permafrost and army autopsy tissues, James Stevens and Ian Wilson of the Scripps Research Institute in La Jolla, California and their collaborators have assembled genes from the 1918 flu virus.

Prostate cancer, the most common cancer in men, is often a localized, slow-growing cancer, which aids treatment and improves survival rates.  However, highly aggressive, metastatic forms of the cancer occur frequently enough to make it the No. 2 cause of death in U.S. men.  Part of the reason for this high mortality rate is the lack of effective drugs to fight these more aggressive cancers. 

When a blood vessel is cut, the body activates a repair mechanism that eventually seals the cut and prevents further blood loss. This life saving process becomes life threatening when clots form inside a functional blood vessel. Arrest of bleeding works through platelet adhesion and thrombin-induced fibrin formation at the site of injury. In order for the platelets to stick to the injured tissues and to each other, they need to be activated. Thrombin is an essential protease (a type of enzyme) that activates platelets and forms blood clots in response to vascular injury.

Autism is considered among the most devastating neurological disorder conditions of early childhood. Now, researchers working in part at SSRL's Beam Line 4-2 have determined a three-dimensional structural model of a complex with the only two extracellular synaptic proteins implicated in autism spectrum disorders and mental retardation. Such a finding could deepen our understanding of this mysterious and debilitating type of disorder. The findings were published in the June 2007 edition of the journal Structure.

The presence of "methyl mercury" in fish is well-known, but until now the detailed chemical identity of the mercury has remained a mystery. In an x-ray absorption spectroscopy study published in the August 29 issue of Science (Science 301, 2003: 1203;Science now: Murky Picture on Fish Mercury), SSRL scientists report that the chemical form of mercury involves a sulfur atom (most likely in a so-called aliphatic form). The study presents significant new knowledge - because the toxic properties of mercury (or any element) are critically dependent upon its chemical form - and represents an important milestone in developing an understanding of how harmful mercury in fish might actually be. The study was carried out by SSRL staff scientists Ingrid Pickering and Graham George and postdoctoral fellow Hugh Harris using SSRL's structural molecular biology beam line 9-3. The very high flux, excellent beam stability and state-of-the-art detector technology allowed the team to measure samples of fish containing micromolar levels of mercury, much lower than had previously been possible.

Proteins containing iron-sulfur clusters are ubiquitous in nature and catalyze one-electron transfer processes. These proteins have evolved into two classes that have large differences in their electrochemical potentials: high potential iron-sulfur proteins (HiPIPs) and bacterial ferredoxins (Fds). The role of the surrounding protein environment in tuning these redox potentials has been a persistent puzzle in the understanding of biological electron transfer. Although high potential iron-sulfur proteins and ferredoxins have the same iron-sulfur structural motif, there are large differences in their electrochemical potentials.

Life depends on the biochemical activity of the thousands of proteins that inhabit and decorate the surface of every one of our cells. Proteins themselves, although simple linear combinations of the twenty amino acids, derive their remarkable properties from the complex three-dimensional structures into which they fold. In this way, enzyme active sites are created, protein-protein recognition surfaces are formed, and the chemistry of life is set in motion.

The development of bacterial resistance to conventional antibiotics is a major public health concern. For example, methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE) and Staphylococcus aureus (VRSA) have emerged as common nosocomial (hospital-originating) infections. Circumvention of such resistance may be possi ble by emulating host defense antimicrobial peptides (AMP's), which are found in a broad range of species and have broad-spectrum antimicrobial properties.

Stanford University School of Medicine scientists working in part at SSRL's Beam Line 11-1 have uncovered new molecular insights to the mechanism behind immune disorders such as asthma. Using protein x-ray crystallography at 3.0 Angstrom resolution, researchers Sherry LaPorte and Chris Garcia solved three structures of two signaling proteins known as "cytokines" in complex with their shared receptors, where these molecules help regulate immune system activity. The study was published as the cover story in the January 25 edition of the journal Cell.

Iron plays an integral role in many biochemical processes essential for life. However excess iron leads to the production of highly reactive hydroxyl radicals by Fenton chemistry (1). These free radicals are deleterious to cells as they react indiscriminately with proteins, DNA and lipids. Hence, iron homeostasis is a highly regulated process and is critical to human health (2). Disorders in iron metabolism, are however, surprisingly common.

Using macromolecular crystallography techniques, the team solved the structure of a protein on the Ebolavirus's surface, called glycoprotein GP, in complex with a rare antibody identified in a human survivor. The glycoprotein-antibody complex proved especially challenging to crystallize and subsequently, to yield well-diffracting crystals. The team grew ~50,000 crystal samples and screened 800 of the largest, using in part the highly-automated robotics hardware and software at the SSRL beam lines, before finding a sample that would diffract to 3.4 Angstroms.

DNA is a relatively stable molecule, but it can be damaged by chemicals generated inside our cells or by radiation originating from outside our cells. Significant amounts of DNA damage can lead to rapid-aging, cancer, and other diseases, so the cell has a fleet of enzymes that specialize in combating this daily wear-and-tear. One important group of DNA repair enzymes is the Rad60 family of proteins that is highly conserved from yeast to humans.

The genome of the human immunodeficiency virus (HIV-1) is bundled inside a capsid composed of about 1,500 copies of the viral Capsid Assembly (CA) protein. These proteins first assemble into substructures, each with six proteins, and these substructures come together to create the cone-shape casing of the virus. Disruption of capsid formation is a natural target for HIV therapies, and knowing the atomic structure of the CA proteins in the capsid would be useful for drug development. However, inherent flexibility in these molecules makes obtaining quality crystals difficult.

UC Irvine researchers have unveiled the mystery behind one of the deadliest toxins that causes liver cancer. Aflatoxins are common contaminants of foods such as nuts and grains, which make up the staple diets of many developing countries. These toxins are produced by moldy fungi during food production, and are considered by the FDA to be an unavoidable food contaminant. Aflatoxin molecules are characterized by the presence of multiple aromatic rings. Chronic ingestion of aflatoxin B1 leads to liver tumors that are a major cause of death in Asia, Africa, and Central America. This toxin wreaks havoc of p53, an important gene in our body that prevents cancer. Without the protective effect of p53, then, aflatoxin further compromises immunity, interferes with our body metabolism, and causes severe malnutrition. It is urgently important to find inexpensive strategies that help protect the world population from aflatoxin food contamination.

An unusual property of the last year's H1N1 "swine flu" virus pandemic is that it disproportionately affected the young. People over the age of around 65 showed much less vulnerability than to more typical flu strains, suggesting that they might have been exposed to a similar virus over three decades ago. Another atypical property of the 2009 H1N1 strain is that its hemagglutinin (HA) subunit is the same subtype as the regular seasonal strains, whereas most pandemics are caused by viruses with novel HA domains.

Semaphorins are a group of proteins known for their critical role in nerve and vascular development and are bound by signaling receptors called Plexins. Some Semaphorins, including Sema7A, are involved in a variety of immune responses. Vaccinia virus, which is used in the smallpox vaccine, has a Sema7A homologue called A39R, which binds PlexinC1, Sema7A's receptor. 

Viruses are dependent on the cellular machinery of their host cells, and often evolve tricks that allow them to sidestep the usual cellular protocols and more efficiently take advantage of cellular resources. Such is the case with a group of viruses that use an RNA sequence called an internal ribosome entry site (IRES), which allows their RNA to be efficiently translated into protein without the normal necessity of a more complicated cap structure. Certain IRESs do this by structurally mimicking a tRNA and mRNA in a way that can fit into the ribosome’s internal tRNA binding site.

While nitrogen in the air is abundant, nitrogen as a form usable to life is limited. Bacteria associated with legumes use an enzyme called nitrogenase to combine N₂ from the atmosphere with water to make ammonia, a form the plant can use. Since the early 1900s, industrial fertilizers have been made through a chemical method called the Haber-Bosch process.  Because these reactions require high temperatures, pressures, and fossil fuels, scientists have renewed interest in learning how the bacteria perform their reactions.

By knowing the structures of proteins and their complexes with other molecules, biomedical scientists and biochemists can better understand how they work.  This knowledge can lead to the design of new drugs and the engineering of faster enzymes for industrial applications, among many other applications. In x-ray crystallography, researchers send x-ray beams generated by a high-energy synchrotron like SSRL at protein crystals; the x-rays are diffracted from the periodic arrangement of protein molecules in the crystal, allowing the researchers to compute a three-dimensional electron density map of the protein molecule—which in turn allows for the mapping of individual atoms. The quality of the electron density map ultimately determines the accuracy of the atomic positions, and hence the overall quality of the protein structure.

Strategies to combat HIV require structural knowledge of how antibodies recognize HIV envelope proteins and how they are used by the immune system to eliminate viruses and virally-infected cells. A few years after infection, some HIV-infected patients develop broadly neutralizing antibodies (bNAbs), which neutralize across many HIV strains and confer protection against simian immunodeficiency virus (SIV) infection in non-human primates when delivered by passive immunization (i.e. purified Abs were injected).

Transport proteins, embedded in lipid membranes, facilitate the import of nutrients into cells or the release of toxic products into the surrounding medium. The largest and arguably the most important family of membrane transport proteins are the ABC transporters. They are ubiquitous in biology and power the translocation of substrates across the membrane, often against a concentration gradient, by hydrolyzing ATP (Higgins, 1992). 

Protein crystallography can routinely determine the 3D structure of protein molecules at near atomic or atomic resolution. The bottleneck of this methodology is to obtain sizable and good quality protein crystals. Overcoming the crystallization difficulty requires the development of the new methodologies. One approach is to use NMR to image protein molecules in solvent. However, it is only applicable primarily to macromolecules in the lower molecular weight range. Another approach under rapid development is single molecule imaging using cryo electron microscopy (cryo-EM).