NONE-No attached Diamond beamline
|
Abstract: Understanding allosteric regulation of proteins is fundamental to our study of protein structure and function. Moreover, allosteric binding pockets have become a major target of drug discovery efforts in recent years. However, even though the function of almost every protein can be influenced by allostery, it remains a challenge to discover, rationalise and validate putative allosteric binding pockets. This review examines how the discovery and analysis of putative allosteric binding sites have been influenced by the availability of centralised facilities for crystallographic fragment screening, along with newly developed computational methods for modelling low occupancy features. We discuss the experimental parameters required for success, and how new methods could influence the field in the future. Finally, we reflect on the general problem of how to translate these findings into actual ligand development programs.
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Dec 2020
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NONE-No attached Diamond beamline
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Tadeo
Moreno Chicano
,
Ali
Ebrahim
,
Danny
Axford
,
Martin V.
Appleby
,
John H.
Beale
,
Amanda K.
Chaplin
,
Helen M. E.
Duyvesteyn
,
Reza A.
Ghiladi
,
Shigeki
Owada
,
Darren A.
Sherrell
,
Richard
Strange
,
Hiroshi
Sugimoto
,
Kensuke
Tono
,
Jonathan A. R.
Worrall
,
Robin L.
Owen
,
Michael A.
Hough
Open Access
Abstract: High-throughput X-ray crystal structures of protein–ligand complexes are critical to pharmaceutical drug development. However, cryocooling of crystals and X-ray radiation damage may distort the observed ligand binding. Serial femtosecond crystallography (SFX) using X-ray free-electron lasers (XFELs) can produce radiation-damage-free room-temperature structures. Ligand-binding studies using SFX have received only modest attention, partly owing to limited beamtime availability and the large quantity of sample that is required per structure determination. Here, a high-throughput approach to determine room-temperature damage-free structures with excellent sample and time efficiency is demonstrated, allowing complexes to be characterized rapidly and without prohibitive sample requirements. This yields high-quality difference density maps allowing unambiguous ligand placement. Crucially, it is demonstrated that ligands similar in size or smaller than those used in fragment-based drug design may be clearly identified in data sets obtained from <1000 diffraction images. This efficiency in both sample and XFEL beamtime opens the door to true high-throughput screening of protein–ligand complexes using SFX.
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Nov 2019
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NONE-No attached Diamond beamline
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Open Access
Abstract: A recent paper in BMC Biology presents a general method for mix-and-inject serial crystallography, to facilitate the visualization of enzyme intermediates via time-resolved serial femtosecond crystallography (tr-SFX). They apply their method to resolve in near atomic detail the cleavage and inactivation of the antibiotic ceftriaxone by a β-lactamase enzyme from Mycobacterium tuberculosis. Their work demonstrates the general applicability of time-resolved crystallography, from which dynamic structures, at atomic resolution, can be obtained.
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May 2018
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NONE-No attached Diamond beamline
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Open Access
Abstract: Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
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May 2018
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NONE-No attached Diamond beamline
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Jonathan M.
Grimes
,
David R.
Hall
,
Alun W.
Ashton
,
Gwyndaf
Evans
,
Robin L.
Owen
,
Armin
Wagner
,
Katherine E.
Mcauley
,
Frank
Von Delft
,
Allen M.
Orville
,
Thomas
Sorensen
,
Martin A.
Walsh
,
Helen
Ginn
,
David I.
Stuart
Open Access
Abstract: Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
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Feb 2018
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NONE-No attached Diamond beamline
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Abstract: The study of micrometeorites—sub-millimetre pieces of debris from asteroids and comets that are found on Earth—can provide insights into the nature of their parent bodies and the Earth’s upper atmosphere. Modern ‘cosmic dust’ particles are relatively easy to capture and examine, but it is much more challenging to study the ancient flux of micrometeorites to Earth. Indeed, pristine micrometeorites are notoriously difficult to identify and separate from their host rocks. In work recently published in Earth and Planetary Science Letters, however, scientists have described and successfully tested a new micrometeorite identification and separation methodology, with which they recovered more than 70 cosmic dust particles from Cretaceous chalk. The distinctive morphologies and textures of the micrometeorite spherules were clearly identifiable from high-resolution electron microscope images obtained as part of the study. Furthermore, from Raman spectroscopy measurements conducted in the offline support Characterisation Laboratory (Lab 91) at Diamond Light Source, it was found that the mineralogy of the particles was distinct from that of modern cosmic dust. The results are thus evidence for replacement of the micrometeorite mineral phases during diagenesis (fossilisation). The authors of the study believe that these ‘pseudomorphic’ micrometeorites should be common within the geologic record and can be recognised through careful observations of particle textures.
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Nov 2017
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NONE-No attached Diamond beamline
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Open Access
Abstract: We report the discovery of fossil micrometeorites from Late Cretaceous chalk. Seventy-six cosmic spherules were recovered from Coniacian (
87±1 Ma
) sediments of the White Chalk Supergroup. Particles vary from pristine silicate and iron-type spherules to pseudomorphic spherules consisting of either single-phase recrystallized magnetite or Fe-silicide. Pristine spherules are readily identified as micrometeorites on the basis of their characteristic mineralogies, textures and compositions. Both magnetite and silicide spherules contain dendritic crystals and spherical morphologies, testifying to rapid crystallisation of high temperature iron-rich metallic and oxide liquids. These particles also contain spherical cavities, representing weathering and removal of metal beads and irregular cavities, representing vesicles formed by trapped gas during crystallization; both features commonly found among modern Antarctic Iron-type (I-type) cosmic spherules. On the basis of textural analysis, the magnetite and Fe-silicide spherules are shown to be I-type cosmic spherules that have experienced complete secondary replacement during diagenesis (fossilization). Our results demonstrate that micrometeorites, preserved in sedimentary rocks, are affected by a suite of complex diagenetic processes, which can result in disparate replacement minerals, even within the same sequence of sedimentary beds. As a result, the identification of fossil micrometeorites requires careful observation of particle textures and comparisons with modern Antarctic collections. Replaced micrometeorites imply that geochemical signatures the extraterrestrial dust are subject to diagenetic remobilisation that limits their stratigraphic resolution. However, this study demonstrates that fossil, pseudomorphic micrometeorites can be recognised and are likely common within the geological record.
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Oct 2017
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NONE-No attached Diamond beamline
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Abstract: Solution-processed organic films are a facile route to high-speed, low cost, large-area deposition of electrically functional components (transistors, solar cells, emitters, etc.) that can enable a diversity of emerging technologies, from Industry 4.0, to the Internet of things, to point-of-use heath care and elder care. The extreme sensitivity of the functional performance of organic films to structure and the general nonequilibrium nature of solution drying result in extreme processing–performance correlations. In this Review, we highlight insights into the fundamentals of solution-based film deposition afforded by recent state-of-the-art in situ measurements of functional film drying. Emphasis is placed on multimodal studies that combine surface-sensitive X-ray scattering (GIWAXS or GISAXS) with optical characterization to clearly define the evolution of solute structure (aggregation, crystallinity, and morphology) with film thickness.
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Apr 2017
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NONE-No attached Diamond beamline
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Franklin D
Fuller
,
Sheraz
Gul
,
Ruchira
Chatterjee
,
E. Sethe
Burgie
,
Iris D.
Young
,
Hugo
Lebrette
,
Vivek
Srinivas
,
Aaron
Brewster
,
Tara
Michels-Clark
,
Jonathan A
Clinger
,
Babak
Andi
,
Mohamed
Ibrahim
,
Ernest
Pastor
,
Casper
De Lichtenberg
,
Rana
Hussein
,
Christopher J
Pollock
,
Miao
Zhang
,
Claudiu A
Stan
,
Thomas
Kroll
,
Thomas
Fransson
,
Clemens
Weninger
,
Markus
Kubin
,
Pierre
Aller
,
Louise
Lassalle
,
Philipp
Braeuer
,
Mitchell D.
Miller
,
Muhamed
Amin
,
Sergey
Koroidov
,
Christian G.
Roessler
,
Marc
Allaire
,
Raymond G
Sierra
,
Peter T.
Docker
,
James M.
Glownia
,
Silke
Nelson
,
Jason E
Koglin
,
Diling
Zhu
,
Matthieu
Chollet
,
Sanghoon
Song
,
Henrik
Lemke
,
Mengning
Liang
,
Dimosthenis
Sokaras
,
Roberto
Alonso-Mori
,
Athina
Zouni
,
Johannes
Messinger
,
Uwe
Bergmann
,
Amie K.
Boal
,
J. Martin
Bollinger
,
Carsten
Krebs
,
Martin
Högbom
,
George N.
Phillips
,
Richard D.
Vierstra
,
Nicholas K
Sauter
,
Allen M.
Orville
,
Jan
Kern
,
Vittal K
Yachandra
,
Junko
Yano
Abstract: X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Feb 2017
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NONE-No attached Diamond beamline
Mechanical Engineering
|
Richard
Walker
,
C
Abraham
,
Cp
Bailey
,
Riccardo
Bartolini
,
P
Coll
,
P
Cox
,
Nigel
Hammond
,
Mark
Heron
,
Se
Hughes
,
James
Kay
,
I
Martin
,
Shriram
Mhaskar
,
A
Miller
,
Aj
Reed
,
Guenther
Rehm
,
E
Rial
,
Austen
Rose
,
A
Shahveh
,
Hugo
Shiers
,
Andrew
Thomson
Open Access
Abstract: We present the status of preparations for a major installation in the Diamond storage ring which is due to take place in 2016, namely the conversion of one cell of the ring from a double bend achromat (DBA) structure, to a double-DBA, or DDBA. We present results of measurements of the new narrow bore, high strength, quadrupoles and sextupoles, as well as the four new gradient dipoles. Fabrication of entirely new narrow-gap vacuum vessel strings, a mixture of copper and stainless steel is also described. The status of assembly of the two 7m long girders is presented, as well as other preparatory engineering, power supply, controls and high level software work.
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Jun 2016
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