cryo-electron microscope – Lightsources.org

Trigger of rare blood clots with AstraZeneca and other COVID vaccines found by scientists

2021/12/092021/12/14

understanding rare blood clots caused by some COVID vaccines – important first to prevention

A collaborative team from the School of Medicine at the University of Cardiff, Wales and a range of US institutions used the UK’s national synchrotron, Diamond Light Source, to help reveal the details of how a protein in the blood is attracted to a key component of Adenovirus based vaccines.

It is believed this protein kicks off a chain reaction, involving the immune system, that can culminate in extremely rare but dangerous blood clots. The Cardiff team were given emergency government funding to find the answers. In collaboration with scientists in the US and from AstraZeneca, they set out to collect data on the structure of the vaccines and perform computer simulations and related experiments to try and uncover why some of the vaccines based on Adenoviruses were causing blood clots in rare cases.

Moderna and BioNTech are based on mRNA, whereas AstraZeneca and Johnson & Johnson are based on Adenoviruses. Blood clots have only been associated with vaccines that use Adenoviruses.

Combatting COVID-19 with crystallography and cryo-EM

2021/05/212021/05/28

Crystallography and cryo-electron microscopy are vital tools in the fight against COVID-19, allowing researchers to reveal the molecular structures and functions of the SARS-CoV-2 virus, paving the way for new drugs and vaccines. Since the start of the pandemic, the ESRF has mobilised its crystallography and cryo-electron microscopy expertise and made its new Extremely Brilliant Source available as part of the collective effort to address this critical global health challenge.

When the WHO declared the outbreak of COVID-19 a public health emergency of international concern in early 2020, it signalled the start of a race against time for scientists to understand how the newly identified SARS-CoV-2 virus functioned and to develop treatments for the disease. Structural biologists around the world pitched in, determining the structures of most of the 28 proteins encoded by the novel coronavirus. This remarkable collective effort resulted in over a thousand 3D structural models of SARS-CoV-1 and SARS-CoV-2 proteins deposited in the Protein Data Bank (PDB) public archive in just one year [1]. Researchers and drug developers rely on these models to design antiviral drugs, therapies and vaccines. However, the speed and urgency with which the SARS-CoV-2 protein structures were solved means that errors could inevitably slip in, with potentially severe consequences for drug designers targeting certain parts of the virus’s structure.

Enter the Coronavirus Structural Task Force, an international team of 25 structural biologists offering their time and expertise to fix errors in structural models of the virus’s proteins in order to give drug designers the best possible templates to work from. Gianluca Santoni, crystallography data scientist in the ESRF’s structural biology group, is part of the task force, whose work is detailed in an article recently published in Nature Structural & Molecular Biology [2]. “Every week, we check the PDB for any new protein structure related to SARS-CoV-2,” he explains. “We push structural biology tools and methods to the limit to get every last bit of information from the data, to evaluate the quality and improve the models where possible.”

To read more visit the ESRF website

Image: The coronavirus research project ‘COVNSP3’ is based on the use of the ESRF’s cryo-electron microscope facility, led by Eaazhisai Kandiah (pictured)

Credit: ESRF/S. Cande.

New targets for antibodies in the fight against SARS-CoV-2

2021/03/262021/03/26

An international team of researchers examined the antibodies from a large cohort of COVID-19 patients. Due to the way antibodies are made, each person that is infected has the potential to produce many antibodies that target the virus in a slightly different way. Furthermore, different people produce a different set of antibodies, so that if we were to analyse the antibodies from many different patients, we would potentially be able to find many different ways to neutralise the virus.

The research article in the journal Cell is one of the most comprehensive studies of its kind so far. It is available online now and will be published in print on 15 April. These new results now show that there are many different opportunities to attack the virus using different antibodies over a much larger area than initially thought/mapped.

Professor Sir Dave Stuart, Life Sciences Director at Diamond and Joint head of Structural Biology at the University of Oxford, said:

SARS CoV-2 is the virus that causes COVID-19. Once infected with this virus, the human immune system begins to fight the virus by producing antibodies. The main target for these antibodies is the spike protein that protrudes from the virus’ spherical surface. The spike is the portion of the virus that interacts with receptors on human cells. This means that if it becomes obstructed by antibodies, then it is less likely that the virus can interact with human cells and cause infection.
By using Diamond Light Source, applying X-ray crystallography and cryo-EM, we were able to visualise and understand antibodies interact with and neutralize the virus. The study narrowed down the 377 antibodies that recognize the spike to focus mainly on 80 of them that bound to the receptor binding domain of the virus, which is where the virus spike docks with human cells.

Read more on the Diamond website

Image: Figure from the publication showing how the receptor binding domain resembles a human torso.

Credit: The authors (Cell DOI: 10.1016/j.cell.2021.02.032)

Diamond helps uncover how an untreatable cancer-causing virus affects immune cells

2020/10/162020/10/16

Scientists have found that human T-cell lymphotropic virus, type 1 (HTLV-1) hijacks cellular machinery to establish an infection.

Research was undertaken using cutting-edge visualisation techniques such as X-ray crystallography, which was undertaken at Diamond, and single-particle cryo-electron microscopy (cryo-EM).

HTLV-1 is a virus that affects T cells, a type of white blood cell which plays a crucial role in our immune system. Currently, between five and 20 million people worldwide are infected by HTLV-1 and no cure or treatment is available. While most people infected with the virus do not experience symptoms, around two to five per cent will go on to develop adult T-cell leukaemia (ATL).

New research, led by a team from Imperial College London and the Francis Crick Institute, shows in atomic detail how HTLV-1 infects immune cells. By providing a more nuanced understanding of how the virus establishes infection in the body, the research will help to support the development of new, targeted therapies.

Read more on the Diamond Light Source website

Image: Scanning electron micrograph of a human T lymphocyte (also called a T cell) from the immune system of a healthy donor. Credit: NIAID

Research could lead to better herbicides and infection treatments

2020/07/302020/08/19

Researchers from the University of Queensland (UQ) have used the Australian Synchrotron and cryo-electron microscopy in China to determine the three-dimensional structure of a complex enzyme found in plants microbes that could be used to develop advanced herbicides and treatments for infection.

A large international team led by Prof Luke Guddat of UQ published the structure of the enzyme acetohydroxyacid synthase (AHAS) in the journal Nature and also explained the first step in how the enzyme regulates the biosynthesis of three essential amino acids, leucine, valine and isoleucine.

“The way that the complex regulates this pathway had been unknown until now. We were finally able to explain it by understanding how the entire structure was assembled,” said Prof Guddat, who has been researching this enzyme for twenty years.

Read more on the Australian Synchrotron website

Image: The 3D structure resembles a ‘Maltese Cross’.

Cryo-electron microscopy for industry coming soon to SOLARIS

2020/02/252020/03/06

The SOLARIS Centre and the Malopolska Centre of Biotechnology (Jagiellonian University) won a two-stage competition for the purchase of an electron microscopy for industrial research.

Funding was awarded by the National Information Processing Institute (OPI PIB) as part of the EU’s Smart Growth Operational Programme.

“We have been trying to purchase a microscope because Polish companies keep asking us about the possibility to carry out measurements using the Cryo-EM technique” – says Michał Młynarczyk, Finance and Administration Deputy Director at SOLARIS. “We expect that the total time allocated for the commercial study will be at least 40% of operational time. The remaining time will be available for academic researchers” – continues the director.

“We are keen to enable Polish companies to access this exciting new technology, which is developing very fast and is currently becoming the most important one used in structural biology. The achievable results facilitate to understand the cellular mechanisms behind human diseases, the design of new drugs, the optimization of existing drug molecules. The technique is also successfully applied in nanotechnology and other fields” – adds Sebastian Glatt, Max Planck Research Group leader at the Malopolska Centre of Biotechnology – the main partner of SOLARIS in the implementation of this project.

>Read more on the SOLARIS website

First structure of a DNA crosslink repair ligase determined

2019/11/042019/11/05

Diamond’s Electron Bio-Imaging Facility (eBIC) has been used to generate the first 3D structure of the Fanconi anaemia (FA) core complex, a multi-subunit E3 ubiquitin ligase required for the repair of damaged DNA. The work, led by Dr Lori Passmore from the MRC Laboratory of Molecular Biology and a team of researchers, has been published today in Nature, and their research provides the molecular architecture of the FA core complex and new insights into how the complex functions.

The FA pathway senses and repairs DNA crosslinks that occur after exposure to chemicals including chemotherapeutic agents and alcohol, but also as a result of normal cellular metabolism. The megadalton FA core complex acts as an E3 ubiquitin ligase to initiate removal of these DNA crosslinks, helping to repair the damage caused. The research team used eBIC’s imaging facilities to make a major breakthrough in understanding the FA core complex by determining its structure using an integrative approach including cryo-electron microscopy and mass spectrometry.

Dr Peijun Zhang, Director of eBIC notes that:

Enabling cutting-edge research like this is exactly why we established eBIC, to provide scientists with state-of-the-art experimental equipment and expertise in the field of cryo-electron microscopy, for both single particle analysis and cryo-electron tomography. Determining the structure of the FA core complex for the first time is a fantastic achievement for the MRC research team.

Image: The FA core complex.
Credit: Phospho Biomedical Animation

Study offers new target for antibiotic resistant bacteria

2019/06/182019/06/24

As antibiotic resistance rises, the search for new antibiotic strategies has become imperative. In 2013, the Centers for Disease Control estimated that antibiotic resistant bacteria cause at least 2 million infections and 23,000 deaths a year in the U.S.; a recent report raised the likely mortality rate to 162,044.
New Cornell research on an enzyme in bacteria essential to making DNA offers a new pathway for targeting pathogens. In “Convergent Allostery in Ribonucleotide Reductase,” published June 14 in Nature Communications, researchers used the MacCHESS research stations at the Cornell High Energy Synchrotron Source (CHESS) to reveal an unexpected mechanism of activation and inactivation in the protein ribonucleotide reductase (RNR).

Understanding the “switch” that turns RNR off provides a possible means to shut off the reproduction of harmful bacteria.
RNRs take ribonucleotides, the building blocks of RNA, and convert them to deoxyribonucleotides, the building blocks of DNA. In all organisms, the regulation of RNRs involves complex mechanisms, and for good reason: These mechanisms prevent errors and dangerous mutations.

>Read more on the CHESS website

Image: William Thomas, a graduate student in the field of chemistry and chemical biology, collects data on ribonucleotide reductase.

Construction starts on new Cryo-EM center

2018/12/132018/12/18

Called the Laboratory of BioMolecular Structure, the new cryo-electron microscope center will offer world-leading imaging capabilities for life sciences research.

Today, the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory broke ground on the Laboratory of BioMolecular Structure (LBMS), a state-of-the-art research center for life science imaging. At the heart of the center will be two new NY-State-funded cryo-electron microscopes (cryo-EM) specialized for studying biomaterials, such as complex protein structures.

“Cryo-electron microscopy is a rapidly-advancing imaging technique that is posting impressive results on a weekly basis,” said LBMS Director Sean McSweeney. “The mission of LBMS is to advance the scientific understanding of key biological processes and fundamental molecular structures.”

“Throughout my career, I have worked hard to make our region of the State a high-tech hub, bringing together the talents and expertise of scientists and facilities across Long Island. I am pleased to have played a part in the creation of the new cryo-EM center, which will add to the incredible facilities at Brookhaven National Lab and enable our scientific community to lead the way in world-class imaging research and discovery,” said NY State Senator Ken LaValle.

Image: New York State Senator Ken LaValle joined leaders of Empire State Development and Brookhaven Lab for the LBMS groundbreaking ceremony. Pictured from left to right are Jim Misewich (Associate Laboratory Director for Energy and Photon Sciences, Brookhaven Lab), Erik Johnson (NSLS-II Deputy for Construction), Sean McSweeney (LBMS Director and NSLS-II Structural Biology Program Manager), Robert Gordon (DOE-Brookhaven Site Office Manager), Ken LaValle, Cara Longworth (Regional Director, Empire State Development), Danah Alexander (Senior Project Manager, Empire State Development), and John Hill (NSLS-II Director).

Secrets of the deadly white-tail virus revealed

2018/12/112018/12/12

The inner workings of a lethal giant freshwater prawn virus have been revealed by an international team of researchers using data gathered at Diamond Light Source. The results reveal a possible new class of virus and presents the prospect of tackling a disease that can devastate prawn farms around the world.

The detailed structure of a virus that can devastate valuable freshwater prawn fisheries has been revealed by an international team using image data collected in the Electron Bio-Imaging Centre (eBIC) based at Diamond Light Source. The researchers produced high-resolution images of virus like particles, VLP’s, composed of virus shell proteins which they compared with lower resolution images of the complete virus purified from prawn larvae. They found strong similarities between the two suggesting that the more detailed VLP images are a good representation of the intact virus. This research, exposing the inner workings of the MrNV, could make it easier to develop ways of combating the economically important disease, but also suggests that it belongs in a new, separate, group of nodaviruses.
The researchers used the rapidly developing technique of cryo-electron microscopy, cryoEM, which has the ability to produce very high-resolution images of frozen virus particles. Images so detailed that the positions of individual atoms could be inferred. Recent breakthroughs in this technique have transformed the study of relatively large biological complexes like viruses allowing researchers to determine their structures comparatively quickly. The data to produce the MrNV structure described here was captured in two days at the eBIC facility.

Image: 3D model of the MrNV
Credit: Dr David Bhella

Fighting malaria with X-rays

2018/04/252018/04/25

Today 25 April, is World Malaria Day.

Considered as one of humanity’s oldest life-threatening diseases, nearly half the world population is at risk, with 216 million people affected in 91 countries worldwide in 2016. Malaria causes 445 000 deaths every year, mainly among children. The ESRF has been involved in research into Malaria since 2005, with different techniques being used in the quest to find ways to prevent or cure the disease.

Malaria in humans is caused by Plasmodium parasites, the greatest threat coming from two species: P. falciparum and P. vivax. The parasites are introduced through the bites of infected female Anopheles mosquitoes. They travel to the liver where they multiply, producing thousands of new parasites. These enter the blood stream and invade red blood cells, where they feed on hemoglobin (Hgb) in order to grow and multiply. After creating up to 20 new parasites, the red blood cells burst, releasing daughter parasites ready for new invasions. This life cycle leads to an exponential growth of infected red blood cells that may cause the death of the human host.

The research carried out over the years at the ESRF has aimed to identify mechanisms critical for the parasite’s survival in the hope of providing an intelligent basis for the development of drugs to stop the parasite’s multiplication and spread.

>Read more on the European Synchrotron website

Image: Inside the experimental hutch of the ESRF’s ID16A nano-analysis beamlin.
Credit: Pierre Jayet