I22-Small angle scattering & Diffraction
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Andrew
Smith
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S. G.
Alcock
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L. S.
Davidson
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J. H.
Emmins
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J. C.
Hiller Bardsley
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P.
Holloway
,
M.
Malfois
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A. R.
Marshall
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C. L.
Pizzey
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S. E.
Rogers
,
O.
Shebanova
,
T.
Snow
,
J. P.
Sutter
,
E. P.
Williams
,
N. J.
Terrill
Open Access
Abstract: Beamline I22 at Diamond Light Source is dedicated to the study of soft-matter systems from both biological and materials science. The beamline can operate in the range 3.7 keV to 22 keV for transmission SAXS and 14 keV to 20 keV for microfocus SAXS with beam sizes of 240 µm × 60 µm [full width half-maximum (FWHM) horizontal (H) × vertical (V)] at the sample for the main beamline, and approximately 10 µm × 10 µm for the dedicated microfocusing platform. There is a versatile sample platform for accommodating a range of facilities and user-developed sample environments. The high brilliance of the insertion device source on I22 allows structural investigation of materials under extreme environments (for example, fluid flow at high pressures and temperatures). I22 provides reliable access to millisecond data acquisition timescales, essential to understanding kinetic processes such as protein folding or structural evolution in polymers and colloids.
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May 2021
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I22-Small angle scattering & Diffraction
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Open Access
Abstract: Coarse-grained simulation models are developed to study both template-bound and free porphyrin nanoring systems. Key interactions are modelled with relatively simple (and physically-motivated) energy functions which allow for relatively facile transfer both between different ring sizes and between the template-bound and free nanoring systems. The effects of varying the model parameters on the respective radii of gyration are determined. The effects of including different templates on the ring structure are investigated both in terms of the detailed geometry of the template and the interaction strength between the template and the metal centres in the nanorings. The role of the template-nanoring interaction strength in controlling potential ``caterpillar track'' rotational motion is discussed. The relationship of the model to experimental small-angle X-ray, exchange spectroscopy and electron spin resonance results is discussed.
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Jul 2017
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I19-Small Molecule Single Crystal Diffraction
I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[7768]
Open Access
Abstract: Vernier templating exploits a mismatch between the number of binding sites in a template and a reactant to direct the formation of a product that is large enough to bind several template units. Here, we present a detailed study of the Vernier-templated synthesis of a 12-porphyrin nanoring. NMR and small-angle X-ray scattering (SAXS) analyses show that Vernier complexes are formed as intermediates in the cyclo-oligomerization reaction. UV/Vis/NIR titrations show that the three-component assembly of the 12-porphyrin nanoring figure-of-eight template complex displays high allosteric cooperativity and chelate cooperativity. This nanoring–template 1:2 complex is among the largest synthetic molecules to have been characterized by single-crystal analysis. It crystallizes as a racemate, with an angle of 27° between the planes of the two template units. The crystal structure reveals many unexpected intramolecular CH???N contacts involving the tert-butyl side chains. Scanning tunneling microscopy (STM) experiments show that molecules of the 12-porphyrin template complex can remain intact on the gold surface, although the majority of the material unfolds into the free nanoring during electrospray deposition.
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Sep 2014
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I22-Small angle scattering & Diffraction
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Abstract: Neurodegenerative diseases constitute a large group of affections characterized by brain dysfunction and degeneration, often occurring with advancing age. Among them, prion diseases are fatal transmissible spongiform encephalopathies (TSEs) affecting Humans (Creutzfeldt-Jacob disease) and animals (BSE or the "Mad cow" disease). The causes of prion diseases have long been debated and it is widely accepted by the scientific community that a protein, namely, the prion protein (PrP), plays a critical role in the disease development. The prion protein or PrP is present in two structurally distinct forms: the natural cellular form (PrPc) and an abnormal polymeric form (PrPsc), which is at the origin of fibrillar deposits found in affected brains. PrPc has been shown to convert into small toxic oligomeric species but the mechanisms of oligomerization are not fully understood. In this study, we have combined Molecular Dynamics (MD) simulations and Small Angle X-ray Scattering (SAXS) to investigate the critical unfolding steps of the ovine prion protein (OvPrP) and to determine the low resolution structure of some of the oligomeric species obtained from various truncated forms of the OvPrP.
We show that the domain formed by Helix2 and Helix3 (H2H3) is critical in the unfolding of OvPrP and its conversion of into a beta-rich conformer. The analysis also suggests the incorporation of 9-10 monomer units for all monomeric species studied. We therefore propose that the minimal β-rich core of OvPrP-O3 oligomer is formed by the H2H3 domain while the N-terminal domain either combines with other N-terminal domains to form a second domain or surrounds the oligomeric core.
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Jan 2014
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I22-Small angle scattering & Diffraction
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Adrian R.
Rennie
,
Maja S.
Hellsing
,
Kathleen
Wood
,
Elliot P.
Gilbert
,
Lionel
Porcar
,
Ralf
Schweins
,
Charles D.
Dewhurst
,
Peter
Lindner
,
Richard K.
Heenan
,
Sarah
Rogers
,
Paul D.
Butler
,
Jeffery R.
Krzywon
,
Ron E.
Ghosh
,
Andrew J.
Jackson
,
Marc
Malfois
Abstract: Measurements of a well-characterised ‘standard’ sample can verify the performance of an instrument.
Typically, small-angle neutron scattering instruments are used to investigate a wide range of samples and may often
be used in a number of configurations. Appropriate ‘standard’ samples are useful to test different aspects of the
performance of hardware as well as that of the data reduction and analysis software. Measurements on a number of
instruments with different intrinsic characteristics and designs in a round robin can not only better characterise the
performance for a wider range of conditions but also, perhaps more importantly, reveal the limits of the current state
of the art of small-angle scattering. The exercise, followed by detailed analysis, tests the limits of current
understanding as well as uncovers often forgotten assumptions, simplifications and approximations that underpin the
current practice of the technique. This paper describes measurements of polystyrene latex, radius 720 Å with a
number of instruments. Scattering from monodisperse, uniform spherical particles is simple to calculate and displays
sharp minima. Such data test the calibrations of intensity, wavelength and resolution as well as the detector response.
Smoothing due to resolution, multiple scattering and polydispersity has been determined. Sources of uncertainty are
often related to systematic deviations and calibrations rather than random counting errors. The study has prompted
2
development of software to treat modest multiple scattering and to better model the instrument resolution. These
measurements also allow checks of data reduction algorithms and have identified how they can be improved. The
reproducibility and the reliability of instruments and the accuracy of parameters derived from the data are described.
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Oct 2013
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Open Access
Abstract: Hfq is a bacterial RNA binding protein that facilitates small RNA-mediated posttranscriptional gene regulation. In Vibrio cholerae, Hfq and four Hfq-dependent small RNAs are essential for the expression of virulence genes, but little is known about this mechanism at the molecular level. To better understand V. cholerae Hfq structure and mechanism, we characterized the protein, alongside Escherichia coli Hfq for comparison, using biochemical and biophysical techniques. The N-terminal domain (NTD) of the two proteins is highly conserved, but the C-terminal regions (CTRs) vary in both sequence and length. Small-angle X-ray scattering studies showed that both proteins adopt a star-shaped hexameric structure in which the conserved NTD adopts the expected Sm fold while the variable CTR is disordered and extends radially outwards from the folded core. Despite their structural similarity, SDS-PAGE stability assays and collision-induced dissociation mass spectrometry revealed that the V. cholerae hexamer is less stable than that of E. coli. We propose that this is due to minor differences between the intersubunit interface formed by the NTDs and the ability of the E. coli CTR to stabilize this interface. However, based on electrophoretic mobility shift assays, the divergent CTRs do appear to perform a common function with regard to RNA-binding specificity. Overall, the similarities and differences in the fundamental properties of V. cholerae and E. coli Hfq provide insight into their assembly and molecular mechanisms.
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Jun 2012
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I19-Small Molecule Single Crystal Diffraction
I22-Small angle scattering & Diffraction
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Johannes
Sprafke
,
Dmitry
Kondratiuk
,
Michael
Wykes
,
Amber
Thompson
,
Marcus
Hoffman
,
Rokas
Drevinskas
,
Wei-Hsin
Chen
,
Chaw
Keong Yong
,
Joakim
Kärnbratt
,
Joseph
Bullock
,
Marc
Malfois
,
Michael
Wasielewski
,
Bo
Albinsson
,
Laura
Herz
,
Donatas
Zigmantas
,
David
Beljonne
,
Harry
Anderson
Abstract: Linear π-conjugated oligomers have been widely investigated, but the behavior of the corresponding cyclic oligomers is poorly understood, despite the recent synthesis of π-conjugated macrocycles such as [n]cycloparaphenylenes and cyclo[n]thiophenes. Here we present an efficient template-directed synthesis of a π-conjugated butadiyne-linked cyclic porphyrin hexamer directly from the monomer. Small-angle X-ray scattering data show that this nanoring is shape-persistent in solution, even without its template, whereas the linear porphyrin hexamer is relatively flexible. The crystal structure of the nanoring–template complex shows that most of the strain is localized in the acetylenes; the porphyrin units are slightly curved, but the zinc coordination sphere is undistorted. The electrochemistry, absorption, and fluorescence spectra indicate that the HOMO–LUMO gap of the nanoring is less than that of the linear hexamer and less than that of the corresponding polymer. The nanoring exhibits six one-electron reductions and six one-electron oxidations, most of which are well resolved. Ultrafast fluorescence anisotropy measurements show that absorption of light generates an excited state that is delocalized over the whole π-system within a time of less than 0.5 ps. The fluorescence spectrum is amazingly structured and red-shifted. A similar, but less dramatic, red-shift has been reported in the fluorescence spectra of cycloparaphenylenes and was attributed to a high exciton binding energy; however the exciton binding energy of the porphyrin nanoring is similar to those of linear oligomers. Quantum-chemical excited state calculations show that the fluorescence spectrum of the nanoring can be fully explained in terms of vibronic Herzberg–Teller (HT) intensity borrowing.
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Sep 2011
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I22-Small angle scattering & Diffraction
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Open Access
Abstract: The CCN (cyr61, ctgf, nov) proteins (CCN1-6) are an important family of matricellular regulatory factors involved in internal and external cell signaling. They are central to essential biological processes such as adhesion, proliferation, angiogenesis, tumorigenesis, wound healing, and modulation of the extracellular matrix. They possess a highly conserved modular structure with four distinct modules that interact with a wide range of regulatory proteins and ligands. However, at the structural level, little is known although their biological function(s) seems to require cooperation between individual modules. Here we present for the first time structural determinants of two of the CCN family members, CCN3 and CCN5 (expressed in Escherichia coli), using small angle x-ray scattering. The results provide a description of the overall molecular shape and possible general three-dimensional modular arrangement for CCN proteins. These data unequivocally provide insight of the nature of CCN protein(s) in solution and thus important insight into their structure-function relationships.
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May 2011
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I22-Small angle scattering & Diffraction
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Clair
Baldock
,
Andres F.
Oberhauser
,
Ling
Ma
,
Donna
Lammie
,
Veronique
Siegler
,
Suzanne M.
Mithieux
,
Yidong
Tu
,
John Yuen Ho
Chow
,
Farhana
Suleman
,
Marc
Malfois
,
Sarah
Rogers
,
Liang
Guo
,
Thomas C.
Irving
,
Tim J.
Wess
,
Anthony S.
Weiss
Abstract: Elastin enables the reversible deformation of elastic tissues and can withstand decades of repetitive forces. Tropoelastin is the soluble precursor to elastin, the main elastic protein found in mammals. Little is known of the shape and mechanism of assembly of tropoelastin as its unique composition and propensity to self-associate has hampered structural studies. In this study, we solve the nanostructure of full-length and corresponding overlapping fragments of tropoelastin using small angle X-ray and neutron scattering, allowing us to identify discrete regions of the molecule. Tropoelastin is an asymmetric coil, with a protruding foot that encompasses the C-terminal cell interaction motif. We show that individual tropoelastin molecules are highly extensible yet elastic without hysteresis to perform as highly efficient molecular nanosprings. Our findings shed light on how biology uses this single protein to build durable elastic structures that allow for cell attachment to an appended foot. We present a unique model for head-to-tail assembly which allows for the propagation of the molecule's asymmetric coil through a stacked spring design.
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Feb 2011
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I22-Small angle scattering & Diffraction
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Melanie C.
O'Sullivan
,
Johannes
Sprafke
,
Dmitry
Kondratiuk
,
Corentin
Rinfray
,
Timothy
Claridge
,
Alex
Saywell
,
Matthew
Blunt
,
James
O'Shea
,
Peter
Beton
,
Marc
Malfois
,
Harry L.
Anderson
Abstract: Templates are widely used to arrange molecular components so they can be covalently linked into complex molecules that are not readily accessible by classical synthetic methods1, 2, 3, 4, 5, 6, 7. Nature uses sophisticated templates such as the ribosome, whereas chemists use simple ions or small molecules. But as we tackle the synthesis of larger targets, we require larger templateswhich themselves become synthetically challenging. Here we show that Vernier complexes can solve this problem: if the number of binding sites on the template, nT, is not a multiple of the number of binding sites on the molecular building blocks, nB, then small templates can direct the assembly of relatively large Vernier complexes where the number of binding sites in the product, nP, is the lowest common multiple of nB and nT (refs 8, 9). We illustrate the value of this concept for the covalent synthesis of challenging targets by using a simple six-site template to direct the synthesis of a 12-porphyrin nano-ring with a diameter of 4.7 nm, thus establishing Vernier templating as a powerful new strategy for the synthesis of large monodisperse macromolecules.
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Jan 2011
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