Circular Dichroism is Sensitive to Monovalent Cation Binding in Monensin Complexes

We present a lock-free version of the light-weight userlevel task management library called Wool, in an aim to show that even extremely well tuned, in terms of synchronization,applications can benefit from lock-free programming.Explicit multi-threading is an efficient way to exploit the offered parallelism of multi-core and multi-processor based systems. However, it can sometimes be hard to expressthe inherited parallelism in programs using a limited number of long lived threads. Often it can be more straightforwardto dynamically create a large number of small tasks that in turn automatically execute on the available threads.Wool is a promising and efficient library and framework that allows the programmer to create user tasks in C with a very low overhead. The library automatically executestasks and balances the load evenly on a given number of threads by utilizing work stealing techniques. However, thesynchronization for stealing tasks is based on mutual exclusion which is known to limit parallelism and efficiency. We have designed and implemented a new lock-free algorithmfor synchronization of stealing tasks in Wool. Experiments show similar or significantly improved performance on a setof benchmarks executed on a multi-core platform

Glucagon-like peptide 1 aggregates into low-molecular-weight oligomers off-pathway to fibrillation

The physical stability of peptide-based drugs is of great interest to the pharmaceutical industry. Glucagon-like peptide 1 (GLP-1) is a 31-amino acid peptide hormone, the analogs of which are frequently used in the treatment of type 2 diabetes. We investigated the physical stability of GLP-1 and its C-terminal amide derivative, GLP-1-Am, both of which aggregate into amyloid fibrils. While off-pathway oligomers have been proposed to explain the unusual aggregation kinetics observed previously for GLP-1 under specific conditions, these oligomers have not been studied in any detail. Such states are important as they may represent potential sources of cytotoxicity and immunogenicity. Here, we identified and isolated stable, low-molecular-weight oligomers of GLP-1 and GLP-1-Am, using size-exclusion chromatography. Under the conditions studied, isolated oligomers were shown to be resistant to fibrillation or dissociation. These oligomers contain between two and five polypeptide chains and they have a highly disordered structure as indicated by a variety of spectroscopic techniques. They are highly stable with respect to time, temperature, or agitation despite their noncovalent character, which was established using liquid chromatography-mass spectrometry and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. These results provide evidence of stable, low-molecular-weight oligomers that are formed by an off-pathway mechanism which competes with amyloid fibril formation

Dependence of the Reactivity of Acridine on Its Substituents: A Computational and Kinetic Study

Aromatic nucleophilic substitution on the C9 carbon of acridine plays an important role in multiple biological and medicinal applications. The rate of the key reaction is strongly dependent on the environment and acridine substituents. In this study, the factors influencing the reaction mechanism were studied theoretically and verified experimentally for simplified systems. Density functional theory was used for the computations. The activation energy of a model derivative was determined experimentally from a kinetic study. Also, the relative reactivities of selected compounds were verified by a competition experiment. The theoretical predictions correlate well with the observations. The computed re

Enantiomeric Discrimination by Surface- Enhanced Raman Scattering- Chiral Anisotropy of Chiral Nanostructured Gold Films

A surface- enhanced Raman scattering- chiral anisotropy (SERS- ChA) effect is reported that combines chiral discrimination and surface Raman scattering enhancement on chiral nanostructured Au films (CNAFs) equipped in the normal Raman scattering Spectrometer. The CNAFs provided remarkably higher enhancement factors of Raman scattering (EFs) for particular enantiomers, and the SERS intensity was proportional to the enantiomeric excesses (ee) values. Except for molecules with mesomeric species, all of the tested enantiomers exhibited high SERS- ChA asymmetry factors (g), ranging between 1.34 and 1.99 regardless of polarities, sizes, chromophores, concentrations and ee. The effect might be attributed to selective resonance coupling between the induced electric and magnetic dipoles associated with enantiomers and chiral plasmonic modes of CNAFs.Absolution by SERS: A surface- enhanced Raman scattering chiral anisotropy effect is presented that combines chiral discrimination and surface Raman scattering enhancement on chiral nanostructured Au films. It is applied in the normal Raman scattering system to identify the absolute configuration and composition of enantiomers, overcoming disadvantages of polarimeter systems and chromatography.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156417/3/anie202006486-sup-0001-misc_information.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156417/2/anie202006486_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156417/1/anie202006486.pd

Enantiomeric Discrimination by Surface- Enhanced Raman Scattering- Chiral Anisotropy of Chiral Nanostructured Gold Films

A surface- enhanced Raman scattering- chiral anisotropy (SERS- ChA) effect is reported that combines chiral discrimination and surface Raman scattering enhancement on chiral nanostructured Au films (CNAFs) equipped in the normal Raman scattering Spectrometer. The CNAFs provided remarkably higher enhancement factors of Raman scattering (EFs) for particular enantiomers, and the SERS intensity was proportional to the enantiomeric excesses (ee) values. Except for molecules with mesomeric species, all of the tested enantiomers exhibited high SERS- ChA asymmetry factors (g), ranging between 1.34 and 1.99 regardless of polarities, sizes, chromophores, concentrations and ee. The effect might be attributed to selective resonance coupling between the induced electric and magnetic dipoles associated with enantiomers and chiral plasmonic modes of CNAFs.Absolution by SERS: A surface- enhanced Raman scattering chiral anisotropy effect is presented that combines chiral discrimination and surface Raman scattering enhancement on chiral nanostructured Au films. It is applied in the normal Raman scattering system to identify the absolute configuration and composition of enantiomers, overcoming disadvantages of polarimeter systems and chromatography.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/156470/3/ange202006486_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156470/2/ange202006486.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/156470/1/ange202006486-sup-0001-misc_information.pd

Solution structure of Mannobioses unravelled by means of Raman optical activity

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible

Computer-Based De Novo Designs of Tripeptides as Novel Neuraminidase Inhibitors

The latest influenza A (H1N1) pandemic attracted worldwide attention and called for the urgent development of novel antiviral drugs. Here, seven tripeptides are designed and explored as neuraminidase (NA) inhibitors on the structural basis of known inhibitors. Their interactions with NA are studied and compared with each other, using flexible docking and molecular dynamics simulations. The various composed tripeptides have respective binding specificities and their interaction energies with NA decrease in the order of FRI > FRV > FRT > FHV > FRS > FRG > YRV (letters corresponding to amino acid code). The Arg and Phe portions of the tripeptides play important roles during the binding process: Arg has strong electrostatic interactions with the key residues Asp151, Glu119, Glu227 and Glu277, whereas Phe fits well in the hydrophobic cave within the NA active site. Owing to the introduction of hydrophobic property, the interaction energies of FRV and FRI are larger; in particular, FRI demonstrates the best binding quality and shows potential as a lead compound. In addition, the influence of the chemical states of the terminal amino acids are clarified: it is revealed that the charged states of the N-terminus (NH3+) and C-terminus (COO−) are crucial for the tripeptide inhibitory activities and longer peptides may not be appropriate. In addition, the medium inhibiting activity by acetylation of the N-terminus indicates the possible chemical modifications of FRI. Experimental efforts are expected in order to actualize the tripeptides as potent NA inhibitors in the near future

The Raman optical activity of β-D-xylose: where experiment and theory meet

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