B22-Multimode InfraRed imaging And Microspectroscopy
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Diamond Proposal Number(s):
[19692]
Abstract: This study aimed at the development of improved drugs against human osteosarcoma, which is the most common primary bone tumor in children and teenagers with a low prognosis available treatment. New insights into the impact of an unconventional Pd(II) anticancer agent on human osteosarcoma cells were obtained by synchrotron-based infrared microspectroscopy (SR-microFTIR) and quasi-elastic neutron scattering (QENS) experiments from its effect on the cellular metabolism to its influence on intracellular water which can be regarded as a potential secondary pharmacological target. Specific infrared biomarkers of drug action were identified, enabling a molecular-level description of variations in cellular biochemistry upon drug exposure. The main changes were detected on the protein and lipid cellular components, namely on the ration of unsaturated-to-saturated fatty acids. QENS revealed a reduced water mobility within the cytoplasm for drug-treated cells, coupled to a disruption of the hydration layers of biomolecules. Additionally, the chemical and dynamical profiles of osteoscarcoma cells were compared to metastatic breast cancer, revealing distinct dissimilarities that may influence drug activity.
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Jul 2019
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[19477]
Abstract: We investigate the impact of lipidation on the self-assembly of two peptide fragments from the gastrointestinal peptide hormone PYY3-36. The lipopeptides C16IKPEAP and C16IKPEAPGE contain the first 6 and 8 amino acid residues respectively from the PYY3-36 peptide sequence, with a palmitoyl C16 tail attached at the N-terminus. These lipopeptides form spherical micelles in aqueous solution, above a critical micelle concentration (cmc), which is pH-dependent. Modelling of small-angle x-ray scattering data along with molecular dynamics simulations shows the formation of micelles with a hydrophobic interior and a well hydrated exterior. The lipopeptides have a disordered conformation over the pH and temperature range studied. The cmc is found to be independent of temperature, pointing to athermal micellization. In contrast to the presence of hydrated micelles in solution, β-sheet amyloid fibrils form in dried samples. Thus, the nanostructure of lipidated PYY3-36 fragment peptides can be tuned by control of pH or concentration, for future applications.
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Jan 2019
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B23-Circular Dichroism
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Parveen
Akhtar
,
Dominik
Lindorfer
,
Monika
Lingvay
,
Krzysztof
Pawlak
,
Otto
Zsiros
,
Giuliano
Siligardi
,
Tamas
Javorfi
,
Márta
Dorogi
,
Bettina
Ughy
,
Gyozo
Garab
,
Thomas
Renger
,
Petar H.
Lambrev
Diamond Proposal Number(s):
[15094, 16232, 17698, 19120, 20644]
Abstract: Anisotropic circular dichroism (ACD) spectroscopy of macroscopically aligned molecules reveals additional information about their excited states that is lost in the CD of randomly-oriented solutions. ACD spectra of light-harvesting complex II (LHCII)—the main peripheral antenna of photosystem II in plants—in oriented lipid bilayers, were recorded from the far-UV to the visible wavelength region. The ACD spectra show a drastically enhanced magnitude and level of detail compared to the isotropic CD spectra, resolving a greater number of bands and weak optical transitions. Exciton calculations show that the spectral features in the chlorophyll Qy region are well reproduced by an existing Hamiltonian for LHCII, providing further evidence for the identity of energy sinks at chlorophylls a603 and a610 in the stromal layer and chlorophylls a604 and a613 in the luminal layer. We propose ACD spectroscopy to be a valuable tool linking the three-dimensional structure and the photophysical properties of pigment–protein complexes.
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Jan 2019
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[15990]
Abstract: The early stage crystallisation behaviour in a triacylglycerol mixture has been investigated on the nanoscale with a novel global small angle X-ray scattering analysis technique. This method has been tailored for the determination of the electron density profiles (EDP) replicating both, (i) the nanostructural texture of molten TAGs (refer to part I ‘Global Small-Angle X-ray Scattering Data Analysis of Triacylglycerols in the Molten State’ of this publication series), and (ii) the lamellar structure of the metastable α-polymorph. In a first stage, the α-phase scattering contribution alone was examined by classical Fourier analysis as well as by globally fitting the data, leading to practically identical EDPs. Based on these findings, we extended our analysis to the entire X-ray scattering contribution arising from molten TAGs and the solid α-phase fraction. Remarkably, the experimental and theoretical data agree very well, providing for the first time a detailed nanostructural understanding about the coexisting molecular assemblies. This allowed in turn, also to quantitatively determine the solid fat content (SFC) with X-ray scattering data. Our new theoretical approach for measurement of SFC is based on the global analysis of small angle scattering/diffraction patterns and the SFC-results are in good agreement with values obtained from other techniques such as NMR spectroscopy.
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Oct 2018
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I22-Small angle scattering & Diffraction
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Diamond Proposal Number(s):
[15990]
Abstract: The study of triacylglycerols (TAGs) in their molten state is of fundamental importance for a deeper understanding of the TAG crystallization processes, being highly relevant for both manufacturing and medical applications. Although different models have been proposed to explain the nanostructured nature of the fluid state of TAGs, none of them are fully satisfactory. In this paper, we propose a new model consisting of positionally uncorrelated lamellar TAG assemblies embedded in an isotropic medium that assist as prenucleating structures. This model was validated by applying a novel global fitting method, resulting in an excellent agreement with the small-angle X-ray scattering data. A deeper analysis of the scattering patterns at different temperatures, both in cooling and heating directions, allowed us further to detect the crystalline traces of TAGs even after heating to 40 °C and record, on cooling, the onset of crystallization at 30–25 °C. The application of the presented novel model not only explains the outstandingly structured fluid of molten TAGs, but also lays the basis for analyzing first the crystallization steps in greater detail, which is outlined in our follow-up paper “Global Small-Angle X-ray Scattering Data Analysis of Triacylglycerols in the α-Phase (Part II)”.
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Oct 2018
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I04-Macromolecular Crystallography
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Abstract: Folding of proteins to their functional conformation is paramount to life. Though 75% of the proteome consists of multidomain proteins, our knowledge of folding has been based primarily on studies conducted on single-domain and fast-folding proteins. Nonetheless, the complexity of folding landscapes exhibited by multidomain proteins has received increased scrutiny in recent years. We study the three-domain protein adenylate kinase from E. coli (AK), which has been shown to fold through a series of pathways involving several intermediate states. We use a protein design method to manipulate the folding landscape of AK, and single-molecule FRET spectroscopy to study the effects on the folding process. Mutations introduced in the NMP binding (NMPbind) domain of the protein are found to have unexpected effects on the folding landscape. Thus, while stabilizing mutations in the core of the NMPbind domain retain the main folding pathways of wild-type AK, a destabilizing mutation at the interface between the NMPbind and the CORE domains causes a significant repartition of the flux between the folding pathways. Our results demonstrate the outstanding plasticity of the folding landscape of AK and reveal how specific mutations in the primary structure are translated into changes in folding dynamics. The combination of methodologies introduced in this work should prove useful for deepening our understanding of the folding process of multidomain proteins.
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Sep 2018
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B21-High Throughput SAXS
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Diamond Proposal Number(s):
[17074]
Abstract: The interplay of degree of methylesterification (DM), pH, temperature, and concentration on the macromolecular interactions of pectin in solution has been explored. Small angle X-ray scattering complemented by atomic force microscopy and molecular dynamics were employed to probe chain dimensions and solution structure. Two length scales have been observed with the first characterising chain clustering with a size ranging between 100-200 nm. The second level of structure arises from single biopolymer chains with radius of gyration between ~6-42 nm. The development of a range of macromolecular dimensions in vitro and in silico shows chain flexibility increases with DM and at acidic pH whereas hydrogen bonding is the responsible thermodynamic driving force for cluster formation. High methyl pectins create structures of lower fractal dimension with less efficient packing. This work unveils pectin conformations covering most of its industrially and biologically relevant environments, enabling rational design of advanced biomaterials based on pectin.
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Jul 2018
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B23-Circular Dichroism
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Diamond Proposal Number(s):
[15146, 13634, 12545, 12923]
Abstract: Thermal unfolding of proteins is used extensively in screening of drug candidates because molecular interactions with ligands and substrates affect strongly protein stability, transition temperature and cooperativity. We use synchrotron radiation circular dichroism to monitor the thermal evolution of secondary structure in proteins as they approach the melting point and the impact of substrate on their thermal behaviour. Using Landau free energy expansion, we quantify transition strength and proximity to a critical point through the relative separation τ+ between the transition temperature Tm and the spinodal T+, obtained from the equation of state. The weakest transition was observed in lysozyme with τ+=0.0167 followed by holo albumin with τ+=0.0208 with a strongest transition in monomeric apo albumin τ+=0.0242. A structural transition at 45°C in apo albumin leads to a non-cooperative melt with τ+=0.00532 and amyloidogenic increase in beta content.
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Feb 2018
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B21-High Throughput SAXS
B23-Circular Dichroism
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Diamond Proposal Number(s):
[1606, 1869]
Abstract: The secondary structure of proline-rich surfactant-like peptides is examined for the first time and is found to be influenced by charged end groups in peptides P6K, P6E, and KP6E and an equimolar mixture of P6K and P6E. The peptides exhibit a conformational transition from unordered to polyproline II (PPII) above a critical concentration, detected from circular dichroism (CD) measurements and unexpectedly from fluorescence dye probe measurements. Isothermal titration calorimetry (ITC) measurements provided the Gibbs energies of hydration of P6K and P6E, which correspond essentially to the hydration energies of the terminal charged residues. A detailed analysis of peptide conformation for these peptides was performed using density functional theory calculations, and this was used as a basis for hybrid quantum mechanics/molecular mechanics molecular dynamics (QM/MM MD) simulations. Quantum mechanics simulations in implicit water show both peptides (and their 1:1 mixture) exhibit PPII conformations. However, hybrid QM/MM MD simulations suggest that some deviations from this conformation are present for P6K and P6E in peptide bonds close to the charged residue, whereas in the 1:1 mixture a PPII structure is observed. Finally, aggregation of the peptides was investigated using replica exchange molecular dynamics simulations. These reveal a tendency for the average aggregate size (as measured by the radius of gyration) to increase with increasing temperature, which is especially marked for P6K, although the fraction of the most populated clusters is larger for P6E.
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Feb 2018
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B21-High Throughput SAXS
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Abstract: The inherent flexibility of carbohydrates is dependent on stereochemical arrangements, and characterization of their influence and importance will give insight into 3D structure and dynamics. In this study, a β-(1→4)/β-(1→3)-linked glucosyl decasaccharide is experimentally investigated by synchrotron small-angle X-ray scattering from which its radius of gyration (Rg) is obtained. Molecular dynamics (MD) simulations of the decasaccharide show four populated states at each glycosidic linkage, namely, syn- and anti-conformations. The calculated Rg values from the MD simulation reveal that in addition to syn-conformers, the presence of anti-ψ conformational states are required to reproduce experimental scattering data, unveiling inherent glycosidic linkage flexibility. The CHARMM36 force field for carbohydrates thus describes the conformational flexibility of the decasaccharide very well and captures the conceptual importance that anti-conformers are to be anticipated at glycosidic linkages of carbohydrates.
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Dec 2017
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