Differential isotope dansylation labeling combined with liquid chromatography mass spectrometry for quantification of intact and N-terminal truncated proteins

The N-terminal amino acids of proteins are important structure units for maintaining the biological function, localization, and interaction networks of proteins. Under different biological conditions, one or several N-terminal amino acids could be cleaved from an intact protein due to processes, such as proteolysis, resulting in the change of protein properties. Thus, the ability to quantify the N-terminal truncated forms of proteins is of great importance, particularly in the area of development and production of protein-based drugs where the relative quantity of the intact protein and its truncated form needs to be monitored. In this work, we describe a rapid method for absolute quantification of protein mixtures containing intact and N-terminal truncated proteins. This method is based on dansylation labeling of the N-terminal amino acids of proteins, followed by microwave-assisted acid hydrolysis of the proteins into amino acids. It is shown that dansyl labeled amino acids are stable in acidic conditions and can be quantified by liquid chromatography mass spectrometry (LC–MS) with the use of isotope analog standards.     

Reactivity Ratios and Sequence Distribution Characterization by Quantitative 13C NMR for RAFT Synthesis of Styrene‐Acrylonitrile Copolymers

The kinetics and reactivity ratios of styrene‐acrylonitrile (SA) copolymerization have been studied extensively in bulk and in a variety of solution media using conventional free radical polymerizations (FRPs). Due to the significant difference in the two reactivity ratios for this monomer pair, at certain feed ratios the copolymers display composition drift with conversion due to monomer depletion. In this study, the kinetics of SA copolymerization using Reversible Addition‐Fragmentation Chain Transfer (RAFT) has been studied in bulk at 80 °C. The reactivity ratios for the terminal model were calculated from the comonomer sequence distributions for the RAFT process at low conversion for nine different compositions and found to be in the same range as those reported for conventional FRP of SA. The changes in the composition and sequence distribution with conversion were studied for three feed compositions. The copolymers show compositional drift with conversion, except at the azeotropic composition, and match the predictions from the reactivity ratios obtained at low conversion. From quantitative ¹³C NMR the triad distributions of these copolymers were estimated and found to match the predicted triad distributions as conversion increased. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017 , 55, 919–927     

Microbial Screening of Copolymers of N‐Vinylimidazole with Phenacyl Methacrylate: Synthesis and Monomer Reactivity Ratios

N‐vinylimidazole (VIM), and phenacyl methacrylate (PAMA) copolymerized with different feed ratios using 1,4‐dioxane as a solvent and α,α'‐azobisisobutyronitrile (AIBN) as an initiator at 60°C. Structure and composition of copolymers for a wide range of monomer feed were determined by elemental analysis (content of N for VIM‐units) and by Fourier transform infrared spectroscopy through recorded analytical absorption bands for VIM (670 cm^?1 for C‐N of imidazole ring) and PAMA (1730 cm^?1 for C?O of ester group) units, respectively. Monomer reactivity ratios for VIM (M₁)‐PAMA (M₂) pair were determined by the application of conventional linearization methods such as Fineman‐Ross (F‐R) and Kelen‐Tüdös (KT) and a nonlinear error invariable model method using a computer program RREVM. The molecular weights (_w and _n) and polydispersity indices of the polymers were determined using gel permeation chromatography (GPC). Thermal behaviors of copolymers with various compositions were investigated by differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA). Also, the apparent thermal decomposition activation energies (ΔE_d) were calculated by Ozawa method using the SETARAM Labsys TGA thermobalance. The antibacterial and antifungal effects of polymers were also tested on various bacteria, fungi and yeast.     

Studies on Synthesis and Characterization of Charge Transfer Polymerization of Styrene and Alkyl Methacrylates

Abstract

Copolymers involving styrene and homologues of alkyl methacrylates (viz., methyl, ethyl, and butyl methacrylates) were synthesized at 60°C by employing a mixture of n‐butylamine and carbontetrachloride as charge transfer (CT) initiators in dimethyl sulphoxide medium. The CT complex was characterized by UV spectroscopy while the respective copolymers were characterized by employing infrared (IR) and ¹H NMR spectroscopy. The copolymer compositions were determined by using ¹H NMR spectroscopy and the reactivity ratios were computed by Fineman–Ross (F–R) and Kelen–Tudos (K–T) methods. The reactivity ratios of Sty‐MMA and Sty‐EMA copolymers indicate that higher level of styrene is incorporated in the copolymer. On the other hand the Sty‐BMA system exhibits different behavior. The higher value of r ₂ is obtained denoting that BMA is more active than styrene and hence, more BMA is present in the copolymer chain. In Sty‐MMA and Sty‐BMA systems, the product of r ₁ and r ₂ is greater than 1, representing the formation of high degree of random copolymers. However, in the case of Sty‐EMA, the product of r ₁ and r ₂ is less than 1 indicating the formation of alternating copolymer.     

Kinetic Study of Radical Polymerization VIII. A Comprehensive Study of Solution Copolymerization of Vinyl Acetate and Methyl Acrylate by 1H‐NMR Spectroscopy

Radical copolymerization reaction of vinyl acetate (VA) and methyl acrylate (MA) was performed in a solution of benzene‐d₆ using benzoyl peroxide (BPO) as the initiator at 60°C. Kinetic studies of this copolymerization reaction were investigated by on‐line ¹H‐NMR spectroscopy. Individual monomer conversions vs. reaction time, which was followed by this technique, were used to calculate the overall monomer conversion, as well as the monomer mixture and the copolymer compositions as a function of time. Monomer reactivity ratios were calculated by various linear and nonlinear terminal models and also by simplified penultimate model with r _2(VA)=0 at low and medium/high conversions. Overall rate coefficient of copolymerization was calculated from the overall monomer conversion vs. time data and k _p  . k _t ^?0.5 was then estimated. It was observed that k _p  . k _t ^?0.5 increases with increasing the mole fraction of MA in the initial feed, indicating the increase in the polymerization rate with increasing MA concentration in the initial monomer mixture. The effect of mole fraction of MA in the initial monomer mixture on the drifts in the monomer mixture and copolymer compositions with reaction progress was also evaluated experimentally and theoretically.     

Copolymerization of 4‐Propanoylphenyl Acrylate with Methyl Methacrylate: Synthesis,Characterization and Reactivity Ratios

The new acrylic monomer 4‐propanoylphenyl acrylate (PPA) was synthesized and copolymerized with methyl methacrylate (MMA) in methyl ethyl ketone at 70±1°C using benzoyl peroxide as a free radical initiator. The copolymers were characterized by FT‐IR, ¹H‐NMR and ¹³C‐NMR spectroscopic techniques. The compositions of the copolymers were determined by ¹H‐NMR analysis. The reactivity ratios of the monomers were determined using Fineman‐Ross (r₁=0.5535 and r₂=1.5428), Kelen‐Tüdös (r₁=0.5307 and r₂=1.4482), and Ext. Kelen‐Tüdös (r₁=0.5044 and r₂=1.4614), as well as by a nonlinear error‐in‐variables model (EVM) method using a computer program, RREVM (r₁=0.5314 and r₂=1.4530). The solubility of the polymers was tested in various polar and non‐polar solvents. The elemental analysis was determined by a Perkin‐Elmer C‐H analyzer. The molecular weights (M_w and M_n) of the copolymers were determined by gel permeation chromatography. Thermogravimetric analysis of the polymers reveals that the thermal stability of the copolymers increases with an increase in the mole fraction of MMA in the copolymers. Glass transition temperatures of the copolymers were found to increase with an increase in the mole fraction of MMA in the copolymers.     

Automation of dimethylation after guanidination labeling chemistry and its compatibility with common buffers and surfactants for mass spectrometry-based shotgun quantitative proteome analysis

Isotope labeling liquid chromatography–mass spectrometry (LC–MS) is a major analytical platform for quantitative proteome analysis. Incorporation of isotopes used to distinguish samples plays a critical role in the success of this strategy. In this work, we optimized and automated a chemical derivatization protocol (dimethylation after guanidination, 2MEGA) to increase the labeling reproducibility and reduce human intervention. We also evaluated the reagent compatibility of this protocol to handle biological samples in different types of buffers and surfactants. A commercially available liquid handler was used for reagent dispensation to minimize analyst intervention and at least twenty protein digest samples could be prepared in a single run. Different front-end sample preparation methods for protein solubilization (SDS, urea, Rapigest™, and ProteaseMAX™) and two commercially available cell lysis buffers were evaluated for compatibility with the automated protocol. It was found that better than 94% desired labeling could be obtained in all conditions studied except urea, where the rate was reduced to about 92% due to carbamylation on the peptide amines. This work illustrates the automated 2MEGA labeling process can be used to handle a wide range of protein samples containing various reagents that are often encountered in protein sample preparation for quantitative proteome analysis.     

Studies on the Uptake of Rare Earth Elements on Polyacrylamidoxime Resins from Natural Concentrate Leachate Solutions

Synthesis of poly(acrylamidoxime) resin from polyacrylonitrile performed with different crosslinking ratios 2, 5, and 10 wt% of divinylbenzene as crosslinking agent, using methylbenzoate and dioctylphthalate as pore producing solvent, the reaction mixture occurred under nitrogen. Studies carried out on diluted solution from rare earth elements (REEs) concentrate contains impurities as Cu²⁺, Ni²⁺, Zn²⁺, Fe³⁺, Al³⁺, Si⁴⁺, Th⁴⁺, U⁶⁺, Ca²⁺, and K⁺. Changing some parameters as pH of the solution, time of feeding and type of acid as HCl, HNO₃, H₂SO₄. The adsorption efficiency of resin is in the order pH 6 > pH 5 > pH 4 > pH 2 with excluding pH 6 due to the precipitation of some of REEs with the impurities and complete precipitation of Dy ion during pH adjustment, the adsorption in HNO₃ > HCl > H₂SO₄ media.     

Accurate measurement of uranium isotope ratios in soil samples using thermal ionization mass spectrometry equipped with a warp energy filter

A chemical and mass-spectrometric procedure for uranium isotopic analysis using a thermal ionisation mass spectrometer equipped with a Wide Aperture Retardation Potential energy filter has been developed and applied to uranium isotopic measurements for various soil samples. Soil samples were digested using a microwave digestor. Uranium was isolated from soil samples by the chemical separation procedure based on the use of anion-exchange resin and UTEVA extraction chromatography column. The isotope ratios were measured for two certified reference materials by using a VG Sector 54-30 thermal ionisation mass spectrometer in dynamic mode with Faraday cup and Daly ion counting system. Replicates of standard reference materials showed excellent analytical agreement with established values supporting the reliability and accuracy of the method. Precision of the ²³⁵U/²³⁸U ratio was achieved by a correction factor of 0.22% amu as a function of ion-beam intensity with sample loads of around 250?ng of U. The resulting reproducibility for standards and soil samples was better than 0.2% at two standard deviations (SD). Uranium isotopic compositions have been determined in several reference soil samples such as Buffalo river sediment, NIST 2704, river sediment SRM 4350b and ocean sediment NIST-4357 and a Chernobyl soil sample. There was a significant deviation from the natural uranium in comparison with Chernobyl soil samples.     

A Spectroscopic Overview of Intramolecular Hydrogen Bonds of NH…O,S,N Type

Intramolecular NH…O,S,N interactions in non-tautomeric systems are reviewed in a broad range of compounds covering a variety of NH donors and hydrogen bond acceptors. ¹H chemical shifts of NH donors are good tools to study intramolecular hydrogen bonding. However in some cases they have to be corrected for ring current effects. Deuterium isotope effects on ¹³C and ¹⁵N chemical shifts and primary isotope effects are usually used to judge the strength of hydrogen bonds. Primary isotope effects are investigated in a new range of magnitudes. Isotope ratios of NH stretching frequencies, νNH/ND, are revisited. Hydrogen bond energies are reviewed and two-bond deuterium isotope effects on ¹³C chemical shifts are investigated as a possible means of estimating hydrogen bond energies.