The latest Business updates from the science industry
by Heather Hobbs Diamond Protein Data Bank Continues to Expand
As the UK’s national synchrotron, Diamond Light Source has a suite of instruments dedicated to solving the 3D structure of large biological molecules – proteins, DNA and RNA. Scientists use the MX beamlines to reveal the shape and arrangement of biological molecules at atomic resolution, knowledge of which provides a highly accurate insight into function. Each 3D structure solved is deposited into the Protein Data Bank (PDB). The depositions are then released on a weekly basis. October’s PDB release took Diamond beyond 10,000 structures deposited with over half of these based on human proteins. From March to early December 2020 over 193 Covid-19 related structures from data collected at Diamond through the pandemic were made publicly available in the PDB including many using the X-Chem fragment screening facility.
Dave Hall Science Group Leader Macromolecular Crystallography Group (Credit Diamond LIght Source)
In late October 2020, Diamond and its scientifi c users achieved a signifi cant milestone by depositing its 10,000th Macromolecular Crystallography (MX) structure in the Protein Data Bank (PDB), a global repository and resource for students and researchers working to understand the molecules of life, highlighting its position as one of the most successful and prolifi c light sources solving biological structures and sharing this information worldwide. In little over a month this total had already jumped up to 10,336 structures.
Dr Dave Hall, MX Science Group Leader at Diamond, said: “This is an incredible milestone for Diamond. Thanks to the continually developing capabilities and dedicated staff, we have been able to consistently serve the UK, European and international structural biology community with access to cutting-edge technology and expertise in the fi eld.”
Professor Dave Stuart, Director of Life Sciences at Diamond Light Source and Joint Head of Structural Biology at University of Oxford, commented on the batch of Diamond MX structures which included the 10,000th: “This is a fantastic demonstration of the breadth and diversity of the science and user base of Diamond’s MX beamlines. Institutes from the UK, Europe, the Middle East, USA and Australia have been involved in these experiments, from both academia and industry. These latest structures will help to progress scientifi c research in a range
of areas, from the discovery of chemotherapeutics for the treatment of metabolic diseases [1] to identifying viral mutants that may become highly contagious and cross the species boundary. Knowing the structure of the biological molecules involved gives us vital information on how they function, which helps us to understand the role they play in health and disease.”
Diamond is one of around 50 synchrotron light source facilities currently in operation
Professor Dave Stuart (Credit: University of Oxford)
worldwide and plays a key role in solving biological structures. In 2019, 35% of all structures solved at synchrotrons in Europe were solved at Diamond along with around 11% of all worldwide synchrotron structures.
More information online:
ilmt.co/PL/zpJJ 1. Mpro, Douangamath et al, 2020
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International Project reveals Structures of Arsenic Compounds
Discovered more than 100 years ago, the structure of yukonite and arseniosiderite have been diffi cult to determine because of their low crystallinity; now using a special technique at the CLS, an international team of researchers from Canada, China, the USA, Italy and Ireland was able to visualize for the fi rst time how atoms are structured in samples of arseniosiderite and yukonite.
For McGill University graduate Mario Alberto Gomez, one of the project’s leads, it’s appropriate the discovery was made using the fi rst Canadian beamline capable of doing this type of analysis. “I think it was quite fi tting that this mineral (yukonite) was discovered in Canada, in the Yukon, a long time ago and then we were doing research on it. And now we were able to fi nally get a clearer picture of it using a Canadian synchrotron.”
Arseniosiderite Specimen BM.62813 from the collections of the Natural History Museum, London (Credit The Trustees of the Natural History Museum, London.
International researchers have used the Canadian Light Source at the University of Saskatchewan to uncover the structure of two arsenic- containing compounds yukonite and arseniosiderite - information that can be used to prevent and predict arsenic contamination in soil sources that might affect waterways.
Originally from Canada but currently a visiting professor at China’s Shenyang University of Chemical Technology, Gomez draws parallels between his team’s fi ndings and how knowing the structure of the COVID-19 coronavirus helps scientists understand how it functions, which in turn enables drug companies to develop vaccines.
For example, other natural and lab-based studies have shown that when yukonite and arseniosiderite are placed in a solution containing calcium, they release less arsenic. “Knowing their structure now will help us better understand why this happens,” he added.
Pictured: Narayan Appathurai, Chelsea-Lea Randall, Beatriz Moreno, and Graham King at the beamline (Credit: CLS)
More information online:
ilmt.co/PL/EMo6 Published in Environmental Science Nano
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