Symmetric Grothendieck polynomials, skew Cauchy identities, and dual filtered Young graphs

Symmetric Grothendieck polynomials are analogues of Schur polynomials in the K-theory of Grassmannians. We build dual families of symmetric Grothendieck polynomials using Schur operators. With this approach we prove skew Cauchy identity and then derive various applications: skew Pieri rules, dual filtrations of Young's lattice, generating series and enumerative identities. We also give a new explanation of the finite expansion property for products of Grothendieck polynomials

Studies toward the Total Synthesis of the Cytotoxic Sponge Alkaloid Pyrinodemin A

The syntheses of the proposed structure of pyrinodemin A (1) and its cis double bond positional isomer (C15‘−C16‘) in racemic form are described. The key reaction involved an intramolecular nitrone/double bond cycloaddition. Our results suggest that neither 1 nor its double positional isomer is the correct structure of pyrinodemin

A Two-Directional Approach to Enantiopure 1,4-Difluoro-cyclohexenes: Synthesis of Difluorinated Cyclitol Analogues

Enantiopure 1,4-difluoro-cyclohexenes were prepared from readily available acetonide-protected (3S,4S)-hexa-1,5-diene-3,4-diol. In a two-directional mode, a double cross-metathesis reaction using allyltrimethylsilane as the olefinic partner, followed by electrophilic fluorination, afforded diastereomeric acetonide-protected 3,6-difluoro-octa-1,7-diene-4,5-diols. These dienes were found to be suitable substrates for ring-closing metathesis, delivering cyclohexenes featuring fluorine atoms on the two allylic positions flanking the double bond. Upon dihydroxylation, novel difluorinated cyclitol analogues were formed

Using NMR Solvent Water Relaxation to Investigate Metalloenzyme−Ligand Binding Interactions

This report demonstrates that solvent water relaxation measurements can be used for quantitative screening of ligand binding and for mechanistic investigations of enzymes containing paramagnetic metal centers by using conventional NMR instrumentation at high field. The method was exemplified using prolyl hydroxylase domain containing enzyme 2 (PHD2), a human enzyme involved in hypoxic sensing, with Mn(II) substituting for Fe(II) at the active site. KD values were determined for inhibitors that hinder access of water to the paramagnetic center. This technique is also useful for investigating the mechanism of suitable metalloenzymes, including order of ligand binding and modes of inhibition

Biomimetic Synthesis of the Crispatene Core

The biomimetic synthesis of the crispatene core is reported. The core framework was efficiently generated from an easily synthesized all (E)-tetraene precursor in one step, in good yield

Tuning the Cavity of Cyclodextrins: Altered Sugar Adaptors in Protein Pores

Cyclodextrins (CDs) have been widely used in host−guest molecular recognition because of their chiral and hydrophobic cavities. For example, β-cyclodextrin (βCD) lodged as a molecular adaptor in protein pores such as α-hemolysin (αHL) is used for stochastic sensing. Here, we have tuned the cavity and overall size of βCD by replacing a single oxygen atom in its ring skeleton by a disulfide unit in two different configurations to both expand our ability to detect analytes and understand the interactions of βCD with protein pores. The three-dimensional structures of the two stereoisomeric CDs have been determined by the combined application of NMR spectroscopy and molecular simulation and show distorted conformations as compared to natural βCD. The interactions of these synthetic βCD analogues with mutant αHL protein pores and guest molecules were studied by single-channel electrical recording. The dissociation rate constants for both disulfide CDs from the mutant pores show ∼1000-fold increase as compared to those of unaltered βCD, but are ∼10-fold lower than the dissociation rate constants for βCD from wild-type αHL. Both of the skeleton-modified CDs show altered selectivity toward guest molecules. Our approach expands the breadth in sensitivity and diversity of sensing with protein pores and suggests structural parameters useful for CD design, particularly in the creation of asymmetric cavities

GFA does not affect HCHO metabolism in <i>E</i>. <i>coli</i> cell lysate.

<p>(A) ¹H NMR (top) and 1D-¹³C-HSQC spectra (bottom) of <i>E</i>. <i>coli</i> BL21 (DE3) cell lysate (0.5 mg/mL in 50 mM Tris buffer pH 7.5) incubated with [¹³C]-HCHO (6 mM). Resonances in the 1D-HSQC spectra are annotated. [¹³C]-satellites for the Tris buffer are observed in the 1D-HSQC spectrum due to its high abundance of in the mixture. The doublet resonance at δ_H 3.25 ppm is assigned to methylamino groups from the lysate. Inset top left and bottom right: ¹H NMR spectra of <i>E</i>. <i>coli</i> BL21 (DE3) cell lysate (0.5 mg/mL in 50 mM Tris buffer pH 7.5) incubated with [¹³C]-HCHO (6 mM) over time. Production of ¹³C-formate (as indicated by the increase in intensity of the doublet resonance at δ_H 8.36 ppm, red top left) and [¹³C]-methanol (as indicated by the increase in intensity of the resonance at δ_H 3.36 ppm, red bottom right) are clearly observed. Only one half of the expected doublet resonance is observed for [¹³C]-methanol in the ¹H spectra due to overlap with the Tris buffer. Note: the relatively high initial [¹³C]-methanol level (relative to the level of [¹³C]-formate) is due to contamination of the commercial source of [¹³C]-HCHO (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145085#pone.0145085.s015" target="_blank">S15 Fig</a>). (B) ¹H NMR spectra of <i>E</i>. <i>coli</i> BL21 (DE3) cell lysate (0.5 mg/mL in 50 mM Tris buffer pH 7.5) incubated with GSH (4 mM) and [¹³C]-HCHO (6 mM) after 5 min (blue) and 45 min (red) respectively. [¹³C]-HMG (as indicated by the resonances at δ_H 2.96 ppm and δ_H 3.09 ppm) was most abundant over early time points and decreased during the experiment, which correlated with time-dependent formation of [¹³C]-formate, [¹³C]-methanol and GSH. Resonances corresponding to [¹³C]-HMG were poorly resolved in the time-course experiments without added GSH due to overlap with other resonances (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145085#pone.0145085.s016" target="_blank">S16 Fig</a>). (C) GFA does not affect the rate of formate production in <i>E</i>. <i>coli</i> cell lysate. Initial [¹³C]-formate production rate is dependent on the concentration of added [¹³C]-HCHO over the tested range; however, addition of recombinant GFA (20 μM) to the lysate before incubation with 1 mM [¹³C]-HCHO (green) does not affect the rate of [¹³C]-formate production (relative to the control without added enzyme, blue).</p

Anatomy of a Simple Acyl Intermediate in Enzyme Catalysis: Combined Biophysical and Modeling Studies on Ornithine Acetyl Transferase

Acyl-enzyme complexes are intermediates in reactions catalyzed by many hydrolases and related enzymes which employ nucleophilic catalysis. However, most of the reported structural data on acyl-enzyme complexes has been acquired under noncatalytic conditions. Recent IR analyses have indicated that some acyl-enzyme complexes may be more flexible than most crystallographic analyses have implied. OAT2 is a member of the N-terminal nucleophile (Ntn) hydrolase enzyme superfamily and catalyzes the reversible transfer of an acetyl group between the α-amino groups of ornithine and glutamate in a mechanism proposed to involve an acyl-enzyme complex. We have carried out biophysical analyses on ornithine acetyl transferase (OAT2), both in solution and in the crystalline state. Mass spectrometric studies identified Thr-181 as the residue acetylated during OAT2 catalysis; 13C NMR analyses implied the presence of an acyl-enzyme complex in solution. Crystallization of OAT2 in the presence of N-α-acetyl-l-glutamate led to a structure in which Thr-181 was acetylated; the carbonyl oxygen of the acyl-enzyme complex was located in an oxyanion hole and positioned to hydrogen bond with the backbone amide NH of Gly-112 and the alcohol of Thr-111. While the crystallographic analyses revealed only one structure, IR spectroscopy demonstrated the presence of two distinct acyl-enzyme complex structures with carbonyl stretching frequencies at 1691 and 1701 cm−1. Modeling studies implied two possible acyl-enzyme complex structures, one of which correlates with that observed in the crystal structure and with the 1691 cm−1 IR absorption. The second acyl-enzyme complex structure, which has only a single oxyanion hole hydrogen bond, is proposed to give rise to the 1701 cm−1 IR absorption. The two acyl-enzyme complex structures can interconvert by movement of the Thr-111 side-chain alcohol hydrogen away from the oxyanion hole to hydrogen bond with the backbone carbonyl of the acylated residue, Thr-181. Overall, the results reveal that acyl-enzyme complex structures may be more dynamic than previously thought and support the use of a comprehensive biophysical and modeling approach in studying such intermediates

α- and α′-Lithiation–Electrophile Trapping of <i>N</i>‑Thiopivaloyl and <i>N</i>-<i>tert</i>-Butoxythiocarbonyl α‑Substituted Azetidines: Rationalization of the Regiodivergence Using NMR and Computation

¹H NMR and computational analyses provide insight into the regiodivergent (α- and α′-) lithiation–electrophile trapping of <i>N</i>-thiopivaloyl- and <i>N</i>-(<i>tert</i>-butoxythiocarbonyl)-α-alkylazetidines. The magnitudes of the rotation barriers in these azetidines indicate that rotamer interconversions do not occur at the temperature and on the time scale of the lithiations. The NMR and computational studies support the origin of regioselectivity as being thiocarbonyl-directed lithiation from the lowest energy amide-like rotameric forms (<i>cis</i> for <i>N</i>-thiopivaloyl and <i>trans</i> for <i>N</i>-<i>tert</i>-butoxythiocarbonyl)

Highly (<i>E</i>)-Selective Wadsworth−Emmons Reactions Promoted by Methylmagnesium Bromide

An experimentally simple protocol for the very highly (E)-selective Wadsworth−Emmons reaction [(E):(Z) selectivities in excess of 180:1 in some cases] of a range of straight-chain and branched aliphatic, substituted aromatic, and base-sensitive aldehydes via reaction with an alkyl diethylphosphonoacetate and MeMgBr is reported