DANGLE: A Bayesian inferential method for predicting protein backbone dihedral angles and secondary structure

This paper introduces DANGLE, a new algorithm that employs Bayesian inference to estimate the likelihood of all possible values of the backbone dihedral angles ? and ψ for each residue in a query protein, based on observed chemical shifts and the conformational preferences of each amino acid type. The method provides robust estimates of ? and ψ within realistic boundary ranges, an indication of the degeneracy in the relationship between shift measurements and conformation at each site, and faithful secondary structure state assignments. When a simple degeneracy-based filtering procedure is applied, DANGLE offers an ideal compromise between accuracy and coverage when compared with other shift-based dihedral angle prediction methods. In addition, per residue analysis of shift/structure degeneracy has potential to be a useful new approach for studying the properties of unfolded proteins, with sufficient sensitivity to identify regions of residual structure in the acid denatured state of apomyoglobin.     

Construction of diverse peptide structural architectures via chemoselective peptide ligation

Herein, we report the development of a facile synthetic strategy for constructing diverse peptide structural architectures via chemoselective peptide ligation. The key advancement involved is to utilize the benzofuran moiety as the peptide salicylaldehyde ester surrogate, and Dap–Ser/Lys–Ser dipeptide as the hydroxyl amino functionality, which could be successfully introduced at the side chain of peptides enabling peptide ligation. With this method, the side chain-to-side chain cyclic peptide, branched/bridged peptides, tailed cyclic peptides and multi-cyclic peptides have been designed and successfully synthesized with native peptidic linkages at the ligation sites. This strategy has provided an alternative strategic opportunity for synthetic peptide development. It also serves as an inspiration for the structural design of PPI inhibitors with new modalities.

Methods of introducing peptide salicylaldehyde esters and hydroxyl amine functionality into the peptide side chain have been developed. Diverse peptide structural motifs were constructed via ligation with native amide linkages at the ligation sites.     

Equilibrium studies of the sorption of Cu(II) ions onto chitosan

Chitosan is a polymer that can be obtained from the shells of seafood such as prawns, crabs, and lobsters. Chitosan has free amino groups, which can attract metal ions, and has been used as an adsorbent for the removal of metal ions from effluents. In this research, the sorption of copper ions from solution onto chitosan at two pHs has been investigated. DSC, TGA, surface area, SEM, and NMR studies have been used to report the pure physical states of chitosan and the chitosan-copper complex. The experimental isotherm data were analyzed using the Langmuir, Freundlich, and Redlich-Peterson equations. Correlation coefficients were determined for each isotherm analysis. Error functions have been used to determine the alternative single component parameters by nonlinear regression due to the inherent bias in using the correlation coefficient resulting from linearization. The error function method provided the best parameters for the isotherm equations in this system and is demonstrated for error comparison purposes.     

A ketone-functionalized aromatic saddle as a potential building block for negatively curved carbon nanobelts

Herein, we report the synthesis and crystal structure of a novel ketone-functionalized aromatic saddle, which is a potential building block for synthesis of negatively curved carbon nanobelts.     

Efficient and regioselective synthesis of 2-alkyl-2H-indazoles

An efficient and regioselective synthesis of 2-methyl-2H-indazoles and 2-ethyl-2H-indazoles using trimethyloxonium tetrafluoroborate or triethyloxonium hexafluorophosphate is reported.     

Near-infrared laser spectroscopy of NiI

Laser-induced fluorescence spectrum of NiI in the near infrared region of 714-770 nm has been recorded. Seven bands belonging to three electronic transition systems were observed and analyzed: the (0,0), (1,0), and (2,0) bands of [13.3] (2)Sigma(+)-A (2)Pi(3/2) system; the (1,1) and (0,1) bands of [13.9] (2)Pi(3/2)-X (2)Delta(5/2) system; and the (0,0) and (1,0) bands of [13.9] (2)Pi(3/2)-A (2)Pi(3/2) system. Spectra of isotopic molecules confirmed the vibrational quantum number assignment of the observed bands. Least-squares fit of rotationally resolved transition lines yielded accurate molecular constants for the v=0-2 levels of the [13.3] (2)Sigma(+) state, the v=0 level of the A (2)Pi(3/2), and the v=1 level of the X (2)Delta(5/2) state. The vibrational separation, DeltaG(1/2), of the ground state was measured to be 276.674 cm(-1). With the observation of the [13.9] (2)Pi(3/2)-A (2)Pi(3/2) and [13.9] (2)Pi(3/2)-X (2)Delta(5/2) transitions, we accurately determined the energy separation between the A (2)Pi(3/2) and the X (2)Delta(5/2) to be 163.847 cm(-1). This confirms that the order of the A (2)Pi(3/2) and X (2)Delta(5/2) states in NiI is reversed when compared with other nickel monohalides.     

Bioprinting of Collagen: Considerations,Potentials, and Applications

Collagen is the most abundant extracellular matrix protein that is widely used in tissue engineering (TE). There is little research done on printing pure collagen. To understand the bottlenecks in printing pure collagen, it is imperative to understand collagen from a bottom‐up approach. Here it is aimed to provide a comprehensive overview of collagen printing, where collagen assembly in vivo and the various sources of collagen available for TE application are first understood. Next, the current printing technologies and strategy for printing collagen‐based materials are highlighted. Considerations and key challenges faced in collagen printing are identified. Finally, the key research areas that would enhance the functionality of printed collagen are presented.     

Determination of a novel antifibrotic small molecule GDC‐3280 in human plasma and urine by liquid chromatography tandem mass spectrometry to support its first‐in‐human clinical trial

A specific and robust LC–MS/MS method was developed and validated for the quantitative determination of GDC‐3280 in human plasma and urine. The nonspecific binding associated with urine samples was overcome by the addition of CHAPS. The sample volume was 25 μL for either matrix, and supported liquid extraction was employed for analyte extraction. d6‐GDC‐3280 was used as the internal standard. Linear standard curves (R² > 0.9956) were established from 5.00 to 5000 ng/mL in both matrices with quantitation extended to 50,000 ng/mL through dilution. In plasma matrix, the precision (RSD) ranged from 1.5 to 9.9% (intra‐run) and from 2.4 to 7.2% (inter‐run); the accuracy (RE) ranged from 96.1 to 107% (intra‐run) and from 96.7 to 104% (inter‐run). Similarly, in urine the precision was 1.5–6.2% (intra‐run) and 1.9–6.1% (inter‐run); the accuracy was 83.1–99.3% (intra‐run) and 87.1–98.3% (inter‐run). Good recovery (>94%) and negligible matrix effect were achieved in both matrices. Long‐term matrix stability was established for at least 703 days in plasma and 477 days in urine. Bench‐top stability of 25 h and five freeze–thaw cycles were also confirmed in both matrices. The method was successfully implemented in GDC‐3280's first‐in‐human trial for assessing its pharmacokinetic profiles.