Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Unzipping Nucleoside Channels by Means of Alcohol Disassembly

Gold nanoparticles capped with simple adenosine derivatives can form colloidal aggregates in nonpolar solvents. Theoretical calculations indicate the formation of organic channels by the supramolecular assembly of the nanoparticles by means of hydrogen bonds between the adenine moieties. The aggregates were only negligibly sensitive to nPrOH, iPrOH, and tBuOH, whereas some showed a similar response to MeOH and EtOH, and others showed high selectivity toward MeOH. DNA nucleoside derivatives (1‐(2‐deoxy‐β‐D ‐ribofuranosyl)‐5‐methyluracil and 2′,3′‐O‐isopropylideneadenosine) as well as thymine and other aromatic compounds such as pyrene derivatives (pyrene, 1‐chloropyrene, 1‐hydroxypyrene, (1‐pyrenyl)methanol, and 2‐hydroxynapthalene) did not induce disassembly of the nanoparticle aggregates. Data suggest that the nucleoside channels allow access to alcohols according to their size, and an efficient interaction between the alcohol and the adenine units destabilizes the hydrogen bonds, which eventually leads to nanoparticle disassembly.     

Epitope Mapping of Monoclonal Antibodies using Synthetic Oligosaccharides Uncovers Novel Aspects of Immune Recognition of the Psl Exopolysaccharide of Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic Gram‐negative bacterium that can cause life‐threatening infections in critically ill and cystic fibrosis patients. The Psl exopolysaccharide of P. aeruginosa offers an attractive serotype‐independent antigen for the development of immunotherapies. Here, the first chemical synthesis of a panel of oligosaccharides derived from the exopolysaccharide of P. aeruginosa by a synthetic strategy that efficiently deals with the stereoselective installation of several β‐mannosides and the formation of a mannoside that is extended by saccharide moieties at C‐1, C‐2, and C‐3 in a crowded 1,2,3‐cis configuration is described. The approach was employed to prepare tetra‐, penta‐, and hexa‐ and decasaccharide part structures. The compounds were employed to define the epitope requirements of several functionally active monoclonal antibodies (mAbs) that can bind three distinct epitopes of Psl (class I, II, and III). The class II mAb reacted potently with each oligosaccharide indicating its epitope resides within the tetrasaccharide and does not require the branched mannoside of Psl. The class III antibody did not bind the tetra‐ or pentasaccharide; however, it did react potently with the hexasaccharide and weakly with the decasaccharide, suggesting a terminal glucoside is required for optimal binding. Unexpectedly, the class I mAb did not bind any of the oligosaccharides indicating that Psl contains a yet to be elucidated sub‐stoichiometric isoform. This study demonstrates that functional activity of a mAb does not only depend on the avidity of binding but also on the location of an epitope within a bacterial polysaccharide. The results also provide a strong impetus to analyze further the structure of Psl to identify the class I epitope, that is expected to provide an attractive target for the development of a synthetic vaccine for P. aeruginosa.     

A Unified Strategy for the Synthesis of Mucin Cores 1–4 Saccharides and the Assembled Multivalent Glycopeptides

By displaying different O‐glycans in a multivalent mode, mucin and mucin‐like glycoproteins are involved in a plethora of protein binding events. The understanding of the roles of the glycans and the identification of potential glycan binding proteins are major challenges. To enable future binding studies of mucin glycan and glycopeptide probes, a method that gives flexible and efficient access to all common mucin core‐glycosylated amino acids was developed. Based on a convergent synthesis strategy starting from a shared early stage intermediate by differentiation in the glycoside acceptor reactivity, a common disaccharide building block allows for the creation of extended glycosylated amino acids carrying the mucin type‐2 cores 1–4 saccharides. Formation of a phenyl‐sulfenyl‐N‐Troc (Troc=trichloroethoxycarbonyl) byproduct during N‐iodosuccinimide‐promoted thioglycoside couplings was further characterized and a new methodology for the removal of the Troc group is described. The obtained glycosylated 9‐fluorenylmethoxycarbonyl (Fmoc)‐protected amino acid building blocks are incorporated into peptides for multivalent glycan display.     

Dual Gold Catalysis: σ,π‐Propyne Acetylide and Hydroxyl‐Bridged Digold Complexes as Easy‐To‐Prepare and Easy‐To‐Handle Precatalysts

A series of dinuclear gold σ,π‐propyne acetylide complexes were prepared and tested for their catalytic ability in dual gold catalysis that was based on the reaction of an electrophilic π‐complex of gold with a gold acetylide. The air‐stable and storable catalysts can be isolated as silver‐free catalysts in their activated form. These dual catalysts allow a fast initiation phase for the dual catalytic cycles without the need for additional additives for acetylide formation. Because propyne serves as a throw‐away ligand, no traces of the precatalyst are generated. Based on the fast initiation process, side products are minimized and reaction rates are higher for these catalysts. A series of test reactions were used to demonstrate the general applicability of these catalysts. Lower catalyst loadings, faster reaction rates, and better selectivity, combined with the practicability of these catalysts, make them ideal catalysts for dual gold catalysis.     

Nickel‐Catalyzed Arylation,Alkenylation, and Alkynylation of Unprotected Thioglycosides at Room Temperature

Unprotected thioglycosides were effective nucleophiles for Ni⁰‐catalyzed C? S bond‐forming reaction with functionalized (hetero)aryl, alkenyl, and alkynyl halides. The functional‐group tolerance on the electrophilic partner was typically high and the anomeric selectivities of the thioglycosides were high in all cases. The efficiency of this general procedure was well‐demonstrated by the synthesis of 4‐methyl‐7‐thioumbelliferyl‐β‐D ‐cellobioside (MUS‐CB).     

Estimation of the surface sulfur content of cellulose nanocrystals prepared by sulfuric acid hydrolysis

The conditions required for the accurate measurement of the sulfur content of cellulose nanocrystals (CNCs) by conductometric titration are discussed. CNCs from sulfuric acid hydrolysis are electrostatically stabilized in aqueous suspension due to the introduction of charged sulfate ester groups onto the surface of the crystallites during reaction. The sulfur content thus largely reflects the surface charge of the crystals, and is crucial to the characterization and understanding of material properties. Conductometric titration is commonly used to quantify the sulfur content of CNCs, however, the exhaustive removal of free acid by dialysis and the necessity, type, quantity and duration of ion-exchange resin treatments are not always consistent. Here we explore the standard conditions of dialysis, ion-exchange, and the reproducibility of titration results. Extensive dialysis is found to be effective in the removal of free acid, but similar results are also achieved in shorter times and with less water using membrane ultrafiltration. It is also shown that the conditions of ion-exchange most commonly employed in the literature can lead to inaccurate sulfur contents. Finally, good agreement is obtained between the sulfur contents of different CNC batches prepared using the same hydrolysis conditions, and from titration and elemental analysis when thoroughly purified, well-dispersed samples, and appropriate resin conditions are used.     

Limit distribution of the coefficients of polynomials with only unit roots

We consider sequences of random variables whose probability generating functions have only roots on the unit circle, which has only been sporadically studied in the literature. We show that the random variables are asymptotically normally distributed if and only if the fourth central and normalized (by the standard deviation) moment tends to 3, in contrast to the common scenario for polynomials with only real roots for which a central limit theorem holds if and only if the variance is unbounded. We also derive a representation theorem for all possible limit laws and apply our results to many concrete examples in the literature, ranging from combinatorial structures to numerical analysis, and from probability to analysis of algorithms. © 2013 Wiley Periodicals, Inc. Random Struct. Alg., 46,707–738, 2015     

Towards a quaternionic function theory linked with the Lamé's wave functions

Over the past few years, considerable attention has been given to the role played by the Lamé's Wave Functions (LWFs) in various problems of mathematical physics and mechanics. The LWFs arise via the method of separation of variables for the wave equation in ellipsoidal coordinates. The present paper introduces the Lamé's Quaternionic Wave Functions (LQWFs), which extend the LWFs to a non‐commutative framework. We show that the theory of the LQWFs is determined by the Moisil‐Theodorescu type operator with quaternionic variable coefficients. As a result, we explain the connections between the solutions of the Lamé's wave equation, on one hand, and the quaternionic hyperholomorphic and anti‐hyperholomorphic functions on the other. We establish analogues of the basic integral formulas of complex analysis such as Borel‐Pompeiu's, Cauchy's, and so on, for this version of quaternionic function theory. We further obtain analogues of the boundary value properties of the LQWFs such as Sokhotski‐Plemelj formulae, the ‐hyperholomorphic extension of a given Hölder function and on the square of the singular integral operator. We address all the text mentioned earlier and explore some basic facts of the arising quaternionic function theory. We conclude the paper showing that the spherical, prolate, and oblate spheroidal quaternionic wave functions can be generated as particular cases of the LQWFs. Copyright © 2015 John Wiley & Sons, Ltd.     

Ideological Complex Systems: Mathematical Theory

The goal of this article is to build an abstract mathematical theory rather than a computational one of the process of transmission of ideology. The basis of much of the argument is Patten's Environment Theory that characterizes a system with its double environment (input or stimulus and output or response) and the existing interactions among them. Ideological processes are semiotic processes, and if in Patten's theory, the two environments are physical, in this theory ideological processes are physical and semiotic, as are stimulus and response. © 2014 Wiley Periodicals, Inc. Complexity 21: 47–65, 2015