2016, Davies, Heather S., Singh, Prabha, Deckert-Gaudig, Tanja, Deckert, Volker, Rousseau, Karine, Ridley, Caroline E., Dowd, Sarah E., Doig, Andrew J., Pudney, Paul D. A., Thornton, David J., Blanch, Ewan W.

The major structural components of protective mucus hydrogels on mucosal surfaces are the secreted polymeric gel-forming mucins. The very high molecular weight and extensive O-glycosylation of gel-forming mucins, which are key to their viscoelastic properties, create problems when studying mucins using conventional biochemical/structural techniques. Thus, key structural information, such as the secondary structure of the various mucin subdomains, and glycosylation patterns along individual molecules, remains to be elucidated. Here, we utilized Raman spectroscopy, Raman optical activity (ROA), circular dichroism (CD), and tip-enhanced Raman spectroscopy (TERS) to study the structure of the secreted polymeric gel-forming mucin MUC5B. ROA indicated that the protein backbone of MUC5B is dominated by unordered conformation, which was found to originate from the heavily glycosylated central mucin domain by isolation of MUC5B O-glycan-rich regions. In sharp contrast, recombinant proteins of the N-terminal region of MUC5B (D1-D2-D′-D3 domains, NT5B), C-terminal region of MUC5B (D4-B-C-CK domains, CT5B) and the Cys-domain (within the central mucin domain of MUC5B) were found to be dominated by the β-sheet. Using these findings, we employed TERS, which combines the chemical specificity of Raman spectroscopy with the spatial resolution of atomic force microscopy to study the secondary structure along 90 nm of an individual MUC5B molecule. Interestingly, the molecule was found to contain a large amount of α-helix/unordered structures and many signatures of glycosylation, pointing to a highly O-glycosylated region on the mucin.

2014, Appelhans, Dietmar, Klajnert-Maculewicz, Barbara, Janaszewska, Anna, Lazniewska, Joanna, Voit, Brigitte

In this review we highlight the potential for biomedical applications of dendritic glycopolymers based on polyamine scaffolds. The complex interplay of the molecular characteristics of the dendritic architectures and their specific interactions with various (bio)molecules are elucidated with various examples. A special role of the individual sugar units attached to the dendritic scaffolds and their density is identified, which govern ionic and H-bond interactions, and biological targeting, but to a large extent are also responsible for the significantly reduced toxicity of the dendritic glycopolymers compared to their polyamine scaffolds. Thus, the application of dendritic glycopolymers in drug delivery systems for gene transfection but also as therapeutics in neurodegenerative diseases has great promise.

2015, Buchner, Franziska, Nakayama, Akira, Yamazaki, Shohei, Ritze, Hans-Hermann, Lübcke, Andrea

Time-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys.2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.

2015, Ciuraru, Raluca, Fine, Ludovic, van Pinxteren, Manuela, D’Anna, Barbara, Herrmann, Hartmut, George, Christian

Isoprene is an important reactive gas that is produced mainly in terrestrial ecosystems but is also produced in marine ecosystems. In the marine environment, isoprene is produced in the seawater by various biological processes. Here, we show that photosensitized reactions involving the sea-surface microlayer lead to the production of significant amounts of isoprene. It is suggested that H-abstraction processes are initiated by photochemically excited dissolved organic matter which will the degrade fatty acids acting as surfactants. This chemical interfacial processing may represent a significant abiotic source of isoprene in the marine boundary layer.

2016, Cowcher, David P., Deckert-Gaudig, Tanja, Brewster, Victoria L., Ashton, Lorna, Deckert, Volker, Goodacre, Royston

The correct glycosylation of biopharmaceutical glycoproteins and their formulations is essential for them to have the desired therapeutic effect on the patient. It has recently been shown that Raman spectroscopy can be used to quantify the proportion of glycosylated protein from mixtures of native and glycosylated forms of bovine pancreatic ribonuclease (RNase). Here we show the first steps toward not only the detection of glycosylation status but the characterization of glycans themselves from just a few protein molecules at a time using tip-enhanced Raman scattering (TERS). While this technique generates complex data that are very dependent on the protein orientation, with the careful development of combined data preprocessing, univariate and multivariate analysis techniques, we have shown that we can distinguish between the native and glycosylated forms of RNase. Many glycoproteins contain populations of subtly different glycoforms; therefore, with stricter orientation control, we believe this has the potential to lead to further glycan characterization using TERS, which would have use in biopharmaceutical synthesis and formulation research.

2015, Boltalina, Olga V., Popov, Alexey A., Kuvychko, Igor V., Shustova, Natalia B., Strauss, Steven H.

New chemical derivatives that possess the greatest variety of addition patterns than any other class of fullerene derivatives represent an important addition to the existing classes of perfluorocarbons, that is, compounds that are composed only of the two types of atoms, carbon and fluorine. These include aromatic and aliphatic perfluorocarbons such as perfluorodecalin, perfluorononane, hexafluorobenzene, etc., which are important as fluorous solvents used in medicine. The propensity of perfluoroalkylfullerenes (PFAFs) to readily crystallize from organic solutions upon slow evaporation in open air provided a straightforward access to their molecular structures via X-ray crystallography. Another crucial aspect that ensures future success in the characterization of numerous PFAFs of higher fullerenes and endohedral metallofullerenes is the possibility to apply HPLC methodologies to the separation of product mixtures. PFAFs, especially those of C60 and C70, are unique fullerene derivatives in terms of the number of structurally characterized derivatives with different number of RF groups and different addition patterns.

2014, Lin, Gungun, Makarov, Denys, Medina-Sánchez, Mariana, Guix, Maria, Baraban, Larysa, Cuniberti, Gianaurelio, Schmidt, Oliver G.

We present a concept of multidimensional magnetic and optical barcoding of droplets based on a magnetofluidic platform. The platform comprises multiple functional areas, such as an encoding area, an encoded droplet pool and a magnetic decoding area with integrated giant magnetoresistive (GMR) sensors. To prove this concept, penicillin functionalized with fluorescent dyes is coencapsulated with magnetic nanoparticles into droplets. While fluorescent dyes are used as conventional optical barcodes which are decoded with an optical decoding setup, an additional dimensionality of barcodes is created by using magnetic nanoparticles as magnetic barcodes for individual droplets and integrated micro-patterned GMR sensors as the corresponding magnetic decoding devices. The strategy of incorporating a magnetic encoding scheme provides a dynamic range of ~40 dB in addition to that of the optical method. When combined with magnetic barcodes, the encoding capacity can be increased by more than 1 order of magnitude compared with using only optical barcodes, that is, the magnetic platform provides more than 10 unique magnetic codes in addition to each optical barcode. Besides being a unique magnetic functional element for droplet microfluidics, the platform is capable of on-demand facile magnetic encoding and real-time decoding of droplets which paves the way for the development of novel non-optical encoding schemes for highly multiplexed droplet-based biological assays.

2015, Beer, Meike V., Hahn, Kathrin, Diederichs, Sylvia, Fabry, Marlies, Singh, Smriti, Spencer, Steve J., Salber, Jochen, Möller, Martin, Shard, Alexander G., Groll, Jürgen

Hydrogels are extensively studied for biomaterials application as they provide water swollen noninteracting matrices in which specific binding motifs and enzyme-sensitive degradation sites can be incorporated to tailor cell adhesion, proliferation, and migration. Hydrogels also serve as excellent basis for surface modification of biomaterials where interfacial characteristics are decisive for implant success or failure. However, the three-dimensional nature of hydrogels makes it hard to distinguish between the bioactive ligand density at the hydrogel-cell interface that is able to interact with cells and the ligands that are immobilized inside the hydrogel and not accessible for cells. Here, the authors compare x-ray photoelectron spectrometry (XPS), time-of-flight secondary ion mass spectroscopy (ToF-SIMS), enzyme linked immunosorbent assay (ELISA), and the correlation with quantitative cell adhesion using primary human dermal fibroblasts (HDF) to gain insight into ligand distribution. The authors show that although XPS provides the most useful quantitative analysis, it lacks the sensitivity to measure biologically meaningful concentrations of ligands. However, ToF-SIMS is able to access this range provided that there are clearly distinguishable secondary ions and a calibration method is found. Detection by ELISA appears to be sensitive to the ligand density on the surface that is necessary to mediate cell adhesion, but the upper limit of detection coincides closely with the minimal ligand spacing required to support cell proliferation. Radioactive measurements and ELISAs were performed on amine reactive well plates as true 2D surfaces to estimate the ligand density necessary to allow cell adhesion onto hydrogel films. Optimal ligand spacing for HDF adhesion and proliferation on ultrathin hydrogel films was determined as 6.5 ± 1.5 nm.

2015, Verkade, Jorge M. M., Quaedflieg, Peter J. L. M., Verzijl, Gerard K. M., Lefort, Laurent, van Delft, Floris L., de Vries, Johannes G., Rutjes, Floris P. J. T.

The γ-amino alcohol structural motif is often encountered in drugs and natural products. We developed two complementary catalytic diastereoselective methods for the synthesis of N-PMP-protected γ-amino alcohols from the corresponding ketones. The anti-products were obtained through Ir-catalyzed asymmetric transfer hydrogenation, the syn-products via Rh-catalyzed asymmetric hydrogenation.

2015, Marciniak, A., Despré, V., Barillot, T., Rouzée, A., Galbraith, M.C.E., Klei, J., Yang, C.-H., Smeenk, C.T.L., Loriot, V., Nagaprasad Reddy, S., Tielens, A.G.G.M., Mahapatra, S., Kuleff, A.I., Vrakking, M.J.J., Lépine, F.

Highly excited molecular species are at play in the chemistry of interstellar media and are involved in the creation of radiation damage in a biological tissue. Recently developed ultrashort extreme ultraviolet light sources offer the high excitation energies and ultrafast time-resolution required for probing the dynamics of highly excited molecular states on femtosecond (fs) (1 fs=10−15s) and even attosecond (as) (1 as=10−18 s) timescales. Here we show that polycyclic aromatic hydrocarbons (PAHs) undergo ultrafast relaxation on a few tens of femtoseconds timescales, involving an interplay between the electronic and vibrational degrees of freedom. Our work reveals a general property of excited radical PAHs that can help to elucidate the assignment of diffuse interstellar absorption bands in astrochemistry, and provides a benchmark for the manner in which coupled electronic and nuclear dynamics determines reaction pathways in large molecules following extreme ultraviolet excitation.