Watch the assembly of the Grand Tube at the APS

The Advanced Photon Source (APS) Upgrade will result in X-ray beams that are up to 500 times brighter than those generated by the original APS. But that’s only half the story. The upgrade team is also building seven new beamlines, constructing critical infrastructure to enable two more beamlines to be built, and updating many other experiment stations around the ring. 

Work on the beamlines is ramping up. One of the most visible recent projects has been the assembly of the Grand Tube at beamline 9-ID. The Grand Tube is a 70-foot-long enclosure that will enable a new X-ray technique called Coherent Surface Scattering Imaging (CSSI). This will allow scientists to image extremely small materials in three dimensions on a scale previously unattainable. 

The Grand Tube, weighing 100,000 pounds, arrived at Argonne in four sections and took three weeks to assemble. The video below shows the scale of the enclosure and the process of putting it together on the APS experiment floor.

Watch the Grand Tube assemly video here

APS to accelerate biological and environmental research

The eBERlight program aims to connect the world-leading X-ray facility with more scientists studying Earth’s climate, environment and bioeconomy crops.

The Earth is a complex ecosystem, and our place in it is dependent on many different factors. From soil health to air quality to the behavior of plants and microorganisms, understanding our natural world and its other inhabitants is vital to our own survival. As the climate continues to change, research into the environment and its diverse forms of life will only become more important.

In October 2023, the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory, will officially launch a new initiative to expand biological and environmental research at the world leading X-ray and analysis facility. The enterprise, dubbed eBERlight, recently received approval from DOE’s Biological and Environmental Research (BER) program. Its goal is to connect researchers conducting experiments within the BER mission with the world-leading X-ray science resources of the APS. By increasing access to multiple capabilities at the APS, the minds behind eBERlight hope to find new scientific approaches and engage new groups of multidisciplinary researchers towards investigating new insights about the world in which we live.

“This is an opportunity to build something new that, until now, hasn’t existed at APS,” said Karolina Michalska, a protein crystallographer at Argonne who is leading the eBERlight effort. ​“We’re broadening the access to accommodate more biological and environmental research, and since this program is so new, the scientists who will use the facility are helping us to develop it.”

Read more on the APS website

Image: The eBERlight program at the Advanced Photon Source will enable research into many areas of biological and environmental science, including studies of crop growth for biofuels and biomanufacturing.

Credit: Shutterstock/JJ. Gouin

New catalyst could cut pollution from millions of engines

Researchers demonstrate a way to remove the potent greenhouse gas from the exhaust of engines that burn natural gas.

Individual palladium atoms attached to the surface of a catalyst can remove 90% of unburned methane from natural-gas engine exhaust at low temperatures, scientists reported today in the journal Nature Catalysis

While more research needs to be done, they said, the advance in single atom catalysis has the potential to lower exhaust emissions of methane, one of the worst greenhouse gases, which traps heat at about 25 times the rate of carbon dioxide. 

Researchers from the Department of Energy’s SLAC National Accelerator Laboratory and Washington State University showed that the catalyst removed methane from engine exhaust at both the lower temperatures where engines start up ­­­and the higher temperatures where they operate most efficiently, but where catalysts often break down. 

“It’s almost a self-modulating process which miraculously overcomes the challenges that people have been fighting – low temperature inactivity and high temperature instability,” said Yong Wang, Regents Professor in WSU’s Gene and Linda Voiland School of Chemical Engineering and Bioengineering and one of four lead authors on the paper. 

A growing source of methane pollution 

Engines that run on natural gas power 30 million to 40 million vehicles worldwide and are popular in Europe and Asia. The natural gas industry also uses them to run compressors that pump gas to people’s homes. They are generally considered cleaner than gasoline or diesel engines, creating less carbon and particulate pollution.

However, when natural-gas engines start up, they emit unburnt, heat-trapping methane because their catalytic converters don’t work well at low temperatures. Today’s catalysts for methane removal are either inefficient at lower exhaust temperatures or they severely degrade at higher temperatures. 

“There’s a big drive towards using natural gas, but when you use it for combustion engines, there will always be unburnt natural gas from the exhaust, and you have to find a way to remove that. If not, you cause more severe global warming,” said co-author Frank Abild-Pedersen, a SLAC staff scientist and co-director of the lab’s SUNCAT Center for Interface Science and Catalysis, which is run jointly with Stanford University. “If you can remove 90% of the methane from the exhaust and keep the reaction stable, that’s tremendous.”

A catalyst with single atoms of the chemically active metal dispersed on a support also uses every atom of the expensive and precious metal, Wang added. 

“If you can make them more reactive,” he said, “that’s the icing on the cake.”

Unexpected help from a fellow pollutant 

In their work, the researchers showed that their catalyst made from single palladium atoms on a cerium oxide support efficiently removed methane from engine exhaust, even when the engine was just starting. 

They also found that trace amounts of carbon monoxide that are always present in engine exhaust played a key role in dynamically forming active sites for the reaction at room temperature. The carbon monoxide helped the single atoms of palladium migrate to form two- or three-atom clusters that efficiently break apart the methane molecules at low temperatures. 

Then, as the exhaust temperatures rose, the clusters broke up into single atoms and redispersed, so that the catalyst was thermally stable. This reversible process enabled the catalyst to work effectively and used every palladium atom the entire time the engine was running – including when it started cold.

Read more on SLAC website

Ready, set, upgrade: Advanced Photon Source’s overhaul is underway

The facility is undergoing a comprehensive upgrade. Afterwards, the new APS will be able to generate X-ray beams 500 times brighter

Over the past three years, thousands of machine parts have been delivered to a low-slung, deceptively plain building in Lemont, Illinois. Once a warehouse, Building 981 is now a workshop — an extremely sophisticated one. Inside, a multitalented team assembles the building blocks of a complicated yet elegant machine, one that will sit at the heart of the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory.

This new machine is part of a comprehensive upgrade to the facility, one that will set it at the forefront of global X-ray science for decades to come.

More than 5,500 scientists in a typical year use the APS for its intensely bright X-ray beams. Since it began operating in the mid-1990s, the APS has enabled advances in the fields of medicine, energy, climate, physics and more. The drug Paxlovid, devised to treat COVID-19, emerged from work at the APS. So did two Nobel Prizes in chemistry. These and many other breakthroughs have resulted from the APS’s ability to illuminate the otherwise invisible.

“The APS Upgrade opens up possibilities that could not be envisioned till now.” — Suresh Narayanan, Argonne Physicist

Now comes a moment more than a decade in the making. The APS’s powerful engines shut down on April 24, to make way for this new machine, called a storage ring, which circulates electrons in order to deliver X-ray beams up to 500 times brighter than the current one. That required first dismantling the existing storage ring, which spanned about two-thirds of a mile around. This phase of the project is now complete. The next phase will see the new components from Building 981 — preassembled into 200 modules weighing up to 50,000 pounds each — moved in this summer, when installation will begin in earnest.

Read more on the Argonne website

Image: Workers remove the final girder of the original APS. The new ring will be made up of 200 modules, each with precisely aligned electromagnets and complex vacuum and electrical systems

Credit: Argonne National Laboratory J.J Starr

Historic Advanced Photon Source magnet sees the light of day for the first time in 29 years

Historic Advanced Photon Source magnet sees the light of day for the first time in 29 years

Many of the Argonne employees who signed the magnet in 1994 still work for the laboratory, and their experiences building the original APS are vital to the ongoing effort to upgrade the facility.

On September 8, 1994, a group of people affixed their signatures in white ink onto a long red magnet. This was the final dipole magnet (of 81, including spares) built and tested for inclusion in a complex machine known as the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory. By sheer chance, it also happened to be part of the final module of magnets to be installed in the APS facility.

Once signed, the magnet took its place next to its fellows and, for the next 28 years, it helped to steer particles called electrons circulating in a large storage ring. Those electrons were manipulated to create bright X-ray beams that thousands of scientists have used over the years to conduct thousands of experiments for the betterment of humankind.

“We expect the new machine to work a hundred times better than the old one. We learned many lessons building the APS, and the best part is that many of the people who learned those lessons are around now to help us build the new one.”  — Glenn Decker, APS Upgrade Project

Now the original APS is undergoing an $815 million upgrade, and the original APS storage ring is being removed to make way for a more modern one. And so, on May 23, the signed dipole magnet was taken back out of the storage ring facility, seeing the light of day for the first time in 29 years. As it emerged, it brought with it many memories, emerging fresh in the minds of those who were there in 1994, building a dream machine.

Read more on the Argonne website

Image: The final module of magnets to be installed in the Advanced Photon Source in September 1994, surrounded by several of the people who signed it at the time. The module was removed in May 2023 as part of the APS Upgrade Project.

Credit: Jason Creps, Argonne National Laboratory

A first step to designing better solid-state batteries

Electrifying transportation is an essential step towards mitigating climate change. To improve the power, efficiency and safety of electric vehicles, researchers must continue to develop better batteries. All-solid-state lithium batteries (SSBs), which have a solid electrolyte instead of a liquid, are safer than traditional lithium-ion batteries because they are less flammable and more stable at higher temperatures. They could also have higher energy densities than lithium-ion batteries, allowing for longer lasting batteries in smaller sizes for portable electronics and other applications.

A research team led by Joshua Gallaway of Northeastern University in Boston and scientists at the Department of Energy’s (DOE) Argonne National Laboratory recently tested how the composition of thick cathodes affected electrochemical reactions in SSBs. The team used the resources of the Advanced Photon Source (APS), a DOE Office of Science user facility at Argonne. Their discoveries were published in the journal ACS Energy Letters.

“How all-solid-state batteries are designed will determine what their applications will be and how they will be optimized moving forward,” — Josh Gallaway, Northeastern University

Gallaway relates batteries to sandwiches — they are comprised of an anode on one side, a cathode on the other, a separator in the middle, and electrolyte solution throughout. When batteries provide power, lithium ions flow from the anode to cathode through the electrolyte. While SSBs don’t require traditional separators because the electrolyte separates the anode and cathode, they do require thick cathodes.

In this study, Gallaway and his colleagues evaluated batteries with thick cathodes that were comprised of two materials: a sulfide solid electrolyte called LPSC and an NMC (nickel, manganese, cobalt) cathode active material (CAM). They altered the composition of these two materials, so some batteries were 80% CAM, 20% LPSC, while others were 70% CAM, 30% LPSC and 40% CAM, 60% LPSC. Then, they used X-ray imaging and scattering at APS beamline 6-BM-A to measure six slices within the cathode and solid-state electrolyte.

Read more on the Argonne website

Image: An all-solid-state battery on an experimental stage used in the study. The battery is compressed in a vise and has a laser shining on it to align the X-ray beam.

Credit: Josh Gallaway/Northeastern University, Boston.

The APS prepares for its renewal

The facility’s ultrabright X-ray beams will turn off for a year to enable a comprehensive upgrade, one that will light the way to new breakthroughs

With the start of the construction period, the Advanced Photon Source is now only a year away from re-emerging as a world-leading X-ray light source. Its brighter beams will lead to new discoveries in energy storage, materials science, medicine and more.

Today, a year-long effort to renew the Advanced Photon Source (APS), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory, officially begins.

After years of planning and preparation, the team behind the APS Upgrade project will now spend the next 12 months removing the old electron storage ring at the heart of the facility, replacing it with a brand new, state-of-the-art storage ring and testing the new ring once it is in place. The team will also build seven new experiment stations, construct the needed infrastructure for two more and update nearly every existing experiment station around the APS ring.

This is an extensive project, representing an $815 million investment from DOE. When complete, the APS will re-emerge as a world leader in global hard X-ray synchrotron science, enabling unimaginable new discoveries. Science conducted at the APS will lead to longer-lasting, faster-charging batteries, more durable airplane engines and better treatments for infectious diseases, among many other discoveries.

“The APS Upgrade is not only an investment in the facility’s future, but in the next 25 years of advancements that will change the way we power our vehicles, harness renewable energy and learn more about the fundamental science that underpins our future technologies.” — Linda Horton, associate director of science for Basic Energy Sciences, U.S. Department of Energy.

“This is a significant day for Argonne,” said Argonne Director Paul Kearns. ​“The APS Upgrade will transform the future of science for America and the world. Once we safely complete construction, the APS will shed new light on how the brain works, develop materials to decarbonize our economy, refine quantum technologies that can power the internet of the future and answer many other questions in numerous other disciplines.”

Read more on the Argonne National Laboratory website

Image: The Advanced Photon Source is undergoing a comprehensive upgrade that will result in X-ray beams that are up to 500 times brighter than the current facility can create. After a year-long shutdown, the upgraded APS will open the door to discoveries we can barely imagine today

Credit: Argonne National Laboratory/JJ Starr

X-rays make 3D metal printing more predictable

Insights into the microscopic details of 3D printing gained using the microXAS beamline of the Swiss Light Source SLS could propel the technology toward wider application.

Researchers have not yet gotten the additive manufacturing, or 3D printing, of metals down to a science completely. Gaps in our understanding of what happens within metal during the process have made results inconsistent. But new research could grant a greater level of mastery over metal 3D printing.

Using powerful x-rays generated by the Swiss Light Source SLS and Argonne National Laboratory’s Advanced Photon Source, researchers at Paul Scherrer Institute PSI, the National Institute of Standards and Technology (NIST), KTH Royal Institute of Technology in Sweden and other institutions have peered into the internal structure of steel as it was melted and then solidified during 3D printing. The findings, published in Acta Materialia, unlock a computational tool for 3D-printing professionals, offering them a greater ability to predict and control the characteristics of printed parts, potentially improving the technology’s consistency and feasibility for large-scale manufacturing. 

“So-called operando measurements with x-rays enable us to capture what is really happening to the microstructure during a rapid process such as printing.” said Steven Van Petegem, senior scientist at PSI, who led the experimental work performed at the SLS using the microXAS beamline.

Read more on the PSI website

Image: Researchers used high-speed X-ray diffraction to identify the crystal structures that form within steel as it is 3D-printed. The angle at which the X-rays exit the metal correspond to types of crystal structures within.

Credit: H. König et al. via Creative Commons (https://creativecommons.org/licenses/by/4.0), adapted by N. Hanacek/NIST

Keeping track of the thousands of components needed to upgrade the APS

As the APS Upgrade’s supply chain coordinator, Aleksander Stankovik conducts detailed planning and forecasting to ensure all the materials are in place.

By Marguerite Huber

The Advanced Photon Source (APS) is shutting down for a year to undergo a complex and extensive upgrade. It’s a major investment in the future of science, as well as a significant investment in the APS, a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Argonne National Laboratory.

Behind the scenes of the upgrade, Aleksander Stankovik keeps track of the tens of thousands of components and materials needed for the project. As supply chain coordinator, Stankovik uses a component database, which includes approximately 30,000 entries, to manage all the inventory and assembly data.

“We cannot spend time searching for something,” explained Stankovik.” All the components we are using, you cannot go to a local store and buy them. You need to know at any given time where something is and how to get it. That’s a non-negotiable for this project.”

Stankovik joined Argonne and the APS in 2020 after spending years in logistics and supply chain management, helping to build energy facilities, chemical plants and refineries around the world as a government contractor. When the COVID-19 pandemic struck, a project he was working on was put on hold and Stankovik looked for another position. He was inspired by the challenge of the APS Upgrade.

“I knew that this was a different industry, but I was confident that my knowledge and experience would be of great value to the project team,” said Stankovik. “I was hoping that if I could join Argonne, I would be able to share my knowledge, learn new things, make a few more friends, and help to successfully complete the project.”

Read more on the APS website

Image: Aleksander Stankovik, supply chain coordinator for the Advanced Photon Source Upgrade.

Treating COVID-19 by inhibiting viral replication

When SARS-CoV-2, the virus that causes COVID-19, enters a person’s cells, it hijacks those cells to make more viruses. First SARS-CoV-2 releases its RNA into the host cell. Then the host ribosomes translate the viral RNA into two giant protein chains (polyproteins). One protein in the giant chain, called MPro, cleaves the chain into smaller proteins, which help create more viruses and, therefore, more infection. Because of MPro’s role in initiating the viral replication process, the protein has become a target for antiviral drug developers. Recently, a team of scientists using high-brightness x-rays at the U.S. Department of Energy’s Advanced Photon Source (APS) has determined x-ray crystallographic structures of MPro cleaving the polyprotein at ten cleavage sites. Their findings, published in the journal Nature Communications, provide information about the mechanistic steps and molecular interactions that initiate viral replication, which can be used to inform antiviral therapeutic development for COVID-19, as well as other conditions for which MPro may be responsible.

Viruses can’t reproduce on their own; they need a human or animal cell to make other viruses and continue their infectious rampage. The SARS-CoV-2 virus, which causes COVID-19, employs its spike protein to enter a human cell. Once inside, the virus’s protective coating dissolves, and it dumps its genetic material—RNA—into the host cell. This RNA contains all the instructions the virus needs to replicate. What’s more, it comes in a handy form that is ready for a human cell to translate into proteins that will compose the next generation of viruses.

The SARS-CoV-2 RNA includes instructions for four proteins that make up the virus’s structure—its spike protein, protective coating, and the like—and sixteen proteins that replicate the virus. The replication process begins when the host’s ribosomes translate the replication genes into two gigantic protein chains called polyproteins.

Before replication can continue, however, these gigantic chains must be chopped up into their constituent proteins. Remarkably, the molecule that does the chopping is itself contained in the polyprotein and must hack its way out of the chain before attending to its neighbors.

Read more on the APS website

Image: Fig. 1. The amino acid residues preceding the SARS-CoV-2 polyprotein cleavage site between non-structural proteins nsp10 and nsp11 are shown in yellow. These residues are bound within the Mpro acceptor active site groove (grey semitransparent molecular surface).

Looking into the heart of an antibiotic killer

β-lactam-based antibiotics currently account for about 65% of all applied antibiotics, due to their broad-spectrum of activity and favorable safety profile, making this class of drugs the most common clinical approach for treating bacterial infections. Examples of these drugs, which contain a β-lactam ring in their structure, include naturally occurring penicillins, and synthetic cephalosporins, monobactams, and carbapenems. Antibiotics with a β-lactam core target bacterial transpeptidases—enzymes necessary for cell-wall synthesis—and they block the formation of cross-bridges between adjacent peptidoglycan chains, leading to bacterial death. Overuse of β-lactam antibiotics has led to an increase in microorganisms with multidrug resistance. In β-lactam antibiotics, this resistance is driven primarily by bacterial enzymes called b-lactamases. Researchers have now revealed the crystal structure, binding, and cleavage of moxalactam antibiotic bound to L1 metallo-β-lactamase (MBL) from the emerging pathogen Stenotrophomonas maltophilia using the U.S. Department of Energy’s Advanced Photon Source (APS). Drug discovery based on the details captured in this study could contribute key information to counteract antimicrobial resistance and provide tools in future pandemics. The results were published in the journal Nature Communications.

Read more on the APS website

Image: Fig. 1. TR-SSX crystal structure of moxalactam of the active site of L1 MBL, L1 active site structure at 150 ms with hydrolyzed moxalactam (in yellow-red-blue), zinc (magenta) and protein residues (in silver-blue-red).

Structure-based Protein Design Advances Vaccine Development for Human Metapneumovirus

When the U.S. Centers for Disease Control and Prevention began investigating several cases of severe respiratory illnesses around the state of North Dakota in 2016, they uncovered the presence of a serious and potentially life-threatening virus known as human metapneumovirus (hMPV). Within four hospitals across the state, 44 cases of hMPV were uncovered impacting both children (17) and adults (27). And although many healthy populations are not severely impacted by hMPV, five of the patients from this outbreak―including two children, succumbed to the illness. hMPV like COVID-19, which would surface only three short years later, and other transient viruses suffer from the same problem: a lack of information. The cases in North Dakota show that hMPV can have serious health implications for some patient populations, but the lack of understanding about this virus, and countless others, means that there are no vaccines or therapeutics available to help protect at-risk groups. Fortunately, this issue is starting to change. In a recent study published in Nature Communications, a team of researchers carrying out experiments at the U.S. Department of Energy’s Advanced Photon Source (APS) have isolated and characterized highly stable hMPV fusion (f) proteins that are critical for viral entry. The insights reported not only provide the structure-function relationship of these fusion proteins, but also highlight the potential for these proteins to advance the development of hMPV vaccines and therapeutics.

COVID-19, which has resulted in the death of more than 6.6 million people around the world, has brought dialogue about vaccines and immunity back to the forefront of public conversation. And although devastating viral infections like polio, hepatitis A&B, Haemophilus influenzae type B, measles, and mumps have essentially been erased from the U.S. vernacular due to successful vaccination programs, few people are aware that many debilitating and long-standing viral pathogens, like chikungunya virus, Dengue virus, eastern equine encephalitis virus, cytomegalovirus, respiratory syncytial virus and a number of other viruses still lack the basic research to develop adequate vaccines and therapeutics.

Similarly, the devastating hMPV virus that struck North Dakota in 2016 lacked the basic research information for vaccine development and remains without a vaccine in 2022.

Read more on the APS website

Image: Fig. 1. Crystal structure of perfusion-stabilized hMPV F (DS-CavES2) made with ChimeraX with substitutions shown as spheres, determined at SBC-XSD.

#SynchroLightAt75 – APS lights the way to 2012 Chemistry Nobel

Thanks in part to research performed at the U.S. Department of Energy’s (DOE) Argonne National Laboratory, the 2012 Nobel Prize in Chemistry was awarded today to Americans Brian Kobilka and Robert Lefkowitz for their work on G-protein-coupled receptors.

G-protein-coupled receptors, or GPCRs, are a large family of proteins embedded in a cell’s membrane that sense molecules outside the cell and activate a cascade of different cellular processes in response. They constitute key components of how cells interact with their environments and are the target of nearly half of today’s pharmaceuticals.

These medicines work by connecting with many of the 800 or so human GPCRs. But to do this well, a drug needs to connect to the protein like a key opens a lock. Improving drugs requires knowing exactly how these proteins work and are structured, which is difficult because the long, slender protein chains are folded in an intricate pattern that threads in and out of the cell’s membrane.

In a study performed at Argonne in 2007, Kobilka, a professor at Stanford University, used intense X-rays produced by the laboratory’s Advanced Photon Source (APS) to make the first discovery of the structure of a human GPCR. This receptor, called the human β2 adrenoreceptor (β2AR), is responsible for a number of different biological responses, including facilitating breathing and dilating the arteries.

Read more on the Argonne National Laboratory website

Image: This is an image of a G-protein-coupled receptor signaling complex whose structure was identified in 2011. The receptor is in magenta while the different G protein subunits are colored green, red and blue. Stanford biochemist Brian Kobilka shared the 2012 Nobel Prize in Chemistry for his work in determining the structure of this activated GPCR using X-rays provided by Argonne’s Advanced Photon Source.

New insights of how the HIV-1 assembles and incorporates the Env protein

Assembly of HIV-1, which causes AIDS, takes place on the inner plasma membrane leaflet of infected cells, a geometric building process that creates hexamers out of trimers of the viral Gag protein, as guided by Gag’s N-terminal matrix domain.

Yet certain details of that virion assembly have been lacking for four decades. In a study published in the journal Proceedings of the National Academy of Sciences of the United States of America, Jamil Saad, Ph.D., University of Alabama at Birmingham (UAB), and colleagues provide the first atomic view of the matrix lattice, a step that advances the understanding of key mechanisms of viral assembly and viral envelope protein incorporation.

“Our findings may facilitate the development of new therapeutic agents that inhibit HIV-1 assembly, envelope incorporation and ultimately virus production,” said Saad, a professor of microbiology at UAB.

The Gag protein is post-translationally modified, in which a lipid-like myristate group is added to help Gag bind to the plasma membrane. How the myristoylated matrix domain, or myrMA, of Gag assembles into lattice eluded detection until now. 

Techniques with low molecular resolution — such as cryo-electron diffraction and cryo-electron tomography — suggested that the myrMA protein organizes as trimers, and these trimers then undergo higher-order organization to form hexamers of trimers. Saad’s study is consistent with a recent study, which suggested that the myrMA protein undergoes dramatic structural changes to allow the formation of distinct hexameric lattices in immature and mature viral particles. Virus maturation is the last step of the virus replication cycle, as the capsid core forms inside the assembled virus, yielding infectious particles.

The envelope protein of HIV-1, or Env, is a transmembrane protein delivered to the plasma membrane by the cell’s secretory pathway. The bulk of the Env protein extends beyond the membrane, but a tail hangs through the membrane back into the inside of the cell. Genetic and biochemical studies have suggested that incorporation of the viral Env protein into the virus particles also depends on interaction between the myrMA domain and the cytoplasmic tail of Env. In 2017, Saad’s lab solved the high-resolution structure of the cytoplasmic tail of Env, which was the last unknown protein structure of HIV-1.

Env is a key infectivity protein. As a mature HIV-1 virus approaches a target cell, Env attaches to proteins on the outside of the uninfected cell, and then the Env protein snaps like a mousetrap to fuse the viral membrane with the cell membrane. 

The structures described by Saad and UAB colleagues showing molecular details at 2.1- angstroms resolution were determined via x-ray diffraction data collected at the Southeast Regional Collaborative Access Team (SER-CAT) beamline 22-ID at the Advance Photon Source. The structures show that the myristic acid of myrMA plays a key role in stabilizing the lattice structure, so the ability to form crystals of myrMA was important. They achieved this elusive technical challenge by removing 20 amino acids from the end of the 132-amino acid myrMA. Formation of a Gag lattice on the plasma membrane is known to be obligatory for the assembly of immature HIV-1 and Env incorporation. 

Read more on the Argonne website

Image: X-ray crystallography revealed the structure of the HIV-1 matrix protein at 2.1 angstroms resolution, advancing understanding of key mechanisms of viral assembly.

Gerold Rosenbaum’s #My1stLight

From Gerold Rosenbaum – Advanced Photon Source user

A Playful Use of the Last 10 Minutes of a Run Turns Out to be Very Educational

In 1967, after finishing data collection on the DESY XUV beamline on the polarizer/polarization analyzer I had built for my diploma thesis, there were 15 minutes to go before the synchrotron was to be shut down. Since I always wanted to know how good the vacuum had to be for working in the XUV, I suggested to bleed up the 1-m-long sample chamber to 1/10000 atm or 0.08 torr. The playful use of the last 10 minutes of the run turned out to be an impressive demonstration of the superiority of the continuous spectrum of synchrotron radiation over other XUV sources (paired with a high-resolution monochromator). The very low intensity below 800 Å, even though at the peak of the monochromator spectrum, told me clearly where vacuum-UV starts.

Journal reference: R.P. Godwin, “Synchrotron radiation as a light source,” Springer-Verlag Tracts in Modern Physics 51, p.66, 1969.

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Understanding the structural implications of genetic mutations in heart-muscle disease

Cardiomyopathies are diseases of the heart muscle in which the muscle of the pumping chamber (ventricle) can become enlarged (dilated cardiomyopathy; DCM) or thickened (hypertrophic cardiomyopathy; HCM), potentially leading to heart failure. There are currently no effective treatments but the disease often has a genetic component related to mutations in the heart muscle proteins that are involved in muscle contraction, so some researchers have focused their therapeutic development efforts on correcting these muscle contraction problems based on the structural basis of the defect. A recent study from a team of researchers using the U.S. Department of Energy’s Advanced Photon Source (APS) employed humanized mouse models expressing mutations observed in patients with HCM and DCM to evaluate the structure-function relationships and the changes observed in cardiac muscle contraction with these mutations. The work, published in the Proceedings of the National Academy of Sciences of the United States of America, provides a deeper understanding of the effects of cardiomyopathy-causing gene mutations on heart muscle contraction that could lead to the development of new therapies for this potentially life-threatening disease.

About 70% of patients with inherited HCM have a defect in the gene for the cardiac myosin protein or the cardiac myosin binding protein C. However, recent genetic evidence has suggested that mutations in the cardiac regulatory light chain (RLC) MYL2 gene are more common than previously thought and can be associated with poor outcomes. In order to understand the structural basis for how mutations in the MYL2 gene can cause HCM, or the less commonly occurring DCM, the research team performed muscle structure and force measurement experiments on heart muscle samples from mice that express mutated human RLC proteins, the HCM-D166V mutation associated with hypertrophic cardiomyopathy or the DCM-D94A mutation associated with dilated cardiomyopathy.

Normally, the cardiac regulatory light chain protein acts as a major subunit of the cardiac myosin protein to regulate calcium-mediated interactions with other muscle proteins and the myosin movements that result in the power stroke of muscle contraction. On this basis, the team set out to understand the relationship between these two mutations in the MYL2 gene and associated defects in the function of RLC in cardiomyopathy.

They used the small-angle x-ray diffraction technique at the Biophysics Collaborative Access Team 18-ID x-ray beamline at the APS to compare the spatial orientation of the thick and thin muscle filaments in left ventricular papillary muscle (LVPM) from mice expressing the mutated human RLC to mice expressing the normal, unmutated wildtype human cardiac RLC. (The APS is an Office of Science user facility at Argonne National Laboratory.)

In this model system, small-angle x-ray diffraction can measure interfilament lattice spacing that is proportional to the distance between two adjacent muscle filaments and equatorial intensity ratios that provide information about the number of myosin heads that are attached to actin-containing thin filaments (cross-bridges). By comparing structural results at different concentrations of calcium and simultaneously recording force traces, they were able to get structure-function information for all three muscle types. The intensity ratios at different calcium concentrations showed that contraction of the HCM mutant muscles were the most sensitive to calcium, forming more cross-bridges at submaximal calcium concentrations than either the DCM mutant or the wildtype muscle.

Read more on the APS website

Image: Mechanism of action for HCM-D166V and DCM-D94A mutations. The HCM-D166V model disrupts the SRX state and promotes the SRX-to-DRX transition increasing the number of DRX heads and leading to hypercontractile behavior. The DCM-D94A model stabilizes the SRX state yielding fewer heads available for contraction and leading to clinical hypocontractility. Abbreviations: ELC, myosin essential light chain; RLC, regulatory light chain; DRX, disordered relaxed; SRX, super-relaxed.