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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Dynamics of ions produced by laser ablation of ceramic Al<Subscript>2</Subscript>O<Subscript>3</Subscript> and Al at 193 nm

We study the dynamics of ions produced upon ablation of Al and ceramic Al₂O₃ targets using nanosecond laser pulses at 193 nm (6.4 eV) as a function of the laser fluence from threshold up to 12 J cm⁻². An electrical (Langmuir) probe located at 40 mm from the target surface has been used for determining the ion yield and calculating the kinetic energy distributions. The results for both targets show the existence of a significant amount of ions having kinetic energies >200 eV (≈20% around threshold fluence), and kinetic energies are up to >1.5 keV. The results are related with the existence of direct photonionization processes caused by the photon energy of the laser being higher than the ionization potential of Al (5.98 eV). Comparison of the ion yield when ablating the two types of targets for fluences above threshold to data reported in the literature suggests that the magnitude of the yield and its threshold are parameters depending on the thermal properties of the target rather than on the laser wavelength. Around threshold, the different behavior of ion yield when ablating Al and Al₂O₃ targets suggests that the threshold for neutral aluminium and ion species in the case of ablation of the Al₂O₃ target must be similar.     

Zinc and Cobalt Complexes Derived from Tetradentate Tripodal Ligands with N2O2 Donorset as Model Compounds for Phosphatases

Starting from the tripodal tetradentate ligands ‐(3,5‐dibromo‐2‐hydroxybenzyl)(2‐hydroxybenzyl)(2‐pyridyl)methylamine (H₂L1), (3,5‐dibromo‐2‐hydroxybenzyl)(2‐hydroxy‐5‐nitrobenzyl)(2‐pyridyl)methylamine (H₂L2), and (3,5‐dichloro2‐hydroxybenzyl)(2‐hydroxy‐5‐nitrobenzyl)(2‐pyridyl)methylamine (H₂L3) the new isostructural dinuclear zinc compounds [Zn₂(L1)₂]·N(CH₂CH₃)₃ ( 1 ), [Zn₂(L2)₂]·2CH₃OH ( 2 ) and [Zn₂(L3)₂]·C₄H₁₀O ( 3 ) were synthesized. Due to their enzyme‐like trigonal bipyramidal N₂O₃ coordination environment of the zinc ions and the similar Zn···Zn distances the complexes can be considered to be structural models for the active sites in phospholipase C and nuclease P1. With H₂L3 also the dinuclear complex [Co₂(L2)₂(CH₃OH)]·2CH₃OH·0.5C₄H₁₀O ( 4 ) could be prepared. The new compounds were isolated and characterized by single crystal X‐ray crystallography as well as infrared spectroscopy. The cobalt compound 4 was additionally characterized by UV‐Vis spectroscopy and magnetic measurements. 1 crystallizes in the monoclinic space group P2₁/n with a = 11.2814(2), b = 28.6154(2), c = 13.1866(3) Å, β = 96.995(1)°, V = 4225.2(2) ų, Z = 4. 2 and 3 are monoclinic, space group C2/c with a = 23.084(5), b = 9.232(2), c = 21.849(4) Å, &β; = 96.83(3)°, V = 4623(2) ų, Z = 4, and a = 22.7834(3), b = 9.2463(1), c = 21.6351(3) Å, &β; = 97.592(1)°, V = 4517.7(2) ų, Z = 4, respectively. 4 crystallizes in the monoclinic space group I2/a with a = 22.4680(4), b = 20.5517(4), c = 22.8910(6) Å, &β; = 111.938(1)°, V = 9804.7(4) ų, Z = 8. 4 shows an effective magnetic moment of 6.72 μ_B at 300 K which clearly indicates the presence of two cobalt(II) high spin ions with Curie‐Weiss behaviour above 80 K. At lower temperatures a decrease of the effective magnetic moment was observed.     

Liquid chromatographic analysis of nucleosides and their mono-, di- and triphosphates using porous graphitic carbon stationary phase coupled with electrospray mass spectrometry

Analysis of nucleosides and nucleotides is desirable in many biological studies, but the task is analytically challenging due to the high polarity of the analytes. In this study, resolution of mixtures containing nucleosides and their mono-, di- and triphosphates was achieved using a porous graphitic carbon (PGC) stationary phase, Hypercarb, under conditions suitable for liquid chromatography/mass spectrometry (LC/MS). Different organic mobile phases and modifiers were evaluated and the separation of 16 nucleosides and nucleotides was optimized using gradient elution with a water/acetonitrile mobile phase containing ammonium acetate and diethylamine as modifiers. The ammonium acetate concentration proved to be critical for retention and diethylamine was found to improve the peak shapes of di- and triphosphates for mass spectrometric detection. A variety of silica-based columns designed for polar compound separation were also tested using optimized LC conditions and compared with results obtained with the Hypercarb column. Only the Hypercarb column provided separations suitable for accurate quantitation of mixed nucleosides and their phosphates.     

Optimal echo spacing for multi-echo imaging measurements of Bi-exponential T2 relaxation

Calculations, analytical solutions, and simulations were used to investigate the trade-off of echo spacing and receiver bandwidth for the characterization of bi-exponential transverse relaxation using a multi-echo imaging pulse sequence. The Cramer–Rao lower bound of the standard deviation of the four parameters of a two-pool model was computed for a wide range of component T₂ values and echo spacing. The results demonstrate that optimal echo spacing (TE_opt) is not generally the minimal available given other pulse sequence constraints. The TE_opt increases with increasing value of the short T₂ time constant and decreases as the ratio of the long and short time constant decreases. A simple model of TE_opt as a function of the two T₂ time constants and four empirically derived scalars is presented.     

Utilization of waste seashells and Camelina sativa oil for biodiesel synthesis

The seafood industry produces over 100 million pounds of seashell waste every year. With landfill space diminishing quickly, ways to recycle waste materials are becoming more sought for. Herein, we utilized waste mussel, clam and oyster shells as heterogeneous catalysts for the transesterification of Camelina sativa oil as a feedstock into biodiesel. Camelina sativa oil provides a reliable solution for biodiesel production because it has high tolerance of cold weather, drought, low-fertility soils and contains approximately 40% oil content. The catalysts from waste seashells were characterized by X-ray powder diffraction and Fourier transform infrared (FTIR) spectroscopy. High biodiesel yields were achieved at a 12:1 (alcohol:oil) molar ratio with 1?wt.% waste seashell catalysts in 2?h at 65°C. Biodiesel was analyzed by ¹H NMR and FTIR spectroscopy and the fuel properties of the biodiesel produced from Camelina sativa oil and waste seashells were compared with American Society for Testing and Materials standards.     

Enantioseparations of non-benzenoid and oligo-Tröger’s bases by HPLC on Whelk O1 column

The separation of enantiomers of several ‘bis- and tris-Tröger’s bases’ by HPLC on commercially available chiral stationary phase Whelk O1 is described for the first time. The observed structure–enantioselectivity relationships are in agreement with the previously established molecular recognition model. For all ‘bis- and tris-Tröger’s bases’ studied, satisfactory to excellent enantioselectivities were observed.