B21-High Throughput SAXS
B23-Circular Dichroism
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Philip
Bardelang
,
Ewan J.
Murray
,
Isobel
Blower
,
Sara
Zandomeneghi
,
Alice
Goode
,
Rohanah
Hussain
,
Divya
Kumari
,
Giuliano
Siligardi
,
Katsuaki
Inoue
,
Jeni
Luckett
,
James
Doutch
,
Jonas
Emsley
,
Weng C.
Chan
,
Philip
Hill
,
Paul
Williams
,
Boyan B.
Bonev
Diamond Proposal Number(s):
[5098, 12923, 13185, 13634, 15146]
Open Access
Abstract: Virulence gene expression in the human pathogen, S. aureus is regulated by the agr (accessory gene regulator) quorum sensing (QS) system which is conserved in diverse Gram-positive bacteria. The agr QS signal molecule is an autoinducing peptide (AIP) generated via the initial processing of the AgrD pro-peptide by the transmembrane peptidase AgrB. Since structural information for AgrB and AgrBD interactions are lacking, we used homology modelling and molecular dynamics (MD) annealing to characterise the conformations of AgrB and AgrD in model membranes and in solution. These revealed a six helical transmembrane domain (6TMD) topology for AgrB. In solution, AgrD behaves as a disordered peptide, which binds N-terminally to membranes in the absence and in the presence of AgrB. In silico, membrane complexes of AgrD and dimeric AgrB show non-equivalent AgrB monomers responsible for initial binding and for processing, respectively. By exploiting split luciferase assays in Staphylococcus aureus, we provide experimental evidence that AgrB interacts directly with itself and with AgrD. We confirmed the in vitro formation of an AgrBD complex and AIP production after Western blotting using either membranes from Escherichia coli expressing AgrB or with purified AgrB and T7-tagged AgrD. AgrB and AgrD formed stable complexes in detergent micelles revealed using synchrotron radiation CD (SRCD) and Landau analysis consistent with the enhanced thermal stability of AgrB in the presence of AgrD. Conformational alteration of AgrB following provision of AgrD was observed by small angle X-ray scattering from proteodetergent micelles. An atomistic description of AgrB and AgrD has been obtained together with confirmation of the AgrB 6TMD membrane topology and existence of AgrBD molecular complexes in vitro and in vivo.
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May 2023
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[31552]
Open Access
Abstract: A non-chiral ferroelectric nematic compound with a 1,3-dioxane unit in the mesogenic core called 2,3',4',5'-tetrafluoro-[1,1'-biphenyl]-4-yl 2,6-difluoro-4-(5-propyl-1,3-dioxan-2-yl) benzoate (DIO) was studied by dielectric spectroscopy in the frequency range 0.1 Hz to 10 MHz over a wide range of temperatures. The compound exhibits three nematic phases on cooling from the isotropic phase, i.e., the ordinary paraelectric nematic N; the intermediate nematic NX and the ferroelectric NF phases. The least frequency process is due to the dynamics of ions. The middle frequency relaxation process P1 is like as observed in other ferronematic compounds and this mode is a continuation of the molecular flip-flop motion in the isotropic phase to the collective dynamics of dipoles which are strongly coupled with the splay fluctuations in nematic phases. In addition to this process, DIO shows an additional collective relaxation process P2 at higher frequencies both in the N and the NX phases. This mode originates from the polar/chiral molecules of the opposite chirality, these arise from the spontaneous symmetry breaking of achiral mesogens in the N phase. Both collective processes, P1 and P2, show soft mode-like characteristic behavior on cooling from the N to the NX-NF phase transition temperature and are shown to contribute independently to the formation of the ferronematic NF phase.
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Mar 2023
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B21-High Throughput SAXS
B23-Circular Dichroism
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Alessandro
Paciaroni
,
Valeria
Libera
,
Francesca
Ripanti
,
Andrea
Orecchini
,
Caterina
Petrillo
,
Daniela
Francisci
,
Elisabetta
Schiaroli
,
Samuele
Sabbatini
,
Anna
Gidari
,
Elisa
Bianconi
,
Antonio
Macchiarulo
,
Rohanah
Hussain
,
Lucia
Silvestrini
,
Paolo
Moretti
,
Norhan
Belhaj
,
Matteo
Vercelli
,
Yessica
Roque
,
Paolo
Mariani
,
Lucia
Comez
,
Francesco
Spinozzi
Diamond Proposal Number(s):
[29982, 32331]
Open Access
Abstract: The main protease (Mpro or 3CLpro) is an enzyme that is evolutionarily conserved among different genera of coronaviruses. As it is essential for processing and maturing viral polyproteins, Mpro has been identified as a promising target for the development of broad-spectrum drugs against coronaviruses. Like SARS-CoV and MERS-CoV, the mature and active form of SARS-CoV-2 Mpro is a dimer composed of identical subunits, each with a single active site. Individual monomers, however, have very low or no catalytic activity. As such, inhibition of Mpro can be achieved by molecules that target the substrate binding pocket to block catalytic activity or target the dimerization process. In this study, we investigated GC376, a transition-state analog inhibitor of the main protease of feline infectious peritonitis coronavirus, and Nirmatrelvir (NMV), an oral, bioavailable SARS-CoV-2 Mpro inhibitor with pan-human coronavirus antiviral activity. Our results show that both GC376 and NMV are capable of strongly binding to SARS-CoV-2 Mpro and altering the monomer-dimer equilibrium by stabilizing the dimeric state. This behavior is proposed to be related to a structured hydrogen-bond network established at the Mpro active site, where hydrogen bonds between Ser1’ and Glu166/Phe140 are formed in addition to those achieved by the latter residues with GC376 or NMV.
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Mar 2023
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[30755, 31552]
Open Access
Abstract: An achiral compound, DIO, known to exhibit three nematic phases namely N, NX and NF, is studied by polarizing microscopy and electro-optics for different surface conditions in confinement. The high temperature N phase assigned initially as a conventional nematic phase, shows two additional unusual features: the optical activity and the linear electro-optic response related to the polar nature of this phase. An appearance of chiral domains is explained by the spontaneous symmetry breaking arising from the saddle-splay elasticity and followed by the formation of helical domains of the opposite chirality. This is the first example of helical segregation observed in calamitic non-chiral molecules in the nematic phase. As reported previously, the ferronematic NF shows strong polar azimuthal surface interaction energy which stabilizes a homogeneous structure in planar aligned LC cells rubbed parallel and exhibits a twisted structure in cells with antiparallel buffing. The transmission spectra are simulated using Berreman's 4 × 4 matrix method. The observed agreement between the experimental and the simulated spectra quantitatively confirms the presence of twisted structures in antiparallel rubbed cells.
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Mar 2023
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[29075, 31797]
Open Access
Abstract: Cyanine dyes are known to form H- and J-aggregates in aqueous solutions. Here we show that the cyanine dye, S0271, assembles in water into vortex induced chiral J-aggregates. The chirality of the J-aggregates depends on the directionality of the vortex. This study utilised both conventional benchtop CD spectropolarimeters and Mueller matrix polarimetry. It was found that J-aggregates have real chirality alongside linear dichroism and linear and circular birefringence. We identify the factors that are key to the formation of metastable chiral J-aggregates and propose a mechanism for their assembly.
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Feb 2023
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B23-Circular Dichroism
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Open Access
Abstract: Chiral diketopyrrolopyrroles appended with enantiomeric ethyl lactate functions through an ether linkage to the aryl backbone of the chromophore were synthesized via the Mitsunobu reaction. The molecules have good solubility and excellent optical properties, high molar absorption coefficients, and fluorescence quantum yields. Helical aggregates with circular dichroism arising from the supramolecular arrangement are seen in both solution and thin films, and the aggregates also display circularly polarized luminescence (glum ≈ ±0.1). The molecules assemble to give monolayers on graphite and precipitate from solution forming supramolecular twisted tapes hundreds of microns long.
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Feb 2023
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[8475, 9567]
Open Access
Abstract: Inhaled nanoparticles (NPs) depositing in the alveolar region of the lung interact initially with a surfactant layer and in vitro studies have demonstrated that NPs can adversely affect the biophysical function of model pulmonary surfactants (PS), of which surfactant protein B (SP-B) is a key component. Other studies have demonstrated the potential for NPs to modify the structure and function of proteins. It was therefore hypothesised that NPs may affect the biophysical function of PS by modifying the structure of SP-B. Synchrotron radiation circular dichroism (SRCD) spectroscopy was used to explore the effect of various concentrations of gold nanoparticles (AuNPs) (5, 10, 20 nm), silver nanoparticles (AgNPs) (10 nm) and silver citrate on the secondary structure of surfactant protein B analogue, SP-B1–25, in a TFE/PB dispersion. For Au and Ag NPs the SRCD spectra indicated a concentration dependent reduction in the α-helical structure of SP-B1–25 (5 nm AuNP ≈ 10 nm AgNP ≫ 10 nm AuNP > 20 nm AuNP). For AuNPs the effect was greater for the 5 nm size, which was not fully explained by consideration of surface area. The impact of the 10 nm AgNPs was greater than that of the 10 nm AuNPs and the effect of AgNPs was greater than that of silver citrate at equivalent Ag mass concentrations. For 10 nm AuNPs, SRCD spectra for dispersions in, the more physiologically relevant, DPPC showed a similar concentration dependent pattern. The results demonstrate the potential for inhaled NPs to modify SP-B1–25 structure and thus potentially adversely impact the physiological function of the lung, however, further studies are necessary to confirm this.
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Feb 2023
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B23-Circular Dichroism
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Abstract: High-resolution calorimetry has played a significant role in providing detailed information on phase transitions in liquid crystals. In particular, adiabatic scanning calorimetry (ASC), capable of providing simultaneous information on the temperature dependence of the specific enthalpy
h
(
T
)
and on the specific heat capacity
c
p
(
T
)
, has proven to be an important tool to determine the order of transitions and render high-resolution information on pretransitional thermal behavior. Here we report on ASC results on the compound 2,3′,4′,5′-tetrafluoro[1,1′-biphenyl]-4-yl 2,6-difluoro-4-(5-propyl-1,3-dioxan-2-yl) benzoate (DIO) and on mixtures with 4-[(4-nitrophenoxy)carbonyl]phenyl 2,4-dimethoxybenzoate (RM734). Both compounds exhibit a low-temperature ferroelectric nematic phase (
N
F
) and a high-temperature paraelectric nematic phase
(
N
)
. However, in DIO these two phases are separated by an intermediate phase (
N
x
). From the detailed data of
h
(
T
)
and
c
p
(
T
)
, we found that the intermediate phase was present in all the mixtures over the complete composition range, albeit with strongly decreasing temperature width for that phase with decreasing mole fraction of DIO (
x
DIO
). The
x
DIO
dependence on the transition temperatures for both transitions could be well described by a quadratic function. Both these transitions were weakly first order. The true latent heat of the
N
x
−
N
transition of DIO was as low as
L
=
0.0075
±
0.0005
J
/
g
and
L
=
0.23
±
0.03
J
/
g
for the
N
F
−
N
x
transition, which is about twice the previously reported value of 0.115 J/g for the
N
F
−
N
transition in RM734. In the mixtures both transition latent heats decrease gradually with decreasing
x
DIO
. At all the
N
x
−
N
transitions pretransition fluctuation effects are absent and these transitions are purely but very weakly first order. As in RM734 the transition from the
N
F
to the higher-temperature phase exhibits substantial pretransitional behavior, in particular, in the high-temperature phase. Power-law analysis of
c
p
(
T
)
resulted in an effective critical exponent
α
=
0.88
±
0.1
for DIO and this value decreased in the mixtures with decreasing
x
DIO
toward
α
=
0.50
±
0.05
reported for RM734. Ideal mixture analysis of the phase diagram was consistent with ideal mixture behavior provided the total transition enthalpy change was used in the analysis.
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Jan 2023
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[24509, 20755, 21202]
Open Access
Abstract: Background: Galectin-9 is a member of the family of lectin proteins and crucially regulates human immune responses, particularly because of its ability to suppress the anticancer activities of T lymphocytes and natural killer cells. Recent evidence demonstrated that galectin-9 is highly expressed in a wide range of human malignancies including the most aggressive tumors, such as high-grade glioblastomas and pancreatic ductal adenocarcinomas, as well as common malignancies such as breast, lung and colorectal cancers. However, solid tumor cells at rest are known to secrete either very low amounts of galectin-9 or, in most of the cases, do not secrete it at all. Our aims were to elucidate whether T cells can induce galectin-9 secretion in human cancer cells derived from solid malignant tumors and whether this soluble form displays higher systemic immunosuppressive activity compared with the cell surface-based protein. Methods: A wide range of human cancer cell lines derived from solid tumours, keratinocytes and primary embryonic cells were employed, together with helper and cytotoxic T cell lines and human as well as mouse primary T cells. Western blot analysis, ELISA, quantitative reverse transcriptase-PCR, on-cell Western and other measurement techniques were used to conduct the study. Results were validated using in vivo mouse model. Results: We discovered that T lymphocytes induce galectin-9 secretion in various types of human cancer cells derived from solid malignant tumors. This was demonstrated to occur via two differential mechanisms: first by translocation of galectin-9 onto the cell surface followed by its proteolytic shedding and second due to autophagy followed by lysosomal secretion. For both mechanisms a protein carrier/trafficker was required, since galectin-9 lacks a secretion sequence. Secreted galectin-9 pre-opsonised T cells and, following interaction with other immune checkpoint proteins, their activity was completely attenuated. As an example, we studied the cooperation of galectin-9 and V-domain Ig-containing suppressor of T cell activation (VISTA) proteins in human cancer cells. Conclusion: Our results underline a crucial role of galectin-9 in anticancer immune evasion. As such, galectin-9 and regulatory pathways controlling its production should be considered as key targets for immunotherapy in a large number of cancers.
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Jan 2023
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[13761]
Abstract: Protein-protein interactions are fundamental to life processes. Complementary computational, structural and biophysical studies of these interactions enable the forces behind their specificity and strength to be understood. Antibody fragments such as single-chain antibodies have the specificity and affinity of full antibodies but a fraction of their size, expediting whole molecule studies and distal effects without exceeding the computational capacity of modelling systems. We previously reported the crystal structure of a high affinity nanobody 59H10 bound to HIV-1 capsid protein p24, and deduced key interactions using all-atom molecular dynamics (MD) simulations. We studied the properties of closely-related medium (37E7) and low (48G11) affinity nanobodies, to understand how changes of three (37E7) or one (48G11) amino acids impacted these interactions, however, the contributions of enthalpy and entropy were not quantified. Here, we report the use of qualitative and quantitative experimental and in silico approaches to separate the contributions of enthalpy and entropy. We used complementary circular dichroism spectroscopy and molecular dynamics simulations to qualitatively delineate changes between nanobodies in isolation and complexed with p24. Using quantitative techniques such as isothermal titration calorimetry alongside WaterMap and Free Energy Perturbation protocols, we found the difference between high (59H10) and medium (37E7) affinity nanobodies on binding to HIV-1 p24 is entropically driven, accounted for by the release of unstable waters from the hydrophobic surface of 59H10. Our results provide an exemplar of the utility of parallel in vitro and in silico studies and highlight that differences in entropic interactions between amino acids and water molecules are sufficient to drive orders of magnitude differences in affinity.
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Dec 2022
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