Recent science highlights from the ALS-ENABLE beamlines

Understanding of the variability within the DHOase family of proteins

 ALS-ENABLE beamline scientist, Jay Nix, contributed to this paper reporting the structural analysis of dihydroorotase (DHOase) from the hyperthermophilic and barophilic archaeon Methanococcus jannaschii. DHOase catalyzes the reversible cyclization of N-carbamoyl-l-aspartate to l-dihydroorotate in the third step of de novo pyrimidine biosynthesis. DHOases form a very diverse family of enzymes and have been classified into types and subtypes with structural similarities and differences among them. This is the first archaeal DHOase studied by x-ray diffraction. Its structure and comparison with known representatives of the other subtypes help define the structural features of the archaeal subtype. The M. jannaschii DHOase is found here to have traits from all subtypes. Contrary to expectations, it has a carboxylated lysine bridging the two Zn ions in the active site, and a long catalytic loop. It is a monomeric protein with a large β sandwich domain adjacent to the TIM barrel. Loop 5 is similar to bacterial type III and the C-terminal extension is long.


X-ray footprinting used for antibody characterization 

Our review made the cover! This article describes how the method of hydroxyl radical protein footprinting, a solution-state method,  can provide structural and kinetic information on antibodies or antibody–antigen interactions useful for therapeutic antibody design.


Evolution and Innovation of RuBisCO

ALS-ENABLE beamline scientists Daniel Rosenberg and Michal Hammel collaborated with the Shih Lab at UC Berkeley to study patterns of oligomerization in rubisco, nature’s most abundant carbon-fixing enzyme. By using SEC-SAXS-MALS, they were able to conduct a diversity-driven structural study across extant and ancestral form II rubisco and retrace the evolutionary trajectory taken during the evolution of the enzyme.


Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement

Two years into the COVID-19 pandemic, several highly infectious variants of SARS-CoV-2 have emerged. To date, the most potent of them is the Omicron variant. In this paper, ALS-ENABLE scientist Dr. Jay Nix (BL 4.2.2) along with others shed light on the Omicron antigenic shift.


The figure to the right shows the molecular basis of human ACE2 recognition by the SARS-CoV-2 Omicron RBD.

The active site of M. jannaschii DHOase superimposed on a 2mFo-DFc map contoured at 1.7σ.

Crystal Structure of an Archaeal Dihydroorotase

 Dr. Jay Nix at ALS-Enable beamline 4.2.2 collected crystallographic data for this first X-ray diffraction study of the archaeal DHOase, a zinc metalloenzyme that functuions in the pyrimidine nucleotide biosynthesis. Dr. Nix was also key in determining the structure, finding both similarities and differences from other known DHOases.


Identifying potential new drugs for SARS-CoV-2

Crystallographic data collected at ALS-ENABLE beamline 8.3.1 was central in this study identifying small chemical fragments that bind to the Nsp3 macrodomain (Mac1) of the SARS-CoV-2 virus. This protein interferes with immunity, so a drug that inhibits it (sticks to it and stops it from doing that) will help the immune system win. By looking at the 3D image of all the bound fragments at once they came up with a new, larger molecule that sticks tighter than any of the fragments alone. Along with computational docking efforts, this result lays a road map for making even better inhibitors that stick even tighter, minimizing potential side effects.


Using SAXS to evaluate radical scavengers

SIBYLS (beamline 12.3.1) user Tim Stachowski and the Snell group make the cover of the Journal of Synchrotron Radiation for their paper describing their work using Small-angle X-ray Scattering to evaluate how three scavengers commonly used in crystallographic experiments perform in solution at 10°C. In this study, they found the SAXS-based method can detect damage at X-ray doses far lower than those accessible crystallographically, thereby providing a detailed picture of scavenger processes. Their approach provides a platform for more systematic and comprehensive screening of radioprotectants that can directly inform mitigation strategies for both solution and crystallographic experiments, while also clarifying fundamental radiation damage mechanisms.


A study of antibodies that inhibit noroviruses

A study using crystallographic data collected at beamline 5.0.1 works towards the development of a vaccine to combat an acute gastroenteritis disease caused by a human norovirus. Since 2010, according the Center for Disease Control, an estimated 19 to 21 million people in the United States annually have been affected by this disease. Worldwide, there were 1.8 billion cases, 18% of which were caused by HuNoVs.

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MX yields access to SARS-CoV-2 Mpro inhibitors

Collaborative Crystallography beamline 5.0.1 used an affinity-based screen of 4 billion DNA-encoded molecules en masse to identify a potent class of virus-specific inhibitors of the SARS-CoV-2 main protease (Mpro) without extensive and time-consuming medicinal chemistry to help combat the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that has, so far, killed more than 4 million humans globally.


A conserved PLPLRT/SD motif of STING mediates the recruitment and activation of TBK1

Crystal structures from diffraction data collected at beamlines 5.0.2 and 8.2.2 provide a structural basis for the development of STING agonists and antagonists for the treatment of cancer and autoimmune disorders.

Structural biology in the spotlight

ALS Enable scientist helps to determine the atomic structure of a coronavirus protein

Using X-ray crystallography at beamline 5.0.2, Marc Allaire, helped to build an atomic model of ORF8, laying the groundwork for other groups to study the protein in more detail.


SIBYLS makes the cover of Protein Science

SIBYLS scientists Michal Hammel and John Tainer describe the mechanistic insights into NHEJ structural biochemistry determined by small angle X-ray scattering (SAXS) data collected at beamline 12.3.1.

SAXS results were combined with with X-ray crystallography (MX) and cryo-electron microscopy (cryo-EM).

The cover

The cover image, like the old car engine malfunctioning without a linchpin and flexible belt, shows the NHEJ efficiency arises from a flexible conformational control principle. The NHEJ components were matched on the SKODA 100 car engine built in 1973 in Czechoslovakia.

probing real-time solvent accessibility

X-ray footprinting

X-ray footprinting of the Orange Carotenoid protein shows the various regions of solvent accessibility changes upon photoactivation of the protein.

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ALS-ENABLE scientist contributes to Cell publication on SARS-CoV-2 spike protein

ALS-ENABLE scientist, Jay Nix at the MBC beamline 4.2.2 participated in the structure solution for a recently published paper in Cell, Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

               Nasal spray prototype

Helping to stop the rise of SARS-CoV-2

Scientists at ALS Enable contribute to groundbreaking research that may help to stop the rise of SARS-CoV-2 infections that have had devastating effect on our health and economy worldwide. In the article (currently in preprint) the authors describe the development of single-domain antibodies (nanobodies) that potently disrupt the interaction between the SARS-CoV-2 Spike and ACE2. This discovery may enable aerosol-mediated delivery of this potent neutralizer directly to the airway epithelia, promising to yield a widely deployable, patient-friendly prophylactic and/or early infection therapeutic agent to stem the worst pandemic in a century.


Guiding the design of COVID-19 vaccines and therapeutics

ALS Enable scientists contribute to an article published in CELL (volume 183, issue 4, November 12, 2020) in which the authors describe the analysis of the specificity and kinetics of neutralizing antibodies (nAbs) elicited by SARS-CoV-2 infection. This discovery is a crucial part of understanding immune protection and identifying targets for vaccine design.

Link to Publication
Fighting bacterial infections

How Proteins Remodel DNA in Bacteria under Stress

ALS-ENABLE beamlines use multiscale, multimodal visualization techniques to clarify how proteins remodel bacterial DNA in response to stressful environments. At the mesoscale, small-angle x-ray scattering (SAXS) at Beamline 12.3.1 made it possible to determine the overall shapes of HU–DNA complexes in solution. At the nanoscale, protein crystallography at Beamline 8.3.1 allowed identification of the molecular-level mechanisms that mediate DNA bundling.


X-ray Experiments zero in on COVID-19 Antibodies

With help from ALS-ENABLE beamline 5.0.2, an international scienctific team has identified an antibody that neutralizes the COVID-19-causing coronavirus. In a paper published in Nature, the scientists note that the antibody is already moving toward clinical trials.


Assembly Lines for Designer Bioactive Compounds

Researchers successfully bioengineered changes to the molecular “assembly line” for bioactive compounds, based in part on insights gained from Small-Angle X-ray Scattering (SAXS) data collected at SIBYLS beamline 12.3.1.


Characterizing the forces that hold membrane proteins together

Designed membrane proteins are used to better understand the competing forces that stabilize this category of protein.


Designer proteins that fit together like DNA

Proteins designed to mimic the structure of DNA can be used as building blocks for self-assembling protein machines.

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Toward defeating influenza

Structures of several influenza antiviral drug molecules bound to their targets in both open and closed conformations provide an atomic-level blueprint from which to design more effective anti-influenza drugs that can overcome growing drug resistance.

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Designing a protein to capture small molecules

For the first time, scientists have created, entirely from scratch, a protein capable of binding to a small target molecule.


Decoding a Calcium dependent switch

Certain voltage-gated proteins in cell membranes are responsible for controlling the flow of ions across the membrane and thus are important in electrical activity in the heart and brain. This study using both diffraction and scattering beamlines of ALS-ENABLE revealed the role of calcium in the regulation of a class of these important proteins.

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How antidepressants block serotonin transport

Serotonin is a diminutive and deceptively simple-looking neurotransmitter molecule, yet a very complex “machinery” is required for neurotransmitter recognition, transmission, and recycling. The malfunctioning of this protein machinery can cause conditions such as depression, obsessive-compulsive disorder, aggression, anxiety, and Parkinson’s disease. In addition, drugs of addiction, such as methamphetamines, act on this system, causing serious damage and profoundly affecting the well-being of individuals. At the ALS, researchers were able to obtain x-ray crystallographic structures of the difficult-to-crystallize human serotonin transporter bound to two commonly prescribed antidepressant drug molecules. The resulting details about the transporter structure and mechanism will help in the design of new, more effective therapeutics for treating depression and anxiety.

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Behind the new gene-editing tool

The CRISPR-Cas system has recently transformed the way that scientists are able to perform gene editing, making it much easier and more accurate than ever before. In this study, the structures of the system with DNA substrates revealed just how specific DNA code is located with such specificity.

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