Proteins and peptides voltammetry: Trends,potential, and limitations

Numerous biological processes are connected with the efficient electron transfer reactions in proteins and peptides. In this review, we discuss briefly the relevance and current challenges associated with the voltammetric analysis of peptides and proteins with and without a metal redox center. Special attention is paid to the integration of electrochemical methods with new nanomaterials which offers amplification of multiplexing capabilities for simultaneous and very sensitive examination of various proteins. After critically discussing the most interesting approaches in the proteins/peptides voltammetric analysis reported so far, for the single or multiplexed examination of such biomolecules with demonstrated applicability in the real-sample analysis, existing challenges still need to be addressed and future directions in this field will be pointed out.     

NMR spectra of salicylohydroxamic acid in DMSO-d6 solution: a DFT study

The ¹H, ¹³C and ¹H, ¹³C COSY NMR spectra of salicylohydroxamic acid (sha) were measured in DMSO-d₆ solution. The B3LYP GIAO method with the 6-311++G(d,p) basis set was chosen to reproduce the experimental spectra. All possible zusammen and entgegen conformers of monomeric sha were computed. After geometry optimisation (B3LYP/6-311++G(d,p)) only nine independent models of the molecule were shown to be stable. Additionally, the NMR chemical shifts of the Onsager model of the most stable monomer were calculated. The computed chemical shifts for the labile protons for all aforementioned geometries meaningfully underestimated experimental results suggesting the existence of the H-bonded structure of sha in DMSO solution. The most probable two dimeric structures along with two solvent-bounded aggregates were subsequently calculated at the same level of theory. The best agreement was obtained for sha H-bonded with two DMSO molecules (confirmed by the absence of concentration effect). The relative error not exceeding 10 and 4% for chemical shifts in ¹H and ¹³C NMR spectra of sha–(DMSO)₂, respectively, showed that the applied method with the B3LYP/6-311++G(d,p) basis set was efficient to predict the NMR shifts of a compound with strong H-bonds. Thus, this allows to assign properly NMR resonances to specific structure formed in DMSO solution.     

Origins of the activity of PAL and LAP enzyme inhibitors: toward ab initio binding affinity prediction

Interaction energies of phenylalanine ammonia-lyase (PAL) active site residues with a series of PAL inhibitors have been partitioned into electrostatic, exchange, delocalization, and correlation components and compared with analogous results obtained previously for leucine aminopeptidase (LAP). In the latter metalloenzyme, either of the two charged residues controls entirely relative inhibitor binding energies, while at least four residues are required to determine ligand relative stabilization in neutral PAL. Significant correlation with experimental inhibitory activity was found between the stabilization energy at gradually decreasing levels of theory (MP2, SCF) down to the first-order Heitler-London term. Contrary to the LAP case, where the electrostatic term was sufficient to reproduce experimentally observed trends, in the case of PAL, exchange repulsion effects also have to be considered. Computational protocol presented herein constitutes a promising way to incorporate the first principle calculation's accuracy into the process of rational binding affinity prediction, revealing the physical nature of the interactions, where successive approximations can be introduced in a systematic and justifiable manner.     

Solubility of Solid 2,3-Dimethylbutane and Cyclopentane in Liquid Argon and Nitrogen at the Standard Boiling Points of the Solvents

The solubilities of solid 2,3-dimethylbutane and cyclopentene in liquid argon at a temperature of 87.3 K and in liquid nitrogen at 77.4 K have been measured by the filtration method. The hydrocarbon contents in solutions were determined using gas chromatography. GC–MS was used to identify impurities in solutes. The experimental value of the mole fraction solubility of solid 2,3-dimethyl-butane in liquid argon at 87.3 K is (8.26 ± 1.60) × 10^–6 and (2.77 ± 0.94) × 10^–8 in liquid nitrogen at 77.4 K. The experimental value of the mole fraction solubility of solid cyclopentene in liquid argon at 87.3 K is (5.11 ± 0.44) × 10^–6 and (4.60 ± 0.76) × 10^–8 in liquid nitrogen at 77.4 K. The Preston–Prausnitz method was used for calculation of the solubilities of solid hydrocarbons in liquid argon in the temperature range 84.0–110.0 K and in liquid nitrogen from 64.0 to 90.0 K. The solvent–solute interaction parameters l ₁₂ were also calculated. At 90.0 K liquid argon is a better solvent for investigated solid hydrocarbons than is liquid nitrogen.     

A Curtin–Hammett pentamethylene chain symmetrization process in the Bergman cyclization of an 11‐membered ring enediyne

Pentamethylene chain conformational effects for the Bergman cyclization of the 11‐membered ring enediyne, (3Z)‐3‐cycloundecene‐1,5‐diyne, 2, are examined theoretically with unrestricted Becke, three‐parameter, Lee–Yang–Parr/6‐31 G(d,p) calculations. A C₁ symmetric enediyne conformation was found to be the global minimum, where its nonsymmetric pentamethylene chain prevented π‐orbital alignment of the acetylene groups for C–C σ bond product formation. The Bergman cyclization of 2 was found to be conformationally dependent. In a Curtin–Hammett type process, the C₁ symmetric 2 inverts to one of the C_S or C₂ symmetric conformers required for the Bergman cyclization, which produced a C_S or C₂ symmetric 1,4‐diradical intermediate. The activation energy for the cyclization is slightly higher to reach the C₂ symmetry diradical compared with the C_S symmetry diradical. Copyright © 2012 John Wiley & Sons, Ltd.     

Butylated hydroxytoluene enediyne: access to diradical and electrophilic quinone methide intermediates

A theoretical study was carried out on the unimolecular reaction of an enediyne with a fused butylated hydroxytoluene to internally scavenge the p‐benzyne diradical sites formed after the Bergman cyclization. The calculations revealed that the conversion of the p‐benzyne diradical (2‐tert‐butyl‐4‐methyl‐5,8‐didehydro‐1‐naphthalenol) to p‐quinone methide is favored over the conversion to a phenoxy/benzene diradical 4 in an approximate 95:5 ratio. Based on this model, the Bergman cyclization leads in a bifunctional manner to intermediates for competing reactivity with intermolecular H‐atom abstraction. Copyright © 2015 John Wiley & Sons, Ltd.     

Ochratoxin A and 2′R-Ochratoxin A in Selected Foodstuffs and Dietary Risk Assessment

The aim of this study was to estimate the contamination of grain coffee, roasted coffee, instant coffee, and cocoa purchased in local markets with ochratoxin A (OTA) and its isomerization product 2′R-ochratoxin A (2′R-OTA), and to assess risk of dietary exposure to the mycotoxins. OTA and 2′R-OTA content was determined using the HPLC chromatography with immunoaffinity columns dedicated to OTA. OTA levels found in all the tested samples were below the maximum limits specified in the European Commission Regulation EC 1881/2006. Average OTA concentrations calculated for positive samples of grain coffee/roasted coffee/instant coffee/cocoa were 0.94/0.79/3.00/0.95 µg/kg, with the concentration ranges: 0.57–1.97/0.44–2.29/0.40–5.15/0.48–1.97 µg/kg, respectively. Average 2′R-OTA concentrations calculated for positive samples of roasted coffee/instant coffee were 0.90/1.48 µg/kg, with concentration ranges: 0.40–1.26/1.00–2.12 µg/kg, respectively. In turn, diastereomer was not found in any of the tested cocoa samples. Daily intake of both mycotoxins with coffee/cocoa would be below the TDI value even if the consumed coffee/cocoa were contaminated with OTA/2′R-OTA at the highest levels found in this study. Up to now only a few papers on both OTA and 2′R-OTA in roasted food products are available in the literature, and this is the first study in Poland.