Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein–ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein–ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.     

Solvent Effects on Acrylate kp in Organic Media?—A Systematic PLP–SEC Study

The Arrhenius parameters of the propagation rate coefficient, k_p, are determined employing high‐frequency pulsed laser polymerization–size exclusion chromatography (PLP–SEC) for the homologous series of five linear alkyl acrylates (i.e., methyl acrylate (MA), butyl acrylate (BA), dodecyl acrylate (DA), stearyl acrylate (SA), and behenyl acrylate (BeA)) in 1 m solution in butyl acetate (BuAc) as well as in toluene. The comparison of the obtained k_p values with the literature known values for bulk demonstrates that no significant solvent influence neither in BuAc nor in toluene on the propagation reaction compared to bulk is detectable. Concomitantly, the k_p values in toluene and in BuAc solution display a similar increase with increasing number of C‐atoms in the ester side chain as was previously reported for the bulk systems. These findings are in clear contrast to earlier studies, which report a decrease of k_p with increasing ester side chain length in toluene. The additional investigation of the longest and shortest ester side chain acrylate (i.e., BeA and MA) over the entire experimentally available concentration range at one temperature (i.e., 50 °C) does not reveal any general concentration dependence and all observed differences in the k_p are within the experimental error.

     

Are calculated enthalpies of formation sometimes more reliable than experimental? A test on alkyl substituted benzoic acids

Energies of 20 alkyl-substituted benzoic acids were calculated at the levels B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p) and MP2/6-311+G(d,p)//MP2/6-311+G(d,p); the pertinent enthalpies at 298 K were calculated at the same levels. Comparison with experimental enthalpies of formation Delta(f)H degrees (g)(298) was carried out in terms of isodesmic reactions, that is, in the relative values. Of the four calculated quantities, the DFT enthalpies yielded best correlation with the standard deviation of 2.1 kJ mol(-1), near to the experimental uncertainty; the DFT energies are only slightly worse and the MP2 enthalpies or energies much worse. However, the DFT method overestimated systematically the substituent effects and had to be calibrated. Comparison with the experimental gas-phase acidities was less telling and the fit was worse because both methods overestimated the substituent effects. Extending the base in selected examples did not give better results. Although the systematic deviations are evidently due to the imperfections of the theoretical models, individual big deviations should be attributed to experimental errors or to the abnormal behavior of certain compounds at the experimental conditions. From this point of view, three examples of the so-called long-range effect claimed in the case of different benzoic acid derivatives, always for substituents in the meta position, must be refused as unproven because the experimental energies were not confirmed by calculations.     

A Sterically Overcrowded,Isopropyl-Substituted,Lanthanide-Chelating Tag for Protein Pseudocontact Shift NMR Spectroscopy: Synthesis of its Macrocyclic Scaffold and Benchmarking on Ubiquitin S57 C and hCA II S166 C

A sterically overcrowded lanthanide-chelating tag has been synthesized in order to investigate the influence on the obtained pseudocontact shifts and the anisotropic part of the magnetic susceptibility tensor compared to those of its predecessor DOTA-M8-(4R,4S)-SSPy. For the first time, a concise synthetic route is presented for isopropyl-substituted cyclen, the macrocyclic scaffold of the lanthanide-chelating tag, delivering the macrocycle in an overall yield of 6 % over 11 steps. The geometry of the lutetium complex has been assigned by ROESY experiments, adopting exclusively a Λ(δδδδ) conformation, and DFT calculations have confirmed a stabilization of 32.6 kJ mol⁻¹ compared to the Δ(δδδδ) conformer. The highly rigidified lanthanide-chelating tag induces strong pseudocontact shifts of up to 6.5 ppm on ubiquitin S57 C, shows significantly improved tensor properties compared to those of its predecessor, and constitutes a highly promising starting point for the further development of lanthanide-chelating tags.     

Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05‐2X computational study

The reduction and oxidation properties of four nitrocompounds (trinitrotoluene [TNT], 2,4‐dinitrotoluene, 2,4‐dinitroanisole, and 5‐nitro‐2,4‐dihydro‐3H‐1,2,4‐triazol‐3‐one [NTO]) dissolved in water as compared with the same properties for compounds adsorbed on a silica surface were studied. To consider the influence of adsorption, cluster models were developed at the M05/tzvp level. A hydroxylated silica (001) surface was chosen to represent a key component of soil. The PCM(Pauling) and SMD solvation models were used to model water bulk influence. The following properties were analyzed: electron affinity, ionization potential, reduction Gibbs free energy, oxidation Gibbs free energy, and reduction and oxidation potentials. It was found that adsorption and solvation decrease gas phase electron affinity, ionization potential, and Gibbs free energy of reduction and oxidation, and thus, promote redox transformation of nitrocompounds. However, in case of solvation, the changes are more significant than for adsorption. This means that nitrocompounds dissolved in water are easier to transform by reduction or oxidation than adsorbed ones. Among the considered compounds, TNT was found to be the most reactive in an electron attachment process and the least reactive for an electron detachment transformation. During ionization, a deprotonation of adsorbed NTO was found to occur. © 2015 Wiley Periodicals, Inc.