Ligand Dilution Analysis Facilitates Aptamer Binding Characterization at the Single-Molecule Level

Cell-specific aptamers offer a powerful tool to study membrane receptors at the single-molecule level. Most target receptors of aptamers are highly expressed on the cell surface, but difficult to analyze in situ because of dense distribution and fast velocity. Therefore, we herein propose a random sampling-based analysis strategy termed ligand dilution analysis (LDA) for easily implemented aptamer-based receptor study. Receptor density on the cell surface can be calculated based on a regression model. By using a synergistic ligand dilution design, colocalization and differentiation of aptamer and monoclonal antibody (mAb) binding on a single receptor can be realized. Once this is accomplished, precise binding site and detailed aptamer-receptor binding mode can be further determined using molecular docking and molecular dynamics simulation. The ligand dilution strategy also sets the stage for an aptamer-based dynamics analysis of two- and three-dimensional motion and fluctuation of highly expressed receptors on the live cell membrane.     

Raman microspectroscopy and SEM/EDS in the investigation of white and red painting layers from Celtic pottery from a Modlniczka site in Poland

Red and white painting layers from Celtic pottery from Southern Poland (Modlniczka 2 site near Kraków) were investigated with the use of Raman microspectroscopy, SEM/EDS and optical microscopy. The painting layers were performed homogeneously for all the examined shards, i.e. red layers as thinner, ca. 0,02 mm and white of 0,04 mm. The white painting layers are very fine grained and amorphous under SEM, prepared of compositionally complex magnesium based raw material, with phosphates and fluorite probably used as fluxes. Unusual phases: fluorite and silicon were identified. Raman spectroscopy of fine grained red painting layers revealed the presence of hematite and anatase/leucoxen. Again, rare phases, of silicon and destinezite were found. Both paints were carefully manufactured by grinding and homogenizing the raw materials. Their preliminary firing cannot be excluded. The painted pottery was fired approx. at 700–900 °C, but multistage firing is possible.     

N‐ and O‐linked glycosylation site profiling of the human basic salivary proline‐rich protein 3M

In the present study, we show that the heterogeneous mixture of glycoforms of the basic salivary proline‐rich protein 3M, encoded by PRB3‐M locus, is a major component of the acidic soluble fraction of human whole saliva in the first years of life. Reversed‐phase high‐performance liquid chromatography with high‐resolution electrospray ionization mass spectrometry analysis of the intact proteoforms before and after N‐deglycosylation with Peptide‐N‐Glycosidase F and tandem mass spectrometry sequencing of peptides obtained after Endoproteinase GluC digestion allowed the structural characterization of the peptide backbone and identification of N‐ and O‐glycosylation sites. The heterogeneous mixture of the proteoforms derives from the combination of 8 different neutral and sialylated glycans O‐linked to Threonine 50, and 33 different glycans N‐linked to Asparagine residues at positions 66, 87, 108, 129, 150, 171, 192, and 213.     

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions

We present results of testing the ability of eleven popular scoring functions to predict native docked positions using a recently developed method (Ruvinsky and Kozintsev, J Comput Chem 2005, 26, 1089) for estimation the entropy contributions of relative motions to protein-ligand binding affinity. The method is based on the integration of the configurational integral over clusters obtained from multiple docked positions. We use a test set of 100 PDB protein-ligand complexes and ensembles of 101 docked positions generated by (Wang et al. J Med Chem 2003, 46, 2287) for each ligand in the test set. To test the suggested method we compared the averaged root-mean square deviations (RMSD) of the top-scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10-21% when used in conjunction with the AutoDock scoring function, by 2-25% with G-Score, by 7-41% with D-Score, by 0-8% with LigScore, by 1-6% with PLP, by 0-12% with LUDI, by 2-8% with F-Score, by 7-29% with ChemScore, by 0-9% with X-Score, by 2-19% with PMF, and by 1-7% with DrugScore. We also compared the performance of the suggested method with the method based on ranking by cluster occupancy only. We analyze how the choice of a clustering-RMSD and a low bound of dense clusters impacts on docking accuracy of the scoring methods. We derive optimal intervals of the clustering-RMSD for 11 scoring functions.     

Chemo-selective Suzuki–Miyaura reactions: Synthesis of highly substituted [1,6]-naphthyridines

The Suzuki-Miyaura reaction of methyl-5-bromo-8-(tosyloxy)-1,6-naphthyridine-7-carboxylate(5),with 2 equiv. of arylboronic acids gave diarylated product, 5,8–diaryl-1,6-naphthyridine-7-carboxylate(7), whereas 1 equiv. of arylboronic acid resulted in site-selective formation of 5-aryl-8-(tosyloxy)-1,6-naphthyridine-7-carboxylate(8). The reactions proceeded with excellent chemo-selectivity in favor of the bromide group. Likewise, one-pot reaction with completely different boronic acids by sequential addition produced 1,6-naphthyridine-7-carboxylates,(10) containing two different aryl groups at 5 and 8 positions.     

Optical Properties of Rare Earth Doped Transparent Oxyfluoride Glass Ceramics

Optical properties of Eu^3? ions in oxyfluoride glasses and glass ceramics doped with low concentration (0.1 mol%) have been analysed and compared with previous results for high concentrated samples (2.5 mol%). The Eu^3? ions in the low dopant concentration glass ceramics are diluted into like crystalline environments with higher symmetry and lower coupled phonons energy than in the precursor glasses. Fluorescence line narrowing measurements indicate the presence of two main fluoride site distributions for the Eu^3? ions in these low concentrated glass ceramics.     

Exact diagonalization study of 2D Hubbard model on honeycomb lattice: Semi-metal to insulator transition

Phase transition in a honeycomb lattice is studied by the means of the two-dimensional Hubbard model and the exact diagonalization dynamical mean field theory at zero temperature. At low energies, the dispersion relation is shown to be a linear function of the momentum. In the limit of weak interactions, the system is in the semi-metal phase. By increasing the on site interaction a semi-metal to insulator transition takes place in the paramagnetic phase. Calculation of double occupancy shows such a phase transition is of the second order. The respective phase transition point and critical on-site interaction are determined using renormalized Fermi velocity factor.     

Time evolution of average rotation axis directions and mean rotation angles of pressurized liquid methyl iodide by molecular dynamics simulation

The rotational motion of liquid methyl iodide has been modelled by molecular dynamics simulations under input parameters optimized from literature values to yield the experimental enthalpy of vaporization and permanent dipole moment of the molecule. First, it is shown that results describing the correlation function of the tumbling motion of the molecules agree reasonably well with some corresponding findings from a spectroscopic Raman study. Second, the rotational motion involving the spinning component around the molecule's symmetry axis was simulated, an effect inaccessible by experiment. Third, and most relevant to the author's interests, a group-theoretical formalism was used that generates the time evolution of the average direction of the average rotation axis as well as the mean rotation angle around it. This approach allowed a more realistic understanding of the effects of density and temperature on molecular rotational motion, as well as a better quantification of the influence of short-time inertial decay, than the common approach of studying orientational correlation data along permanently molecule-fixed axis directions. Fourth, site–site radial distribution functions between neighbouring molecules were simulated, establishing a shielding effect that prevents a carbon atom from approaching any other site by their closest distance.     

Observation of magnetic cluster phase above Curie temperature in Fe2CrAl Heusler alloy

We present a detailed magnetic critical behavior study of Fe₂CrAl Heusler alloy, for the first time, with rigorous analysis of high precision magnetization data obtained over the critical temperature region. Our studies confirm that B2 type site-disordered in Fe₂CrAl alloy exhibits long-range ferromagnetic order below a well defined Curie temperature (T=208 K). Though the nature of this transition is found to be of second order, the estimated critical exponents β=0.42, γ=1.356 and δ=4.25, are in between the theoretically predicted values for three-dimensional Heisenberg and mean-field interaction models. However, it is noteworthy that the scaling relations are obeyed indicating renormalization of interactions around the Curie temperature (T_C), where magnetization data collapse into two separate branches, above and below T_C. This conclusively shows that calculated critical exponents as well as critical temperature are unambiguous and intrinsic to the system. However, magnetization vs temperature data shows another magnetic transition (at T=313 K) above the Curie temperature. It is shown that the short range magnetic correlation exist even beyond T_C with cluster moment ∼10² μ_B. This is attributed to a site disorder which results in formation of Cr clusters with short range ferromagnetic order.     

On the number of empty boxes in the Bernoulli sieve II

The Bernoulli sieve is the infinite “balls-in-boxes” occupancy scheme with random frequencies _Pk=_W1?_Wk−1(1−_Wk)$P_k=W_1?W_{k-1}(1-W_k)$, where _(Wk)k∈N${\left(W_k\right)}_{k\in \mathbb{N}}$ are independent copies of a random variable W$W$ taking values in (0,1)$(0,1)$. Assuming that the number of balls equals n$n$, let _Ln$L_n$ denote the number of empty boxes within the occupancy range. In this paper, we investigate convergence in distribution of _Ln$L_n$ in the two cases which remained open after the previous studies. In particular, provided that E|logW|=E|log(1−W)|=∞$\mathbb{E}|logW|=\mathbb{E}|log(1-W)|=\infty$ and that the law of W$W$ assigns comparable masses to the neighborhoods of 0 and 1, it is shown that _Ln$L_n$ weakly converges to a geometric law. This result is derived as a corollary to a more general assertion concerning the number of zero decrements of nonincreasing Markov chains. In the case that E|logW|<∞$\mathbb{E}|logW|<\infty$ and E|log(1−W)|=∞$\mathbb{E}|log(1-W)|=\infty$, we derive several further possible modes of convergence in distribution of _Ln$L_n$. It turns out that the class of possible limiting laws for _Ln$L_n$, properly normalized and centered, includes normal laws and spectrally negative stable laws with finite mean. While investigating the second problem, we develop some general results concerning the weak convergence of renewal shot-noise processes. This allows us to answer a question asked by Mikosch and Resnick (2006) [18].