Locating hydrogen atoms in single crystal and uniaxially aligned amino acids by solid-state NMR

We demonstrate a novel method to locate hydrogen atoms in amino acids, which involves measuring the C(alpha)H(alpha) bond vector geometry through orientationally dependent dipolar coupling frequencies measured by Lee-Goldburg cross polarization (LGCP). A 2D LGCP experiment is used to measure the polar angle of the C(alpha)H(alpha) bond vector in a single crystal of the model compound L-alanine. It is also demonstrated that by coupling the 13C(alpha)1H(alpha) LGCP experiment to a 13C(alpha)15N REDOR experiment, one can determine the complete three-dimensional geometry of the C(alpha)H(alpha) and C(alpha)N vectors in a single crystal. These measurements allow for location of hydrogen atoms in crystalline biological macromolecules.     

Fast Photochemical Oxidation of Proteins (FPOP) Maps the Epitope of EGFR Binding to Adnectin

Epitope mapping is an important tool for the development of monoclonal antibodies, mAbs, as therapeutic drugs. Recently, a class of therapeutic mAb alternatives, adnectins, has been developed as targeted biologics. They are derived from the 10th type III domain of human fibronectin (¹⁰Fn3). A common approach to map the epitope binding of these therapeutic proteins to their binding partners is X-ray crystallography. Although the crystal structure is known for Adnectin 1 binding to human epidermal growth factor receptor (EGFR), we seek to determine complementary binding in solution and to test the efficacy of footprinting for this purpose. As a relatively new tool in structural biology and complementary to X-ray crystallography, protein footprinting coupled with mass spectrometry is promising for protein–protein interaction studies. We report here the use of fast photochemical oxidation of proteins (FPOP) coupled with MS to map the epitope of EGFR-Adnectin 1 at both the peptide and amino-acid residue levels. The data correlate well with the previously determined epitopes from the crystal structure and are consistent with HDX MS data, which are presented in an accompanying paper. The FPOP-determined binding interface involves various amino-acid and peptide regions near the N terminus of EGFR. The outcome adds credibility to oxidative labeling by FPOP for epitope mapping and motivates more applications in the therapeutic protein area as a stand-alone method or in conjunction with X-ray crystallography, NMR, site-directed mutagenesis, and other orthogonal methods. Figure

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Enzymatic Conversion of Flavonoids using Bacterial Chalcone Isomerase and Enoate Reductase

Flavonoids are a large group of plant secondary metabolites with a variety of biological properties and are therefore of interest to many scientists, as they can lead to industrially interesting intermediates. The anaerobic gut bacterium Eubacterium ramulus can catabolize flavonoids, but until now, the pathway has not been experimentally confirmed. In the present work, a chalcone isomerase (CHI) and an enoate reductase (ERED) could be identified through whole genome sequencing and gene motif search. These two enzymes were successfully cloned and expressed in Escherichia coli in their active form, even under aerobic conditions. The catabolic pathway of E. ramulus was confirmed by biotransformations of flavanones into dihydrochalcones. The engineered E. coli strain that expresses both enzymes was used for the conversion of several flavanones, underlining the applicability of this biocatalytic cascade reaction.     

Stereospecific and Chemoselective Copper‐Catalyzed Deaminative Silylation of Benzylic Ammonium Triflates

A method for the synthesis of benzylsilanes starting from the corresponding ammonium triflates is reported. Silyl boronic esters are employed as silicon pronucleophiles, and the reaction is catalyzed by copper(I) salts. Enantioenriched benzylic ammonium salts react stereospecifically through an S_N2‐type displacement of the ammonium group to afford α‐chiral silanes with inversion of the configuration. A cyclopropyl‐substituted substrate does not undergo ring opening, thus suggesting an ionic reaction mechanism with no benzyl radical intermediate.     

Dependence of calibration sensitivity of a polysulfone/Ru(II)-tris(4,7-diphenyl-1,10-phenanthroline)-based oxygen optical sensor on its structural parameters

The optimum performance of an optical oxygen sensor based on polysulfone (PSF)/[Ru(II)-Tris(4,7-diphenyl-1,10-phenanthroline)] octylsulfonate (Ru(dpp)OS) was checked by carefully tuning the parameters affecting the membrane preparation. In particular, membranes having thickness ranging between 0.2 and 8.0 μm with various luminophore concentrations were prepared by dip-coating and tested. The membrane thickness was controlled by tuning the solution viscosity, and was measured both by secondary ion mass spectrometry (SIMS) and by visible spectroscopy (Vis). Luminescence-quenching-based calibration was a single value of the Stern-Volmer constant (K^′SV) for membranes containing up to 20 mmol Ru(dpp) g⁻¹ PSF (1.35 μm average thickness). The K^′SV value decreased for larger concentration. The highest sensitivity was obtained with membrane thickness around 1.6 μm, having a response time close to 1 s. Thicker membranes exhibited an emission saturation effect and were characterized by longer response time. The K^′SV behavior was interpreted on the basis of a mathematical approach accounting for the contribution of luminescence lifetime (τ₀), oxygen diffusion coefficient (DO₂) and oxygen solubility inside the membrane (sO₂) establishing the role of all of them and allowing their experimental determination. Moreover, a simple experimental way to estimate K^′SV without needing calibration was proposed. It was based either on the light emission asymmetry or on the percent variation of light emission on passing from pure nitrogen to pure oxygen.     

Gas-phase anionic complexes of alkali metal ions and peptides: Structure and collision activated decompositions

Alkali metal ions and anionic peptides can be desorbed into the gas phase to give metal-bound peptides and bis(peptide) complexes bearing a ? 1 charge. Although amide nitrogens of peptide bonds are deprotonated in the gas phase by alkali metal ions, this reacion does not occur in solution. Metal-bound dipeptide anions exist as a single structure, whereas those of tripeptide complexes have three structures as revealed by tandem mass spectrometric studies. Ions of bis(peptide) complexes of alkali metals decompose upon collisional activation principally to form deprotonated peptides, in contrast to bis(peptide) complexes of alkaline earth metal ions, which undergo elimination of a neutral peptide.     

Fast-atom bombardment and tandem mass spectrometry of macrolide antibiotics

Molecular weights of macrolide antibiotics can be determined from either (M + H)⁺ or (M + Met)⁺, the latter desorbed from alkali metal salt-saturated matrices. The ion chemistry of macrolides, as determined by tandem mass spectrometry (MS/MS), is different for ions produced as metallated than those formed as (M + H)⁺ species. An explanation for these differences is the location of the charge. For protonated species, the charge is most likely situated on a functional group with high proton affinity, such as the dimethylamino group of the ammo sugar. The alkali metal ion, however, is bonded to the highly oxygenated aglycone. As a result, the collision-activated dissociation spectra of protonated macrolides are simple with readily identifiable fragment ions in both the high and low mass regions but no fragments in the middle mass range. In contrast, the cationized species give complex spectra with many abundant ions, most of which are located in the high mass range. The complementary nature of the fragmentation of these two species recommends the study of both by MS/MS when determining the structure or confirming the identity of these biomaterials.     

High pressure trapping in Fourier transform mass spectrometry: A radiofrequency-only-mode event

A new event for the Fourier transform mass spectrometry (FTMS) sequence is developed and demonstrated. During this event, called a radiofrequency (RF)-only mode event, the typical passive cubic trap of a Fourier transform mass spectrometer is made to operate as an active quadrupole ion trap. The transition between active and passive modes is developed so that ion loss as a consequence of the transition can be held to 15% or less. The adduct of the ion-molecule reaction of the 1,3-butadiene radical cation and methyl vinyl ether was detected during the Rf-only-mode event at a helium pressure of ～1×10^?3 torr even though this adduct is not detectable under standard FTMS operating conditions.