Ewan Blanch - Academia.edu (original) (raw)

Papers by Ewan Blanch

Journal of the American Chemical Society, 2011

Raman optical activity (ROA) spectroscopy, which measures a small difference in Raman scattering ... more Raman optical activity (ROA) spectroscopy, which measures a small difference in Raman scattering intensities from chiral molecules using circularly polarized light, 1À3 either in the incident or scattered beams or even both, has proven to be an informative probe of molecular conformation. In recent years, the development of ROA has benefited greatly from computational modeling, 4,5 which has improved our understanding of the underlying principles behind this chiroptical technique and revealed information on vibrational motion and protein conformation. As ROA spectral calculations are highly sensitive to even small differences in molecular geometry, they can also serve as a gold standard in force field design and computational methods in general. Most of the recent published studies on computational modeling of ROA spectra have concentrated on amino acids and peptides, 6À12 reflecting the main direction of ROA experimental research, protein structure analysis. However, the structures of other classes of biological molecules are now also beginning to be explored by ROA spectroscopy, and the potential impact of such chiroptical techniques may be even greater for these other biological molecules than for proteins. For example, complex carbohydrates such as glycoproteins and peptidoglycans perform a diverse range of functions in living systems and have generally proven more difficult to structurally characterize than proteins. Although relatively few ROA studies have so far been conducted for carbohydrates, the spectra have been shown to be highly informative on carbohydrate structure. However, interpretation of the spectra is currently limited by our incomplete understanding of spectrumÀstructure correlations. Following the example of advances in computational modeling of peptide ROA spectra, the potential of carbohydrate ROA spectral modeling is obvious but there have been few studies of this type to date. Pecul and co-workers 13 conducted the first study using linear response SCF theory into parameters influencing ROA spectra of L-lactic acid and D-glyceraldehyde and found that the spectra were particularly sensitive to both intramolecular hydrogen bonding of hydroxyl groups and solvation. The effects of both conformational averaging and solvent interactions were further highlighted by Macleod et al. 14 in their study on D-lactose, D-glucose, and D-galactose. Luber and Reiher 15 have recently considered the effects of interactions of the carbohydrate with solvent water on the spectra of 1,6-anhydro-β-D-glucopyranose, a ABSTRACT: We report calculations of the Raman and Raman optical activity (ROA) spectra of methyl-β-D-glucose utilizing density functional theory combined with molecular dynamics (MD) simulations to provide an explicit hydration environment. This is the first report of such combination of MD simulations with ROA ab initio calculations. We achieve a significant improvement in accuracy over the more commonly used gas phase and polarizable continuum model (PCM) approaches, resulting in an excellent level of agreement with the experimental spectrum. Modeling the ROA spectra of carbohydrates has until now proven a notoriously difficult challenge due to their sensitivity to the effects of hydration on the molecular vibrations involving each of the chiral centers. The details of the ROA spectrum of methyl-β-D-glucose are found to be highly sensitive to solvation effects, and these are correctly predicted for the first time including those originating from the highly sensitive low frequency vibrational modes. This work shows that a thorough consideration of the role of water is pivotal for understanding the vibrational structure of carbohydrates and presents a new and powerful tool for characterizing carbohydrate structure and conformational dynamics in solution.

Biophysical Journal, Feb 1, 2010

By directly monitoring stirred protein solutions with Raman spectroscopy, the reversible unfoldin... more By directly monitoring stirred protein solutions with Raman spectroscopy, the reversible unfolding of proteins caused by fluid shear is examined for several natural proteins with varying structural properties and molecular weight. While complete denaturation is not observed, a wide range of spectral variances occur for the different proteins, indicating subtle conformational changes that appear to be protein-specific. A number of significant overall trends are apparent from the study. For globular proteins, the overall extent of spectral variance increases with protein size and the proportion of b-structure. For two less structured proteins, fetuin and a-casein, the observed changes are of relatively low magnitude, despite the greater molecular structural mobility of these proteins. This implies that other protein-specific factors, such as posttranslational modifications, may also be significant. Individual band changes occurring in the spectral profiles of each individual protein are also discussed in detail.

In Champion Pm and Ziegler Ld Xxii International Conference on Raman Spectroscopy Amer Inst Physics, Jul 30, 2010

The ability to detect chirality gives stereochemically attuned nanosensors the potential to revol... more The ability to detect chirality gives stereochemically attuned nanosensors the potential to revolutionize the study of biomolecular processes. Such devices may structurally characterize the mechanisms of protein-ligand binding, the intermediates of amyloidogenic diseases and the effects of phosphorylation and glycosylation. We demonstrate that single nanoparticle plasmonic reporters, or nanotags, can enable a stereochemical response to be transmitted from a chiral analyte to an achiral benzotriazole dye molecule in the vicinity of a plasmon resonance from an achiral metallic nanostructure. The transfer of chirality was verified by the measurement of mirror image surface enhanced resonance Raman optical activity spectra for the two enantiomers of both ribose and tryptophan. Computational modelling confirms these observations and reveals the novel chirality transfer mechanism responsible. This is the first report of colloidal metal nanoparticles in the form of single plasmonic substrates displaying an intrinsic chiral sensitivity once attached to a chiral molecule.

Journal of the American Chemical Society 2011 133 4991 4997, Mar 1, 2011

Phys. Chem. Chem. Phys., 2015

Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharid... more Besides its applications in bioenergy and biosynthesis, β-d-xylose is a very simple monosaccharide that exhibits relatively high rigidity. As such, it provides the best basis to study the impact of different solvation shell radii on the computation of its Raman optical activity (ROA) spectrum. Indeed, this chiroptical spectroscopic technique provides exquisite sensitivity to stereochemistry, and benefits much from theoretical support for interpretation. Our simulation approach combines density functional theory (DFT) and molecular dynamics (MD) in order to efficiently account for the crucial hydration effects in the simulation of carbohydrates and their spectroscopic response predictions. Excellent agreement between the simulated spectrum and the experiment was obtained with a solvation radius of 10 Å. Vibrational bands have been resolved from the computed ROA data, and compared with previous results on different monosaccharides in order to identify specific structure-spectrum relationships and to investigate the effect of the solvation environment on the conformational dynamics of small sugars. From the comparison with ROA analytical results, a shortcoming of the classical force field used for the MD simulations has been identified and overcome, again highlighting the complementary role of experiment and theory in the structural characterisation of complex biomolecules. Indeed, due to unphysical puckering, a spurious ring conformation initially led to erroneous conformer ratios, which are used as weights for the averaging of the spectral average, and only by removing this contribution was near perfect comparison between theory and experiment achieved.

Nature Chemistry, 2015

Journal of Natural Products, 2015

Chemical investigations of the ethanolic extracts from the flowers and leaves of Hymenaea stigono... more Chemical investigations of the ethanolic extracts from the flowers and leaves of Hymenaea stigonocarpa Mart. ex Hayne afforded one new ent-halimane diterpenoid, 18-hydroxy-enthalima-1(10),13-(E)-dien-15-oic acid (1), together with five known compounds (2−6). The structural elucidation was performed by means of NMR (COSY, HSQC, HMBC, and NOESY) and MS analyses. Complete 1 H and 13 C NMR data assignments are also reported for labd-13-en-8β-ol-15-oic (2) and labd-7,13-dien-15-oic (3) acids. The absolute configurations of 1 and 2 were established by comparison of experimental and calculated Raman optical activity spectra.

Physical chemistry chemical physics : PCCP, Jan 28, 2015

As two biologically and medically relevant monosaccharides, the constituents of hyaluronic acid, ... more As two biologically and medically relevant monosaccharides, the constituents of hyaluronic acid, d-glucuronic acid and N-acetyl-d-glucosamine, constitute perfect test cases for the development of carbohydrate-specific structural methods. These two molecules have been analysed by Raman optical activity (ROA), a spectroscopic technique exhibiting exquisite sensitivity to stereochemistry. We show that it is possible to support the experiment with a simulation approach combining density functional theory (DFT) and molecular dynamics (MD), both using explicit solvation. Thus, we have gained new insight into the crucial hydration effects that contribute to the conformational dynamics of carbohydrates and managed to characterize in detail the poorly understood vibrational nature of this class of biomolecules. Experimental and calculated ROA spectra of these two molecules are reported and excellent agreement has been found. More specifically, comparison has been made with the more commonly ...

Journal of natural products, Jan 20, 2015

A new orbitide named ribifolin was isolated and characterized from Jatropha ribifolia using mass ... more A new orbitide named ribifolin was isolated and characterized from Jatropha ribifolia using mass spectrometry, NMR spectroscopy, quantitative amino acid analysis, molecular dynamics/simulated annealing, and Raman optical activity measurements and calculations. Ribifolin (1) and its linear form (1a) were synthesized by solid-phase peptide synthesis, followed by evaluation of its antiplasmodial and cytotoxicity activities. Compound 1 was moderately effective (IC50 = 42 μM) against the Plasmodium falciparum strain 3D7.

PloS one, 2014

The salivary mucins that include MUC5B (gel-forming) and MUC7 (non-gel-forming) are major contrib... more The salivary mucins that include MUC5B (gel-forming) and MUC7 (non-gel-forming) are major contributors to the protective mucus barrier in the oral cavity, and it is possible that dietary components may influence barrier properties. We show how one dietary compound, the green tea polyphenol epigallocatechin gallate (EGCG), can substantially alter the properties of both the polymeric MUC5B network and monomeric MUC7. Using rate-zonal centrifugation, MUC5B in human whole saliva and MUC5B purified from saliva sedimented faster in the presence of EGCG. The faster sedimentation by EGCG was shown to be greater with increasing MUC5B concentration. Particle tracking microrheology was employed to determine the viscosity of purified MUC5B solutions and showed that for MUC5B solutions of 200-1600 µg/mL, EGCG caused a significant increase in mucin viscosity, which was greater at higher MUC5B concentrations. Visualisation of the changes to the MUC5B network by EGCG was performed using atomic forc...

The paper reports on a novel study of shear induced protein conformational changes by a combinati... more The paper reports on a novel study of shear induced protein conformational changes by a combination of two powerful laser based techniques. A Taylor-Couette flow device has been designed to subject protein solutions to well-controlled shear conditions and to facilitate real time protein structure measurements by means of Raman spectroscopy, while the flow field and viscous stress distributions have been

Colloidal-based surface-enhanced Raman scattering (SERS) is a complex technique, where interactio... more Colloidal-based surface-enhanced Raman scattering (SERS) is a complex technique, where interaction between multiple parameters, such as colloid type, its concentration, and aggregating agent, is poorly understood. As a result SERS has so far achieved limited reproducibility. Therefore the aim of this study was to improve enhancement and reproducibility in SERS, and to achieve this, we have developed a multiobjective evolutionary algorithm (MOEA) based on Pareto optimality. In this MOEA approach, we tested a combination of five different colloids with six different aggregating agents, and a wide range of concentrations for both were explored; in addition we included in the optimization process three laser excitation wavelengths. For this optimization of experimental conditions for SERS, we chose the β-adrenergic blocker drug propranolol as the target analyte. The objective functions chosen suitable for this multiobjective problem were the ratio between the full width at half-maximum and the half-maximum intensity for enhancement and correlation coefficient for reproducibility. To analyze a full search of all the experimental conditions, 7785 experiments would have to be performed empirically; however, we demonstrated the search for acceptable experimental conditions of SERS can be achieved using only 4% of these possible experiments. The MOEA identified several experimental conditions for each objective which allowed a limit of detection of 2.36 ng/mL (7.97 nM) propranolol, and this is significantly lower (>25 times) than previous SERS studies aimed at detecting this β-blocker.

Coherent anti-Stokes Raman scattering (CARS) microscopy is applied for the first time for the eva... more Coherent anti-Stokes Raman scattering (CARS) microscopy is applied for the first time for the evaluation of the protein secondary structure of polyglutamine (polyQ) aggregates in vivo. Our approach demonstrates the potential for translating information about protein structure that has been obtained in vitro by X-ray diffraction into a microscopy technique that allows the same protein structure to be detected in vivo. For these studies, fibres of polyQ containing peptides (D 2 Q 15 K 2 ) were assembled in vitro and examined by electron microscopy and X-ray diffraction methods; the fibril structure was shown to be cross b-sheet. The same polyQ fibres were evaluated by Raman spectroscopy and this further confirmed the b-sheet structure, but indicated that the structure is highly rigid, as indicated by the strong Amide I signal at 1659 cm 21 . CARS spectra were simulated using the Raman spectrum taking into account potential non-resonant contributions, providing evidence that the Amide I signal remains strong, but slightly shifted to lower wavenumbers. Combined CARS (1657 cm 21 ) and multi-photon fluorescence microscopy of chimeric fusions of yellow fluorescent protein (YFP) with polyQ (Q40) expressed in the body wall muscle cells of Caenorhabditis elegans nematodes (1 day old adult hermaphrodites) revealed diffuse and foci patterns of Q40-YFP that were both fluorescent and exhibited stronger CARS (1657 cm 21 ) signals than in surrounding tissues at the resonance for the cross b-sheet polyQ in vitro.

Carbohydrate Research, 2014

Synthesis of a heparin-related GlcN-IdoA sulfation-site variable disaccharide library and analysi... more Synthesis of a heparin-related GlcN-IdoA sulfation-site variable disaccharide library and analysis by Raman and ROA spectroscopy, Carbohydrate Research (2014), doi: http://dx.Scheme 1. a) NIS, AgOTf, DCM, 92% for 4 via 2, 77% for 6 (6/1 α/β), 80% for 8 (12/1, α/β). b) TMSOTf, DCM, 95% for 4 via 3.

El magnetisme i en particular el camp magnètic de la Terra s’ensenya als alumnes des de la primàr... more El magnetisme i en particular el camp magnètic de la Terra s’ensenya als alumnes des de la primària fins al batxillerat en diferents moments i amb un aprofundiment progressiu. Aquest article pretén complementar l’estudi del camp magnètic al batxillerat amb una acti-vitat pràctica sobre una tempesta magnètica enregistrada a l’Observatori de l’Ebre. El treball consta d’una introducció als conceptes bàsics

Chirality, 2014

Recent Raman and Raman optical activity (ROA) results have demonstrated that dimethyl sulfoxide (... more Recent Raman and Raman optical activity (ROA) results have demonstrated that dimethyl sulfoxide (DMSO) induces the selective conversion of α-helix motifs into the poly(L-proline) II (PPII) helix conformation in an array of proteins, while β-sheets remain mostly unaffected. Human serum albumin (HSA), a highly α-helical protein, underwent the most dramatic changes and, therefore, was selected as a model for further investigations into the mechanism of this conformational change. Herein we report the use of two-dimensional ROA correlation analysis applying synchronous, autocorrelation, and moving windows approaches in order to understand the conformational transitions in HSA as a function of DMSO concentration. Our results indicate that the destabilization of native α-helix starts at DMSO concentrations as little as 20% in water (v/v), with the transition to PPII helix being complete at ~80% DMSO. These results clearly indicate that any protein preparation containing relatively low con...