protein structure – Lightsources.org

Structure-based Protein Design Advances Vaccine Development for Human Metapneumovirus

2022/10/242022/10/26

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.

Creating tastier vegan cheese using synchrotron X-rays

2022/09/302022/10/12

The quest for tastier, more sustainable vegan cheese has led Swedish food company Cassius AB to take a closer look at cheese protein structures. Using synchrotron X-rays at MAX IV, Cassius are searching for the perfect scientific recipe for plant-based cheese.

When regular cheese is produced, the milk proteins react with rennet and form a cheese curd. These specific proteins, formed in a certain structure, are unique to mammalian milk, which makes them difficult to mimic.

Cassius AB:s research project focuses on getting a deeper understanding of how the proteins in regular cheese form structures spontaneously. It also investigates whether this could happen with mammalian milk proteins produced by genetically engineered microorganisms, in a process called precision fermentation.

Since mimicking all proteins in regular cheese is not necessary, Cassius is concentrating on two of the protein types that play a key role in how cheese coagulates.

Cheese gel balls as protein samples

Johan Krakau, founder of Cassius and brands like GoVego, has teamed up with researchers from RISE within the NextBioForm center to perform the experiment at the MAX IV CoSAXS beamline.

Using Small-Angle X-ray Scattering techniques (SAXS), the research team studies different types of protein samples in the form of micelles – spherical protein aggregations that resemble gel balls – and how different conditions affect their shape and size. For example, when mixed with different amounts of salt, or when the pH value is changed. The team also investigates if these proteins coagulate into a curd structure in the same way that mammalian milk proteins do.

Read more on the MAX IV website

SARS-CoV-2 protein caught severing critical immunity pathway

2022/09/082022/09/15

Powerful X-rays from SLAC’s synchrotron reveal that our immune system’s primary wiring seems to be no match for a brutal SARS-CoV-2 protein.

BY DAVID KRAUSE

Over the past two years, scientists have studied the SARS-CoV-2 virus in great detail, laying the foundation for developing COVID-19 vaccines and antiviral treatments. Now, for the first time, scientists at the Department of Energy’s SLAC National Accelerator Laboratory have seen one of the virus’s most critical interactions, which could help researchers develop more precise treatments.

The team caught the moment when a virus protein, called Mpro, cuts a protective protein, known as NEMO, in an infected person. Without NEMO, an immune system is slower to respond to increasing viral loads or new infections. Seeing how Mpro attacks NEMO at the molecular level could inspire new therapeutic approaches.

To see how Mpro cuts NEMO, researchers funneled powerful X-rays from SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL) onto crystallized samples of the protein complex. The X-rays struck the protein samples, revealing what Mpro looks like when it dismantles NEMO’s primary function of helping our immune system communicate.

“We saw that the virus protein cuts through NEMO as easily as sharp scissors through thin paper,” said co-senior author Soichi Wakatsuki, professor at SLAC and Stanford. “Imagine the bad things that happen when good proteins in our bodies start getting cut into pieces.”

The images from SSRL show the exact location of NEMO’s cut and provide the first structure of SARS-CoV-2 Mpro bound to a human protein.

“If you can block the sites where Mpro binds to NEMO, you can stop this cut from happening over and over,” SSRL lead scientist and co-author Irimpan Mathews said. “Stopping Mpro could slow down how fast the virus takes over a body. Solving the crystal structure revealed Mpro’s binding sites and was one of the first steps to stopping the protein.”

The research team from SLAC, DOE’s Oak Ridge National Laboratory, and other institutions published their results today in Nature Communications.

Read more on the SLAC website

Light sources have demonstrated huge adaptability during the pandemic

2022/01/132022/01/13

Johanna Hakanpää is the beamline scientist for P11, one of the macromolecular crystallography beamlines at PETRAIII at DESY in Hamburg. Originally from Finland, she studied chemistry and then did her masters and PhD work in protein crystallography. Johanna was drawn to the field because she wanted to understand how life really works. Supporting health related research is important to her and Johanna is especially inspired by her son who is a patient of celiac disease. Together they hope that one day, with the help of science, he will be able to eat normally without having to think about what is contained in his food. Johanna started her light source journey as a user and was really impressed by the staff scientists who supported her during her experiments. This led her to apply for a beamline scientist position and she successfully made the transition, learning the technical aspects of the beamlines on the job.

In her #LightSourceSelfie, Johanna highlights the adaptability of light sources during the pandemic as a key strength. Being part of a team that was able to keep the lights on for users via remote experiments is a reflection of the commitment that Johanna and her colleagues have when it comes to facilitating science. Thousands of staff at light sources all around the world have shown the same commitment, ensuring scientific advances can continue. This is particularly true for vital research on the SARS-CoV-2 virus itself. Learn more about this research here: https://lightsources.org/lightsource-research-and-sars-cov-2/

Be curious and stay curious!

2021/12/152021/12/15

Luisa Napolitano is a staff scientist working in the structural biology lab at the Elettra Sincrotrone in Trieste, Italy.

In her #LightSourceSelfie, Luisa talks about switching from cellular biology to structural biology and how proud moments come when you solve a structure that you have been working on for years.

Her fantastic lab tour explains how the equipment enables you to prepare proteins for a range of experimental techniques, including crystallography, electron microscopy, SAXS and NMR. Luisa also explains why it is so valuable to have a structural biology lab located at the synchrotron where beamline staff are on hand to give you advice about your research.

Finally Luisa touches on the way her work as a scientist is helping to inspire her 9 year old son. She offers this advice to younger peers, “Be curious and stay curious! Don’t be afraid and try, even if you think something is too much for you. Try it because you never know. It was like me when I started in structural biology at the beginning, I was scared but at the end of the story I like structural biology a lot, and I don’t think I will change my field of action anymore.”

Science Advances cover dedicated to research results on Cryo-EM

2021/09/102021/10/28

The research carried out at NCPS SOLARIS with the use of electron cryomicroscopy and at the Malopolska Biotechnology Centre, and at the British National Electron Bioimaging Center eBIC (Diamond Light Source) allowed to solve the structure of the protein responsible for introducing compounds necessary for the life of bacterial cells. The exceptional importance of the research was honored with a dedicated, unique image by Alina Kurokhtina published on the cover of Science Advances!

Bacterial species are under continuous warfare with each other for access to nutrients. To gain an advantage in this struggle, they produce antibacterial compounds that target and kill their competitors. Different species of bacteria, including ones that live inside us, can battle each other for scarce resources using a variety of tactics. Now, researchers from the laboratories of Prof Jonathan Heddle from Malopolska Centre of Biotechnology, Jagiellonian University, Krakow and Dr Konstantinos Beis at Research Complex at Harwell /Imperial College, London, have uncovered the mechanism of one such tactic in work that may eventually lead to the development of new antibacterials.

The egg in the X-ray beam

2021/04/012021/04/01

Innovative time-resolved method reveals network formation by and dynamics of proteins.

A team of scientists has been using DESY’s X-ray source PETRA III to analyse the structural changes that take place in an egg when you cook it. The work reveals how the proteins in the white of a chicken egg unfold and cross-link with each other to form a solid structure when heated. Their innovative method can be of interest to the food industry as well as to the broad field of research surrounding protein analysis. The cooperation of two groups, headed by Frank Schreiber from the University of Tübingen and Christian Gutt from the University of Siegen, with scientists at DESY and European XFEL, reports the research in two articles in the journal Physical Review Letters.

Eggs are among the most versatile food ingredients. They can take the form of a gel or a foam, they can be comparatively solid and also serve as the basis for emulsions. At about 80 degrees Celsius, egg white becomes solid and opaque. This is because the proteins in the egg white form a network structure. Studying the exact molecular structure of egg white calls for energetic radiation, such as X-rays which is able to penetrate the opaque egg white and has a wavelength that is not longer than the structures being examined.

Read more on the DESY website

Image: When heated, the proteins in the originally transparent chicken egg white form a tightly meshed, opaque network.

Credit: DESY, Gesine Born

Experimental drug targets HIV in a novel way

2020/10/272020/10/29

SCIENTIFIC ACHIEVEMENT

Using the Advanced Light Source (ALS), researchers from Gilead Sciences Inc. solved the structure of an experimental HIV drug bound to a novel target: the capsid protein that forms a shield around the viral RNA.

SIGNIFICANCE AND IMPACT

The work could lead to a long-lasting treatment for HIV that overcomes the problem of drug resistance and avoids the need for burdensome daily pill-taking.

Progress in HIV treatment still needed

Over the past couple of decades, safe and effective treatment for HIV infection has turned what was once a death sentence into a chronic disease. Today, people on the latest HIV drugs have near-normal life expectancy.

However, many people are still living with multidrug-resistant HIV, unable to control their virus loads with currently available HIV drugs. The virus develops resistance when people take their pills inconsistently due to forgetfulness, side effects, or a complex schedule. To some, taking a pill every day is a burden: they schedule their lives around it for fear of missing a dose. To others, it is a stigma, as it makes it difficult to hide one’s HIV status from close friends and family.

Read more on the Advanced Light Source website

Image: An experimental small-molecule drug (GS-6207) targets the protein building blocks of the HIV capsid—a conical shell (colored red in this artistic rendering) that encloses and protects the viral RNA—making the virus unable to replicate in cells. Credit Advanced Light Source

Expansion of SOLARIS experimental hall

2020/08/032020/08/11

The SOLARIS Centre has been awarded by the Ministry of Science and Higher Education a grant for the expansion of the experimental hall. This long-awaited decision opens up new perspectives for the development of the Centre.

The area of the synchrotron hall will be increased by over two thousand square meters. This space will enable the construction of four new beamlines, which require a long distance of the sample from the synchrotron radiation source. These new facilities include the SOLCRYS beamline for the structural research. The beamline end stations will enable analyses of the structure of proteins, viruses, nucleic acids, and polymers. These studies provide knowledge on the molecular structure of the basic building blocks of living organisms, including the architecture of macromolecules. Research carried out on the beamline will be used, among others, in biological sciences, medicine (drug design and discovery), chemistry, and materials science. SOLCRYS will be the only research infrastructure of this type not only in Poland, but also in the entire Central and Eastern Europe.

Read more on the SOLARIS website

Image: Visualisation of the new building.

New detector accelerates protein crystallography

2020/02/172020/02/20

In Feburary a new detector was installed at one of the three MX beamlines at HZB.

Compared to the old detector the new one is better, faster and more sensitive. It allows to acquire complete data sets of complex proteins within a very short time.

Proteins consist of thousands of building blocks that can form complex architectures with folded or entangled regions. However, their shape plays a decisive role in the function of the protein in the organism. Using macromolecular crystallography at BESSY II, it is possible to decipher the architecture of protein molecules. For this purpose, tiny protein crystals are irradiated with X-ray light from the synchrotron source BESSY II. From the obtained diffraction patterns, the morphology of the molecules can be calculated.

>Read more on the BESSY II at HZB website

Image: 60s on the new detector were sufficient to obtain the electron density of the PETase enzyme.
Credit: HZB

The future of fighting infections

2019/08/212019/08/22

Scientists analyze 3D model of proteins from disease-causing bacteria at the CLS.

Millions of people are affected by the Streptococcus pneumoniae bacterium, which can cause sinus infections, middle ear infections and more serious life-threatening diseases, like pneumonia, bacteremia, and meningitis. Up to forty percent of the population are carriers of this bacterium.
Researchers from the University of Victoria (UVic) used the Canadian Light Source (CLS) at the University of Saskatchewan to study proteins that the pathogen uses to break down sugar chains (glycans) present in human tissue during infections. These proteins are key tools the bacterium uses to cause disease.

They used the Canadian Macromolecular Crystallography Facility (CMCF) at the CLS to determine the three-dimensional structure of a specific protein, an enzyme, that the bacterium produces to figure out how it interacts with and breaks down glycans.

Image: The 3D structure of an enzyme from the disease-causing bacterium Streptococcus pneumoniae.

New approach for solving protein structures from tiny crystals

2019/05/032019/05/08

Technique opens door for studies of countless hard-to-crystallize proteins involved in health and disease

Using x-rays to reveal the atomic-scale 3-D structures of proteins has led to countless advances in understanding how these molecules work in bacteria, viruses, plants, and humans—and has guided the development of precision drugs to combat diseases such as cancer and AIDS. But many proteins can’t be grown into crystals large enough for their atomic arrangements to be deciphered. To tackle this challenge, scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and colleagues at Columbia University have developed a new approach for solving protein structures from tiny crystals.

The method relies on unique sample-handling, signal-extraction, and data-assembly approaches, and a beamline capable of focusing intense x-rays at Brookhaven’s National Synchrotron Light Source II (NSLS-II)—a DOE Office of Science user facility—to a millionth-of-a-meter spot, about one-fiftieth the width of a human hair.

Image: Wuxian Shi, Martin Fuchs, Sean McSweeney, Babak Andi, and Qun Liu at the FMX beamline at Brookhaven Lab’s National Synchrotron Light Source II, which was used to determine a protein structure from thousands of tiny crystals.

SwissFEL makes protein structures visible

2018/10/102018/10/18

Successful pilot experiment on biomolecules at the newest large research facility of PSI

For the development of new medicinal agents, accurate knowledge of biological processes in the body is a prerequisite. Here proteins play a crucial role. At the Paul Scherrer Institute PSI, the X-ray free-electron laser SwissFEL has now, for the first time, directed its strong light onto protein crystals and made their structures visible. The special characteristics of the X-ray laser enable completely novel experiments in which scientists can watch how proteins move and change their shape. The new method, which in Switzerland is only possible at PSI, will in the future aid in the discovery of new drugs.

Less than two years after the X-ray free-electron laser SwissFEL started operations, PSI researchers, together with the Swiss company leadXpro, have successfully completed their first experiment using it to study biological molecules. With that, they have achieved another milestone before this new PSI large research facility becomes available for experiments, at the beginning of 2019, to all users from academia and industry. SwissFEL is one of only five facilities worldwide in which researchers can investigate biological processes in proteins or protein complexes with high-energy X-ray laser light.

>Read more on the SwissFEL website

Image: Michael Hennig (left) and Karol Nass at the experiment station in SwissFEL where their pilot experiment was conducted.
Credit: Paul Scherrer Institute/Mahir Dzambegovic

First European XFEL research results published

2018/08/28

High number of X-ray pulses per second reduces time needed for the study of biological structures.

Just days before the first anniversary of the start of European XFEL user operation, the first results based on research performed at the facility have been published. In the journal Nature Communications, the scientists, headed by Prof. Ilme Schlichting from Max-Planck-Institute for Medical Research in Heidelberg, Germany, together with colleagues from Rutgers State University of New Jersey, USA, France, DESY and European XFEL, describe their work using the intense X-ray laser beam to determine the 3D structure of several proteins. They demonstrate, for the first time that, under the conditions used at the time of the experiment an increased number of X-ray pulses per second as produced by the European XFEL can be successfully used to determine the structure of biomolecules. As much faster data collection is therefore possible, the time needed for an experiment could be significantly shortened. The detailed determination of the 3D structure of biomolecules is crucial for providing insights into informing the development of novel drugs to treat diseases.

Prof. Ilme Schlichting said: “Our work shows that under the conditions used data can be collected at European XFEL at a rate much faster than has ever been previously possible. As the time and cost of experiments decrease, very soon many more researchers will be able to perform experiments at high repetition rate X-ray lasers. Our results are therefore of interest not only tor the fields of biology and medicine, but also physics, chemistry and other disciplines.”

>Read more on the European XFEL website

Image: Guest scientist Tokushi Sato working at the sample chamber of the SPB/SFX instrument.
Credit: European XFEL

ALS passes the 7000-protein milestone

2018/05/302018/06/11

The eight structural biology beamlines at the ALS have now collectively deposited over 7000 proteins into the Protein Data Bank (PDB), a worldwide, open-access repository of protein structures. The 7000th ALS protein structure (entry no. 6C7C) is an enzyme from Mycobacterium ulcerans (strain Agy99), solved with data from Beamline 5.0.2. This bacterium produces a toxin that eats away at skin tissue, causing what’s known as Buruli ulcers (Google at your own risk!). The bacterium is antibiotic-resistant, and treatment involves the surgical removal of infected tissues, including amputation.

The enzyme structure was solved by a group from the Seattle Structural Genomics Center for Infectious Disease (SSGID), whose mission is to obtain crystal structures of potential drug targets on the priority pathogen list of the National Institute of Allergy and Infectious Diseases (NIAID). As of May 2018, SSGCID has deposited 1090 structures in the PDB, with data for more than a quarter of those collected at ALS beamlines.

Image: PDB 6C7C: Enoyl-CoA hydratase, an enzyme from M. ulcerans (strain Agy99).

With help from a few friends

2018/02/152018/02/19

Researchers discover the precise make-up of a molecular chaperone complex

A complex made up of three proteins, Hsp90, Sgt1, and Rar1, is thought to stabilise an important immune protein known as nucleotide-binding domain and leucine-rich repeat containing protein. While the structure of the Sgt1-Hsp90-Rar1 protein is known, the stoichiometry of the complex has remained elusive. In a paper published in Frontiers in Molecular Biosciences, Dr Chrisostomos Prodromou of the University of Sussex and Dr Minghao Zhang of the University of Oxford worked with Professor Giuliano Siligardi at the Circular Dichroism beamline (B23) at Diamond Light Source to clarify the detailed make-up of the complex. Using synchrotron radiation circular dichroism, they revealed that it consists of an Hsp90 dimer, two Sgt1 molecules, and a single Rar1 molecule. The stoichiometry of the full complex potentially allows two NLR molecules to bind, a finding which may open avenues of research into how these proteins form dimers.

Figure: (extract) The structure of the Sgt1-Hsp90-Rar1 complex with an Hsp90 dimer, two Sgt1 molecules, and a single Rar1. Entire image here.