Mysteries of enzyme mechanism revealed
An international research team led by the University of Leicester has made a breakthrough advance by trapping an intermediate in the mechanism of enzymes called heme peroxidases and determining its structure using a beam of neutrons from the heart of a nuclear reactor.
The advance is announced today (29 November) in an online publication in Nature Communications. The Leicester team members say they are delighted by their finding which could change the way we understand how these enzymes work through 'wonderful collaborations' with scientists at European facilities such as the Institut Laue-Langevin (ILL) in Grenoble and FRM-II in Munich, as well as the Diamond Light Source in Oxfordshire and the EPR centre at Manchester University. Professors Emma Raven and Peter Moody from the University of Leicester's Institute of Structural and Chemical Biology led the team that developed a new method to trap and analyse the enzyme's reaction steps.
Professor Moody of the Department of Molecular and Cell Biology, said: "Using beams of neutrons instead of X-rays lets us see the position of hydrogen atoms without altering the chemical state. These enzymes go through two intermediate steps, a couple of years ago we used neutron cryo-crystallography to show the hydrogens in the first step (published in Science), and since then a great deal of work by our team has allowed us find a way to trap the next step. It had been believed that this second step did not hold hydrogen at the reactive centre, however this work clearly shows the hydrogen and so we have to re-think the way the enzyme works."
Heme enzymes have an iron atom in a special chemical group called a porphyrin, this is the same as in hemoglobin, the molecule that carries oxygen in our blood, but in heme peroxidase enzymes it is used to pull apart peroxide for many different biochemical processes, these include getting rid of damaging compounds in the cell and the making of new molecules that the cell needs.
Professor Raven from the University's Department of Chemistry said: "The exact nature of these enzyme intermediates has been the subject of a long-standing controversy and conflicting interpretation of indirect evidence. At least we have been able to see these directly, this really is the 'holy grail' of heme enzyme research."
- The work has been funded by a BBSRC project grant to Professors Moody and Raven, an equipment grant from Wellcome Trust and beamtime awarded by the ILL for LADI-III and by FRM-II for BioDIFF.
- This work was mainly conducted by Dr Hanna Kwon (University of Leicester) with the support of the other authors, the neutron data were collected and processed with Dr Matthew Blakeley at the LADI-III beamline at ILL.
The online publication will be on the Nature Communications website on the 29th of November. The DOI for this article is: DOI: 10.1038/ncomms13445
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About the Leicester Institute of Structural and Chemical Biology
The Leicester Institute of Structural and Chemical Biology was created in 2016 with the aim of bringing together established strengths in structural biology, chemical biology and single-molecule research. The new Institute will take advantages of synergies in research technologies and approaches to deliver major advances in both fundamental and translational research.
The Institute's research is organised into four inter-related research strands:
Understanding the structure and mechanism of macromolecular complexes
Some of the most challenging questions in biology involve understanding the structures and mechanism of action of the molecular machines that carry out the processes of life.
Structure-based drug discovery and design
Structural biology provides us enormous insight into the mechanism of action of macromolecules and complexes. At the same time it provides detailed insights into strategies to develop small and medium-sized molecules that can alter protein functions and serve as effective therapeutics.
Using single molecule techniques to understand complex and dynamic biological processes
Many fundamental cellular processes rely on highly dynamic interactions between macromolecules and macromolecular complexes. Single molecule techniques allow us to observe and understand these processes in real time.
Chemical probes and compound libraries development
Understanding how macromolecules carry out their many diverse activities requires an understanding of the underlying chemistry which determines the behaviour of these complexes. By exploiting this chemistry we are able to manipulate macromolecular function and activity. This is important both for drug development, but also the development of research tools.
About Institut Laue-Langevin – the Institut Laue-Langevin (ILL) is an international research centre based in Grenoble, France. It has led the world in neutron-scattering science and technology for almost 40 years, since experiments began in 1972. ILL operates one of the most intense neutron sources in the world, feeding beams of neutrons to a suite of 40 high-performance instruments that are constantly upgraded. Each year 1,200 researchers from over 40 countries visit ILL to conduct research into condensed matter physics, (green) chemistry, biology, nuclear physics, and materials science. The UK, along with France and Germany is an associate and major funder of the ILL.