I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[19880]
Open Access
Abstract: Von Willebrand factor (VWF) activates in response to shear flow to initiate hemostasis, while aberrant activation could lead to thrombosis. Above a critical shear force, the A1 domain of VWF becomes activated and captures platelets via the GPIb-IX complex. Here we show that the shear-responsive element controlling VWF activation resides in the discontinuous autoinhibitory module (AIM) flanking A1. Application of tensile force in a single-molecule setting induces cooperative unfolding of the AIM to expose A1. The AIM-unfolding force is lowered by truncating either N- or C-terminal AIM region, type 2B VWD mutations, or binding of a ristocetin-mimicking monoclonal antibody, all of which could activate A1. Furthermore, the AIM is mechanically stabilized by the nanobody that comprises caplacizumab, the only FDA-approved anti-thrombotic drug to-date that targets VWF. Thus, the AIM is a mechano-regulator of VWF activity. Its conformational dynamics may define the extent of VWF autoinhibition and subsequent activation under force.
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Apr 2021
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B21-High Throughput SAXS
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[14980, 19844]
Abstract: Ubiquitin-specific protease 1 (USP1) acts together with the cofactor UAF1 during DNA repair processes to specifically remove monoubiquitin signals. One substrate of the USP1−UAF1 complex is the monoubiquitinated FANCI−FANCD2 heterodimer, which is involved in the repair of DNA interstrand crosslinks via the Fanconi anemia pathway. Here we determine structures of human USP1−UAF1 with and without ubiquitin and bound to monoubiquitinated FANCI−FANCD2. The crystal structures of USP1−UAF1 reveal plasticity in USP1 and key differences to USP12−UAF1 and USP46−UAF1, two related proteases. A cryo-EM reconstruction of USP1−UAF1 in complex with monoubiquitinated FANCI−FANCD2 highlights a highly orchestrated deubiquitination process, with USP1−UAF1 driving conformational changes in the substrate. An extensive interface between UAF1 and FANCI, confirmed by mutagenesis and biochemical assays, provides a molecular explanation for the requirement of both proteins, despite neither being directly involved in catalysis. Overall, our data provide molecular details of USP1−UAF1 regulation and substrate recognition.
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Apr 2021
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I11-High Resolution Powder Diffraction
I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[15777, 17193]
Abstract: The discovery of new structural and functional materials is driven by phase identification, often using X-ray diffraction (XRD). Automation has accelerated the rate of XRD measurements, greatly outpacing XRD analysis techniques that remain manual, time-consuming, error-prone and impossible to scale. With the advent of autonomous robotic scientists or self-driving laboratories, contemporary techniques prohibit the integration of XRD. Here, we describe a computer program for the autonomous characterization of XRD data, driven by artificial intelligence (AI), for the discovery of new materials. Starting from structural databases, we train an ensemble model using a physically accurate synthetic dataset, which outputs probabilistic classifications—rather than absolutes—to overcome the overconfidence in traditional neural networks. This AI agent behaves as a companion to the researcher, improving accuracy and offering substantial time savings. It is demonstrated on a diverse set of organic and inorganic materials characterization challenges. This method is directly applicable to inverse design approaches and robotic discovery systems, and can be immediately considered for other forms of characterization such as spectroscopy and the pair distribution function.
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Apr 2021
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E02-JEM ARM 300CF
I15-1-X-ray Pair Distribution Function (XPDF)
I22-Small angle scattering & Diffraction
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Adam F.
Sapnik
,
Irene
Bechis
,
Sean M.
Collins
,
Duncan N.
Johnstone
,
Giorgio
Divitini
,
Andrew J.
Smith
,
Philip A.
Chater
,
Matthew A.
Addicoat
,
Timothy
Johnson
,
David A.
Keen
,
Kim E.
Jelfs
,
Thomas D.
Bennett
Diamond Proposal Number(s):
[20038, 24563]
Open Access
Abstract: Amorphous metal–organic frameworks (MOFs) are an emerging class of materials. However, their structural characterisation represents a significant challenge. Fe-BTC, and the commercial equivalent Basolite® F300, are MOFs with incredibly diverse catalytic ability, yet their disordered structures remain poorly understood. Here, we use advanced electron microscopy to identify a nanocomposite structure of Fe-BTC where nanocrystalline domains are embedded within an amorphous matrix, whilst synchrotron total scattering measurements reveal the extent of local atomic order within Fe-BTC. We use a polymerisation-based algorithm to generate an atomistic structure for Fe-BTC, the first example of this methodology applied to the amorphous MOF field outside the well-studied zeolitic imidazolate framework family. This demonstrates the applicability of this computational approach towards the modelling of other amorphous MOF systems with potential generality towards all MOF chemistries and connectivities. We find that the structures of Fe-BTC and Basolite® F300 can be represented by models containing a mixture of short- and medium-range order with a greater proportion of medium-range order in Basolite® F300 than in Fe-BTC. We conclude by discussing how our approach may allow for high-throughput computational discovery of functional, amorphous MOFs.
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Apr 2021
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I12-JEEP: Joint Engineering, Environmental and Processing
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Ziyang
Ning
,
Dominic Spencer
Jolly
,
Guanchen
Li
,
Robin
De Meyere
,
Shengda D.
Pu
,
Yang
Chen
,
Jitti
Kasemchainan
,
Johannes
Ihli
,
Chen
Gong
,
Boyang
Liu
,
Dominic L. R.
Melvin
,
Anne
Bonnin
,
Oxana
Magdysyuk
,
Paul
Adamson
,
Gareth O.
Hartley
,
Charles W.
Monroe
,
James
Marrow
,
Peter G.
Bruce
Diamond Proposal Number(s):
[20795]
Abstract: Lithium dendrite (filament) propagation through ceramic electrolytes, leading to short circuits at high rates of charge, is one of the greatest barriers to realizing high-energy-density all-solid-state lithium-anode batteries. Utilizing in situ X-ray computed tomography coupled with spatially mapped X-ray diffraction, the propagation of cracks and the propagation of lithium dendrites through the solid electrolyte have been tracked in a Li/Li6PS5Cl/Li cell as a function of the charge passed. On plating, cracking initiates with spallation, conical ‘pothole’-like cracks that form in the ceramic electrolyte near the surface with the plated electrode. The spallations form predominantly at the lithium electrode edges where local fields are high. Transverse cracks then propagate from the spallations across the electrolyte from the plated to the stripped electrode. Lithium ingress drives the propagation of the spallation and transverse cracks by widening the crack from the rear; that is, the crack front propagates ahead of the Li. As a result, cracks traverse the entire electrolyte before the Li arrives at the other electrode, and therefore before a short circuit occurs.
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Apr 2021
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I04-Macromolecular Crystallography
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Oyvind
Stromland
,
Juha P.
Kallio
,
Annica
Pschibul
,
Renate H.
Skoge
,
Hulda M.
Harðardóttir
,
Lars J.
Sverkeli
,
Thorsten
Heinekamp
,
Olaf
Kniemeyer
,
Marie
Migaud
,
Mikhail V.
Makarov
,
Toni I.
Gossmann
,
Axel A.
Brakhage
,
Mathias
Ziegler
Open Access
Abstract: Nicotinamide adenine dinucleotide (NAD) is a key molecule in cellular bioenergetics and signalling. Various bacterial pathogens release NADase enzymes into the host cell that deplete the host’s NAD+ pool, thereby causing rapid cell death. Here, we report the identification of NADases on the surface of fungi such as the pathogen Aspergillus fumigatus and the saprophyte Neurospora crassa. The enzymes harbour a tuberculosis necrotizing toxin (TNT) domain and are predominately present in pathogenic species. The 1.6 Å X-ray structure of the homodimeric A. fumigatus protein reveals unique properties including N-linked glycosylation and a Ca2+-binding site whose occupancy regulates activity. The structure in complex with a substrate analogue suggests a catalytic mechanism that is distinct from those of known NADases, ADP-ribosyl cyclases and transferases. We propose that fungal NADases may convey advantages during interaction with the host or competing microorganisms.
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Mar 2021
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I04-1-Macromolecular Crystallography (fixed wavelength)
I04-Macromolecular Crystallography
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Diamond Proposal Number(s):
[8492, 11265]
Open Access
Abstract: Microsomal glutathione S-transferase 2 (MGST2) produces leukotriene C4, key for intracrine signaling of endoplasmic reticulum (ER) stress, oxidative DNA damage and cell death. MGST2 trimer restricts catalysis to only one out of three active sites at a time, but the molecular basis is unknown. Here, we present crystal structures of human MGST2 combined with biochemical and computational evidence for a concerted mechanism, involving local unfolding coupled to global conformational changes that regulate catalysis. Furthermore, synchronized changes in the biconical central pore modulate the hydrophobicity and control solvent influx to optimize reaction conditions at the active site. These unique mechanistic insights pertain to other, structurally related, drug targets.
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Mar 2021
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I24-Microfocus Macromolecular Crystallography
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Open Access
Abstract: De novo protein design is advancing rapidly. However, most designs are for single states. Here we report a de novo designed peptide that forms multiple α-helical-bundle states that are accessible and interconvertible under the same conditions. Usually in such designs amphipathic α helices associate to form compact structures with consolidated hydrophobic cores. However, recent rational and computational designs have delivered open α-helical barrels with functionalisable cavities. By placing glycine judiciously in the helical interfaces of an α-helical barrel, we obtain both open and compact states in a single protein crystal. Molecular dynamics simulations indicate a free-energy landscape with multiple and interconverting states. Together, these findings suggest a frustrated system in which steric interactions that maintain the open barrel and the hydrophobic effect that drives complete collapse are traded-off. Indeed, addition of a hydrophobic co-solvent that can bind within the barrel affects the switch between the states both in silico and experimentally.
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Mar 2021
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Open Access
Abstract: Bicyclo[1.1.1]pentanes (BCPs) are important motifs in contemporary drug design as linear spacer units that improve pharmacokinetic profiles. The synthesis of BCPs featuring adjacent stereocenters is highly challenging, but desirable due to the fundamental importance of 3D chemical space in medicinal chemistry. Current methods to access these high-value chiral molecules typically involve transformations of pre-formed BCPs, and can display limitations in substrate scope. Here we describe an approach to synthesize α-chiral BCPs involving the direct, asymmetric addition of simple aldehydes to [1.1.1]propellane, the predominant BCP precursor. This is achieved by combining a photocatalyst and an organocatalyst to generate a chiral α-iminyl radical cation intermediate, which installs a stereocenter simultaneously with ring-opening of [1.1.1]propellane. The reaction proceeds under mild conditions, displays broad scope, and provides an array of α-chiral BCPs in high yield and enantioselectivity. We also present a theoretical model for stereoinduction in this mode of photoredox organocatalysis.
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Mar 2021
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I03-Macromolecular Crystallography
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Diamond Proposal Number(s):
[15916, 21426]
Open Access
Abstract: Attachment of ubiquitin (Ub) to proteins is one of the most abundant and versatile of all posttranslational modifications and affects outcomes in essentially all physiological processes. RING E3 ligases target E2 Ub-conjugating enzymes to the substrate, resulting in its ubiquitination. However, the mechanism by which a ubiquitin chain is formed on the substrate remains elusive. Here we demonstrate how substrate binding can induce a specific RING topology that enables self-ubiquitination. By analyzing a catalytically trapped structure showing the initiation of TRIM21 RING-anchored ubiquitin chain elongation, and in combination with a kinetic study, we illuminate the chemical mechanism of ubiquitin conjugation. Moreover, biochemical and cellular experiments show that the topology found in the structure can be induced by substrate binding. Our results provide insights into ubiquitin chain formation on a structural, biochemical and cellular level with broad implications for targeted protein degradation.
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Feb 2021
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