Efficient chemoenzymatic synthesis of an N-glycan isomer library

Quantification, characterization and biofunctional studies of N-glycans on proteins remain challenging tasks due to the complexity, diversity and low abundance of these glycans. The availability of structurally defined N-glycan (especially isomer) libraries is essential to help solve these tasks. We report herein an efficient chemoenzymatic strategy, namely Core Synthesis/Enzymatic Extension (CSEE), for rapid production of diverse N-glycans. Starting with 5 chemically prepared building blocks, 8 N-glycan core structures containing one or two terminal N-acetyl-d-glucosamine (GlcNAc) residue(s) were chemically synthesized via consistent use of oligosaccharyl thioethers as glycosylation donors in a convergent fragment coupling strategy. Each of these core structures was then extended to 5 to 15 N-glycan sequences by enzymatic reactions catalyzed by 4 robust glycosyltransferases. Success in synthesizing N-glycans with Neu5Gc and core-fucosylation further expanded the ability of the enzymatic extension. Meanwhile, high performance liquid chromatography with an amide column enabled rapid and efficient purification (>98% purity) of N-glycans in milligram scales. A total of 73 N-glycans (63 isomers) were successfully prepared and characterized by MS² and NMR. In summary, the CSEE strategy provides a practical approach for “mass production” of structurally defined N-glycans, which are important standards and probes for glycoscience.     

Origins of the Intermediate Spectral Form in M100 Mutants of Photoactive Yellow Protein

Numerous single‐site mutants of photoactive yellow protein (PYP) from Halorhodospira halophila and as well as PYP homologs from other species exhibit a shoulder on the short wavelength side of the absorbance maximum in their dark‐adapted states. The structural basis for the occurrence of this shoulder, called the “intermediate spectral form,” has only been investigated in detail for the Y42F mutation. Here we explore the structural basis for occurrence of the intermediate spectral form in a M121E derivative of a circularly permuted H. halophila PYP (M121E‐cPYP). The M121 site in M121E‐cPYP corresponds to the M100 site in wild‐type H. halophila PYP. High‐resolution NMR measurements with a salt‐tolerant cryoprobe enabled identification of those residues directly affected by increasing concentrations of ammonium chloride, a salt that greatly enhances the fraction of the intermediate spectra form. Residues in the surface loop containing the M121E (M100E) mutation were found to be affected by ammonium chloride as well as a discrete set of residues that link this surface loop to the buried hydroxyl group of the chromophore via a hydrogen bond network. Localized changes in the conformational dynamics of a surface loop can thereby produce structural rearrangements near the buried hydroxyl group chromophore while leaving the large majority of residues in the protein unaffected.     

Comparison of structural,thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

The prevalence of Mg²⁺ ions in biology and their essential role in nucleic acid structure and function has motivated the development of various Mg²⁺ ion models for use in molecular simulations. Currently, the most widely used models in biomolecular simulations represent a nonbonded metal ion as an ion‐centered point charge surrounded by a nonelectrostatic pairwise potential that takes into account dispersion interactions and exchange effects that give rise to the ion's excluded volume. One strategy toward developing improved models for biomolecular simulations is to first identify a Mg²⁺ model that is consistent with the simulation force fields that closely reproduces a range of properties in aqueous solution, and then, in a second step, balance the ion–water and ion–solute interactions by tuning parameters in a pairwise fashion where necessary. The present work addresses the first step in which we compare 17 different nonbonded single‐site Mg²⁺ ion models with respect to their ability to simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. None of the models based on a 12‐6 nonelectrostatic nonbonded potential was able to reproduce the experimental radial distribution function, solvation free energy, exchange barrier and diffusion constant. The models based on a 12‐6‐4 potential offered improvement, and one model in particular, in conjunction with the SPC/E water model, performed exceptionally well for all properties. The results reported here establish useful benchmark calculations for Mg²⁺ ion models that provide insight into the origin of the behavior in aqueous solution, and may aid in the development of next‐generation models that target specific binding sites in biomolecules. © 2015 Wiley Periodicals, Inc.     

Radiofluorination of a Pre‐formed Gallium(III) Aza‐macrocyclic Complex: Towards Next‐Generation Positron Emission Tomography (PET) Imaging Agents

As part of a study to investigate the factors influencing the development of new, more effective metal‐complex‐based positron emission tomography (PET) imaging agents, the distorted octahedral complex, [GaCl(L)]?2 H₂O has been prepared by reaction of 1‐benzyl‐1,4,7‐triazacyclononane‐4,7‐dicarboxylic acid hydrochloride (H₂L?HCl) with Ga(NO₃)₃?9 H₂O, which is a convenient source of Ga^III for reactions in water. Spectroscopic and crystallographic data for [GaCl(L)]?2 H₂O are described, together with the crystal structure of [GaCl(L)]?MeCN. Fluorination of this complex by Cl^?/F^? exchange was achieved in high yield by treatment with KF in water at room temperature over 90 minutes, although the reaction was complete in approximately 30 minutes if heated to 80 °C, giving [GaF(L)]?2 H₂O in good yield. The same complex was obtained by hydrothermal synthesis from GaF₃?3 H₂O and Li₂L, and has been characterised by single‐crystal X‐ray analysis, IR, ¹H and ¹⁹F{¹H} NMR spectroscopy and ESI⁺ MS. Radiofluorination of the pre‐formed [GaCl(L)]?2 H₂O has been demonstrated on a 210 nanomolar scale in aqueous NaOAc at pH 4 by using carrier‐free ¹⁸F^?, leading to 60–70 % ¹⁸F‐incorporation after heating to 80 °C for 30 minutes. The resulting radioproduct was purified easily by using a solid‐phase extraction (SPE) cartridge, leading to 98–99 % radiochemical purity. The [Ga¹⁸F(L)] is stable for at least 90 minutes in 10 % EtOH/NaOAc solution at pH 6, but defluorinates over this time scale at pH of approximately 7.5 in phosphate buffered saline (PBS) or human serum albumin (HSA). The subtle role of the Group 13 metal ion and co‐ligand donor set in influencing the pH dependence of this system is discussed in the context of developing potential new imaging agents for PET.     

High‐performance liquid chromatography separation of unsaturated organic compounds by a monolithic silica column embedded with silver nanoparticles

The optimization of a porous structure to ensure good separation performances is always a significant issue in high‐performance liquid chromatography column design. Recently we reported the homogeneous embedment of Ag nanoparticles in periodic mesoporous silica monolith and the application of such Ag nanoparticles embedded silica monolith for the high‐performance liquid chromatography separation of polyaromatic hydrocarbons. However, the separation performance remains to be improved and the retention mechanism as compared with the Ag ion high‐performance liquid chromatography technique still needs to be clarified. In this research, Ag nanoparticles were introduced into a macro/mesoporous silica monolith with optimized pore parameters for high‐performance liquid chromatography separations. Baseline separation of benzene, naphthalene, anthracene, and pyrene was achieved with the theoretical plate number for analyte naphthalene as 36 000 m^?1. Its separation function was further extended to cis/trans isomers of aromatic compounds where cis/trans stilbenes were chosen as a benchmark. Good separation of cis/trans‐stilbene with separation factor as 7 and theoretical plate number as 76 000 m^?1 for cis‐stilbene was obtained. The trans isomer, however, is retained more strongly, which contradicts the long‐ established retention rule of Ag ion chromatography. Such behavior of Ag nanoparticles embedded in a silica column can be attributed to the differences in the molecular geometric configuration of cis/trans stilbenes.     

Strategic customer behavior in a queueing system with delayed observations

We consider the single-server Markovian queue with infinite waiting space and assume that there exists a certain reward-cost structure that reflects the customers’ desire for service and their dislike for waiting. The system is unobservable for the customers at their arrival instants, but the administrator provides them with periodic announcements of their current positions at rate \(\theta \), so that they may renege if it is preferable for them to do so. The customers are strategic, and their decision problem is whether to join or not the system upon arrival and whether to stay or renege later. Their strategies are specified by a join probability q and a reneging threshold n. We determine the equilibrium strategies \((n_e,q_e)\) and study the socially optimal strategies \((n_\mathrm{soc},q_\mathrm{soc})\). Extensive numerical experiments provide interesting qualitative insight about the model. In particular, the equilibrium throughput of the system is a unimodal function of \(\theta \). Moreover, despite the fact that we have an avoid-the-crowd situation, it is possible that \(q_\mathrm{soc}>q_e\), in contrast to the classical unobservable model.     

Certain properties related to well posedness of switching diffusions

This work is devoted to switching diffusions that have two components (a continuous component and a discrete component). Different from the so-called Markovian switching diffusions, in the setup, the discrete component (the switching) depends on the continuous component (the diffusion process). The objective of this paper is to provide a number of properties related to the well posedness. First, the differentiability with respect to initial data of the continuous component is established. Then, further properties including uniform continuity with respect to initial data, and smoothness of certain functionals are obtained. Moreover, Feller property is obtained under only local Lipschitz continuity. Finally, an example of Lotka–Volterra model under regime switching is provided as an illustration.     

Regulatory capital decisions in the Context of consumer loan portfolios

A topic of interest in recent literature is regulatory capital requirements for consumer loan portfolios. Banks are required to hold regulatory capital for unexpected losses, while expected losses are to be covered by either provisions or future income. In this paper, we show the set of efficient operating points in the market share and profit space for a portfolio manager operating under Basel II capital requirement and under capital constraints are a union of single-cutoff-score and double-cutoff-score operating points. For a portfolio manager to increase market-share beyond the maximum allowable under a single-cutoff score policy (eg, with binding capital constraints) requires granting loans to higher than optimal risk applicants. We show this result in greater portfolio risk but without an increase in regulatory capital requirement amount. The increase in forecasted losses is assumed to be absorbed by provisions or future margin income. Given portfolio managers take on higher risk under the same regulatory capital amount, our findings call for greater focus on provision amounts and future margin income under the supervisory review pillar of Basel II. This research raises the issue of whether the design of the regulatory formula for consumer loan portfolios is flawed.     

Shear dependence of viscosity for perfluoropolyether fluids

The shear dependence of the bulk viscosities of two structurally different types of perfluoropolyether fluids was determined by two different techniques. The first involved direct measurement in a high shear Couette viscometer, the second utilized the time-temperature superposition principle to establish master curves from viscosity determinations at low shear rates and temperature; the results are comparable. Both fluids begin to show non-Newtonian behavior at shear rates above 10,000 s^–1.