Molecular IgG3 structure paves the way for new applications of antibodies

A combination of scattering and analytical techniques has provided the first atomic-level structural model for the IgG3 antibody

In humans, Immunoglobulin (IgG) is the most common type of antibody found in blood circulation. IgG molecules are created by plasma B cells, and there are four subclasses. Of the four, IgG3 is the least understood. It has a uniquely long hinge region separating its Fab antigen-binding and Fc receptor-binding regions. The presence of this elongated hinge makes it challenging to perform structural studies, for example, with X-ray crystallography. Due to this lack of structural information, IgG3 is the only subclass not currently exploited for therapeutic uses. In work recently published in the Journal of Biological Chemistry, researchers from University College London and the University of Birmingham have used a combination of imaging and analytical methods to provide the first experimentally determined molecular structural model for a full-length IgG3 antibody. This new information should enable the use of IgG3 to develop new therapies and antibody tests. 

Getting a good look at IgG3

A high-resolution structure for part of the IgG3 molecule, the globular IgG3-Fc fragment, is available. And previous studies of the whole molecule using Small Angle X-ray Scattering (SAXS) and analytical ultracentrifugation (AUC) showed that IgG3 is elongated compared to IgG1, IgG2 and IgG4. SAXS also showed that IgG3 has a more extended central hinge than IgG1 and IgG2 that links its three globular regions together.  

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Image: The IgG3 structural model is formed from two globular Fab regions, a long hinge in the centre, and one Fc region, as shown from the scattering modelling fits. The structure is reminiscent of a giraffe with an extended and semi-rigid neck.

Credit:
Dr Valentina Spiteri, UCL.

Diamond-II programme set to transform UK science

Diamond Light Source has established itself as a world-class synchrotron facility enabling research by leading academic and industrial groups in physical and life sciences. Diamond has pioneered a model of highly efficient and uncompromised infrastructure offered as a user-focussed service driven by technical and engineering innovation.

To continue delivering the world-changing science that Diamond leads and enables, Diamond-II is a co-ordinated programme of development that combines a new machine and new beamlines with a comprehensive series of upgrades to optics, detectors, sample environments, sample delivery capabilities and computing. The user experience will be further enhanced through access to integrated and correlative methods as well as broad application of automation in both instrumentation and analysis. Diamond-II will be transformative in both spatial resolution and throughput and will offer users streamlined access to enhanced instruments for life and physical sciences.

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Image: Diamond’s synchrotron building

Credit: Diamond Light Source

Critical data of insect specimens to be unlocked through 3D imaging

The Natural History Museum is collaborating with Diamond Light Source, the UK’s national synchrotron science facility, on an ambitious project to generate and share immense data from the Museum’s vast insect collections to help further research into their evolution, diversity and extinctions. The Natural History Museum is collaborating with Diamond Light Source, the UK’s national synchrotron science facility, on an ambitious project to generate and share immense data from the Museum’s vast insect collections to help further research into their evolution, diversity and extinctions.

Over 1.6 million of the Museum’s 35 million insects have already been digitised using 2D photography. These specimens have had their images and collections data (information about where in time and space they were collected and what species they are) made available to the public via the Museum’s Data Portal. However, this landmark project is expected to provide valuable new insights and information by providing the beginnings of a high-resolution 3D dataset for all living and fossil insects and their close relatives.

Read more on the Diamond website

Image: Hairy Fungus Beetle – Prepared by Malte Storm

Credit: Diamond Light Source Ltd

Diamond helps find a way to improve accuracy of Lateral Flow Tests

A recent study has found a way to help reduce false-negative results in Lateral Flow Tests by a simple modification.

Using X-ray fluorescence imaging at Diamond, researchers from King’s College London set out to identify what could be causing these false-negative results, and what potential modifications could enable increased accuracy.

They identified that the underlying technology of the Lateral Flow Devices is highly accurate and able to theoretically detect trace amounts of the COVID-19 virus, but the limitations fall to the read-out of the device – the technology used to communicate the result of the test.

The study, published in ACS Materials and Interfaces, suggests  several potentially simple modifications to the Lateral Flow Devices that could lead to improved performance.

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Diamond helps discover microscopic metallic particles in the brain

A UK-led international team of researchers has discovered elemental metallic copper and iron in the human brain for the first time. The team, comprised of scientists from Keele University and the University of Warwick in collaboration with the University of Texas at San Antonio (UTSA), used Diamond, and the Advanced Light Source located in California (USA) to identify elemental metallic copper and magnetic elemental iron within the amyloid plaques, chemical forms of copper and iron previously undocumented in human biology.

The study, published in Science Advances and funded by the UKRI’s Engineering and Physical Sciences Research Council, looked at amyloid plaques isolated from the brain tissue of deceased Alzheimer’s patients. Amyloid plaques, a hallmark feature of Alzheimer’s disease, act as a site of disrupted metal chemistry in the Alzheimer’s brain, and are believed by many to be integral to disease progression.

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Image: X-ray microscope images and X-ray absorption spectra obtained from two Alzheimer’s disease plaque cores, measured at Diamond’s beamline I08. Image: Science Advances.

Credit: Science Advances.

Physicists uncover secrets of world’s thinnest superconductor

Physicists report the first experimental evidence to explain the unusual electronic behaviour behind the world’s thinnest superconductor, a material with myriad applications because it conducts electricity extremely efficiently. In this case the superconductor is only an atomic layer thick. 

The research, led by Massachusetts Institute of Technology and Brookhaven National Laboratory, was possible thanks to new instrumentation available at Diamond.  

Diamond is one of only a few facilities in the world to use the new experimental technique, Resonant Inelastic X-ray Scattering (RIXS), which is a combination of X-ray Absorption Spectroscopy (XAS) and X-ray Emission Spectroscopy (XES), where both the incident and emitted energies are scanned. This state-of-the-art facility is where the team from three continents conducted their experiment.  

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Image: Members of the RIXS team at Diamond. Left to right: Jaewon Choi (Postdoc), Abhishek Nag (Postdoc), Mirian Garcia Fernandez (Beamline Scientist), Charles Tam (joint PhD student), Thomas Rice (Beamline technician), Ke-Jin Zhou (Principal Beamline Scientist), Stefano Agrestini (Beamline Scientist).

Report reveals impact of over £1.8bn on UK science & economy by Diamond

A recent study by Technopolis and Diamond estimates a cumulative monetised impact of at least £1.8 billion from the UK’s synchrotron, reflecting very favourably with the £1.2 billion investment made in the facility to date.  And it costs less than a cup of coffee as each taxpayer contributes only £2.45 a year towards it.  The study, published today (26 May), set out to measure and demonstrate Diamond’s scientific, technological, societal, and economic benefits.  The report summarises the findings and highlights the significant impact it has achieved to date.  

Diamond’s mission is to keep the UK at the forefront of scientific research. We do this by providing our users in academia and industry access to our state-of-the-art facilities enabling them to fulfil their research goals across a wide variety of scientific disciplines. This report illustrates the fantastic benefits the facility has delivered and brilliant science being achieved by our 14,000-strong user community, who are tackling some of the most challenging scientific questions of the 21st century.  We are so grateful to our funding agencies UKRI’s STFC and the Wellcome for their trust and ongoing support.Chief Executive of Diamond, Professor Andrew Harrison OBE

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Image: Aerial image of Diamond Light Source

Credit: Diamond Light Source

X-rays get a grip on why erucamide slips

X-Ray Reflectivity measurements offer insights into a slippery industrial additive

Slip additives have a wide range of industrial uses, finding their way into everything from lubricants to healthcare products. Fatty acid amides have been used as slip additives since the 1960s, and erucamide is widely used in polymer manufacturing. Research into erucamide migration and distribution and its nanomechanical properties has shown that the assembly and performance of the slip-additive surface depend on concentration and application method, as well as the substrate surface chemistry. However, questions remain regarding the nanostructure of organised erucamide surface layers, including the molecular orientation of the outermost erucamide layer. In work recently published in the Journal of Colloid and Interface Science, a team of researchers from the University of Bristol and Procter & Gamble used a combination of techniques to investigate the erucamide nanostructure formed in a model system. Their findings will allow the use of rigorous scientific methods in real-world scenarios. 

Essential erucamide

Manufacturers use slip additives to modify the surface structure of a wide range of materials, reducing friction without compromising the material’s other properties (e.g. modulus). Slip additives are included in everything from food packaging and textiles, dyes and lubricants, to hygiene products such as nappies.

Read on the Diamond website

Image:Multiscale characterisation of polypropylene (PP) fibre vs polypropylene fibre + 1.5 % erucamide: (A) Optical microscopy, (B) Scanning Electron Microscopy, (C) Atomic Force Microscopy (height image)

X-ray Ptychography performed for first time at small-scale Laboratory Source

In recent years, X-ray ptychography has revolutionised nanoscale phase contrast imaging at large-scale synchrotron sources.  The technique produces quantitative phase images with the highest possible spatial resolutions (10’s nm) – going well beyond the conventional limitations of the available X-ray optics – and has wide reaching applications across the physical and life sciences. A paper published in Physical Review Letters on 12 May 2021, reveals that an international collaboration of scientists has demonstrated for the first time how the technique of high-resolution phase contrast diffraction imaging can be performed with small-scale laboratory sources.

The team from Diamond, Ghent University, University of Sheffield, and University College London conducted an experiment with a compact liquid metal-jet (LMJ) X-ray source. Laboratory X-ray sources have significantly lower levels of brilliance but currently provide the X-ray synchrotron user community with access to micro-CT, where they can gain a great deal of experience and produce preliminary data, at their home institutions. Until now, no such equivalent has existed for nano-scale imaging through coherent diffraction imaging and ptychography. The team’s paper outlines such an experiment and the first proof of concept for far field X-ray ptychography performed using an X-ray laboratory source. 

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Image: A reduced selection of the four-dimensional intensity data recorded during the experiment.

Credit: Diamond Light Source Ltd.

Giving rice new weapons to fight rice blast disease

Understanding how a fungal pathogen interacts with rice cells could help us engineer new defences 

Rice is one of the world’s most important agricultural crops, with 741.5 million tonnes produced in 2014. A large proportion of the global population relies on rice as a staple food, particularly in Asia and Africa. However, harvests are threatened by rice blast disease, caused by the fungus Magnaporthe oryzae, which destroys enough rice to feed around 200 million people every year. Rice and the rice blast fungus are involved in a co-evolutionary arms race, fighting for the upper hand. As the fungus relies on effector proteins to help it infect and reproduce within rice plants, rice has evolved immune receptors that allow it to detect and prevent the spread of the fungus. However, the rice blast fungus has evolved stealthy effector proteins that remain undetected by the rice immune system but can still promote disease. In work recently published in the Journal of Biological Chemistry, an international team of scientists has investigated how one stealthy effector protein might maintain its disease-promoting activity but evade immune detection. This research has an ultimate aim of engineering a receptor that would allow rice plants to better defend themselves. 

A pain in the paddy field

We’re familiar with images of the rice paddies of Asia, but this impressive sight represents an irresistible target for the rice blast fungus, Magnaporthe oryzae. Unable to run away from pests and pathogens, plants have evolved immune systems to detect and defend against attack. However, huge swathes planted with the same variety creates an evolutionary pressure for pests and pathogens; a feast is at hand if they can evade those defences. 

One way that pathogens try and gain an advantage is through the use of effector proteins. These proteins can suppress the plant’s immune system and manipulate the plant’s own systems to help the pathogen infect and replicate. However, the mechanisms they employ to do so are not fully understood.  

In collaboration with scientists from Japan and Thailand, researchers at the UK’s John Innes Centre and The Sainsbury Laboratory have been investigating the interaction between rice plants and the rice blast fungus, with the ultimate goal of engineering new genetic resources that will help rice fight this damaging disease.

Read more on the Diamond website

Image: Rice fields in Asia

A novel approach offers hope for an HCV vaccine

An HCV vaccine is needed, but hard to develop. A structural mimic may be the key to enhancing our immune response

Globally, more than 70 million people were struggling with a chronic hepatitis C virus (HCV) infection in 2015. Although effective drugs are available to treat chronic infections, only 13% of cases received curative treatment. The fact that only 20% have been diagnosed is of even greater concern. Although a minority of newly-infected individuals (10–40%) manage to overcome the disease, most develop a chronic infection. Most acute cases of HCV are asymptomatic, leading to undetected virus transmission. Left untreated chronic HCV can lead to serious liver damage and an increased risk of liver cancer. As curative therapies alone cannot eliminate the virus, a vaccine is required. However, because HCV is very diverse and evolves rapidly to evade the immune system, developing an effective vaccine is challenging. In work recently published in npj Vaccines, scientists from the MRC-University of Glasgow Centre for Virus Research, the University of St. Andrews and Imperial College London describe an alternative strategy that uses a structural mimic to encourage the immune system to make antibodies that can recognise multiple strains of the virus i.e. broadly-neutralising antibodies (bNAbs) against HCV. 

A moving target

With its high genetic diversity and an envelope of ever-changing glycoproteins, HCV is challenging for the human immune system to detect and counteract. The minority of cases in which the virus is successfully cleared from the body show a broad, strong T-cell response and neutralising antibodies during the early phase of infection. Individuals who have previously cleared an HCV infection have an 80% chance of successfully fighting off reinfection, indicating that a protective immune response has been induced and that vaccination is a realistic goal. However, with seven distinct genotypes and more than 60 subtypes, the genetic variation makes it challenging to produce a vaccine that would protect against all infections. 

Read more on the Diamond website

Image: I03 beamline at Diamond

Credit: Diamond Light Source

Massive fragment screen points way to new SARS-CoV-2 inhibitors

Experiment with 2533 fragments compounds generates chemical map to future antiviral agents 

New research published in Science Advances provides a template for how to develop directly-acting antivirals with novel modes of action, that would combat COVID-19 by suppressing the SARS-CoV-2 viral infection. The study focused on the macrodomain part of the Nsp3 gene product that SARS-CoV-2 uses to suppress the host cell’s natural antiviral response. This part of the virus’s machinery, also known as Mac1, is essential for its reproduction: previous studies have shown that viruses that lack it cannot replicate in human cells, suggesting that blocking it with a drug would have the same effect.  

The study involved a crystallographic fragment screen of the Nsp3 Mac1 protein by an open science collaboration between researchers from the University of Oxford, the XChem platform at Diamond, and researchers from the QCRG Structural Biology Consortium at the University of California San Francisco.  The international effort discovered 234 fragment compounds that directly bind to sites of interest on the surface of the protein, and map out chemical motifs and protein-compound interactions that researchers and pharmaceutical companies can draw on to design compounds that could be developed into antiviral drugs.  This work is thus foundational for preparing for future pandemics.   

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Image: Principal Beamline Scientist on I04-1, Frank von Delft

Credit: Diamond Light Source

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

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.

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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)

First glimpse of intricate details of Little Foot’s life

In June 2019, an international team brought the complete skull of the 3.67-million-year-old ‘Little Foot’ Australopithecus skeleton, from South Africa to the UK and achieved unprecedented imaging resolution of its bony structures and dentition in an X-ray synchrotron-based investigation at Diamond. The X-ray work is highlighted in a new paper in e-Life, published today focusing on the inner craniodental features of ‘Little Foot’. The remarkable completeness and great age of the ‘Little Foot’ skeleton makes it a crucially important specimen in human origins research and a prime candidate for exploring human evolution through high-resolution virtual analysis.

To recover the smallest possible details from a fairly large and very fragile fossil, the team decided to image the skull using synchrotron X-ray micro computed tomography at the I12 beamline at Diamond, revealing new information about human evolution and origins. This paper outlines preliminary results of the X-ray synchrotron-based investigation of the dentition and bones of the skull (i.e., cranial vault and mandible).

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Image: Fossil skull in Diamond’s beamline I12

Credit: Diamond Light Source

New Data sheds light on genesis of our body’s powerhouses

The mitochondria and its protein making “plants” – mitoribosomes

Scientists uncover for the first time how the body’s energy makers are made using Cryo-Electron Microscopy (cryo-EM) at eBIC within Diamond.

A new paper, published in Science on the 19th February, by an international team of researchers reports an insight into ‘the molecular mechanism of membrane-tethered protein synthesis in mitochondria’. This is a fundamental understanding of how the human mitoribosome functions and could explain how it is affected by mutations and deregulation that lead to disorders such as deafness and diseases including cancer development. 

Mitochondria are intracellular organelles which serve as tiny but potent powerhouses in our body. They use oxygen which we inhale and derivatives from food we eat to produce more than 90% of our energy, and therefore effectively support our life. Mitochondria are particularly important in high-energy demanding organs such as heart, liver, muscles and brain. For example, almost 40% of each heart muscle cell is made up of mitochondria.

Read more on the Diamond website

Image: The mitoribosome is attached to its membrane adaptor as it synthesises a bioenergetic protein (glow yellow).

Credit: Dan W. Nowakowski and Alexey Amunts

Diamond celebrates 10,000th paper – A breakthrough in chiral polymer thin films research

This could fundamentally change the technology landscape by enabling a new generation of devices

A recent paper in Nature Communications by an international team of collaborative researchers marks the 10,000th published as a result of innovative research at Diamond Light Source, the UK’s national synchrotron. This study presents disruptive insights into chiral polymer films, which emit and absorb circularly polarised light, and offers the promise of achieving important technological advances, including high-performance displays, 3D imaging and quantum computing.https://player.vimeo.com/video/502596383

Chirality is a fundamental symmetry property of the universe. We see left-handed (LH) and right-handed (RH) mirror image pairs in everything from snails and small molecules to giant spiral galaxies. Light can also have chirality. As light is travelling, its internal electric field can rotate left or right creating LH or RH circular polarisation. The ability to control and manipulate this chiral, circularly-polarised light presents opportunities in next-generation optoelectronics (Figs 1a and 1b). However, the origin of the large chiroptical effects in polymer thin films (Figs 1c and 2) has remained elusive for almost three decades. In this study, a group of researchers from Imperial College London, the University of Nottingham, the University of Barcelona, the Diamond Light Source and the J.A. Woollam Company made use of Diamond’s Synchrotron Radiation Circular Dichroism beamline (B23) and the Advanced Light Source in California.

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Image: In situ chiroptical response of ACPCA and cholesteric chiral sidechain polymers (CSCP) thin films. In situ CD spectra recorded during heating and cooling of ACPCA (F8BT: aza[6]H) and CSCP (cPFBT) thin films (note blue represents low temperatures and red represents high temperatures), (c) and (d) the CD intensity recorded at 480nm as a function of temperature during heating (red) and cooling (blue), and (e) and (f) CD intensity of thin films held at 140°C as a function of time for [P] (turquoise) and [M] (purple) systems (note the different time on-axis).