Evaluation and comparison of n‐alkyl chain and polar ligand bonded stationary phases for protein separation in reversed‐phase liquid chromatography

Protein retention is very sensitive to the change of solvent composition in reversed‐phase liquid chromatography for so called “on–off” mechanism, leading to difficulty in mobile phase optimization. In this study, a novel 3‐chloropropyl trichlorosilane ligand bonded column was prepared for protein separation. The differences in retention characteristics between the 3‐chloropropyl trichlorosilane ligand bonded column and n‐alkyl chain modified (C₂, C₄, C₈) stationary phases were elucidated by the retention equation . Retention parameters (a and c) of nine standard proteins with different molecular weights were calculated by using homemade software. Results showed that retention times of nine proteins were similar on four columns, but the 3‐chloropropyl trichlorosilane ligand bonded column obtained the lowest retention parameter values of larger proteins. It meant that their retention behavior affected by acetonitrile concentration would be different due to lower |c| values. More specifically, protein elution windows were broader, and retentions were less sensitive to the change of acetonitrile concentration on the 3‐chloropropyl trichlorosilane ligand bonded column than that on other columns. Meanwhile, the 3‐chloropropyl trichlorosilane ligand bonded column displayed distinctive selectivity for some proteins. Our results indicated that stationary phase with polar ligand provided potential solutions to the “on–off” problem and optimization in protein separation.     

Rapid determination of globin chains in red blood cells by capillary electrophoresis using INSTCoated fused‐silica capillary

A laboratory‐made INSTCoated fused‐silica capillary has been newly used for CE separation of four mixtures of proteins in sodium phosphate BGEs at pH 3.0 and 2.5, respectively. The obtained separation efficiencies range from 145 000 theoretical plates per meter for myoglobin to 1 216 000 m^?1 for lysozyme. A total of 49–89% of the number of theoretical plates was obtained in a commercial polyvinyl alcohol coated capillary compared to the INSTCoated capillary under the same experimental conditions, 0–86% was obtained in a laboratory polyacrylamide‐coated capillary, and only 0–6% was obtained in an uncoated fused‐silica capillary. The RSD values for the intraday repeatability for an INSTCoated capillary were 0.1–1.0% (migration time) and 0.3–2.4% (peak area); RSD values for the interday repeatability in the same capillary are 0.6–1.4% (migration time) and 2.4–5.5% (peak area); RSD values for interday repeatability between different capillaries equaled 1.7–2.1% (migration time) and 2.8–10.9% (peak area). The INSTCoated capillary has been further used for rapid determination of globin chains isolated from red blood cells. A separation of α and β chains prepared from adult blood has been completed in 3 min with a peak resolution of 1.3, and the separation of α and ^Gγ chains prepared from newborn blood took 3 min with a peak resolution of 3.6.     

On‐chip protein isoelectric focusing using a photoimmobilized pH gradient†

An immobilized pH gradient was directly constructed on the inner wall of a microfluidic chip channel by photoimmobilizing focused carrier ampholytes onto the wall. A mixture of carbonic anhydrase, myoglobin, and trypsin inhibitor was successfully isoelectric‐focused and separated with good linearity between the pI values of proteins and the location of the focused bands. Furthermore, coating methods for the resistance of protein nonselective adsorption and simultaneously for pH gradient photocoupling were screened. The PEG‐silane coating method was found to be better than the cross‐linked polyacrylamide coating and aminosilane modification methods. Finally, based on the open tubular column mode of carrier ampholytes’ immobilization and effective antiadsorption coating, the immobilized pH gradient was reused and the chip was recycled for the first time. By virtue of its remarkable features including simplicity, convenience, high efficiency of protein enrichment and separation, and potential for coupling site‐selective IEF with other analytical or separation techniques, this novel method promises to be useful in several applications related with zwitterionic biomolecules.     

Response of peptide intensity to concentration in ESI–MS-based proteome

High-throughput quantification with label-free methods has received considerable attention in electrospray ionization(ESI)-mass spectrometry(MS),but the manner by which MS signals respond to peptide concentration remains unclear in proteomics.We developed a new mathematical formula to describe the intrinsic log-log relationship between the MS intensity response and peptide concentration in an analytical ESI process.Experimental results showed that the calibration curve is fairly fit to the log-log formula with a linear dynamic range of approximate four to five orders of magnitude.However,we found that the ionization of analytical peptides can be severely suppressed by coexisting matrix peptides,such that the calibration curve can be poorly leveled off on both ends.Our study suggests that the interferences from coexisting matrix peptides should be reduced in the ESI process to use the log-log calibration curve successfully for the high-throughput quantification.     

Absolute quantification of NAD(P)H:quinone oxidoreductase 1 in human tumor cell lines and tissues by liquid chromatography–mass spectrometry/mass spectrometry using both isotopic and non-isotopic internal standards

NAD(P)H:quinone oxidoreductase 1 (NQO1, DT-diaphorase) is a prognostic biomarker and a potential therapeutic target for various tumors. Therefore, it is of significance to develop a robust method for the absolute quantification of NQO1. This study aimed to develop and validate a LC–MS/MS based method and to test the appropriateness of using non-isotopic analog peptide as the internal standard (IS) by comparing with a stable isotope labeled (SIL) peptide. The chromatographic performance and mass spectra between the selected signature peptide of NQO1 and the non-isotopic peptide were observed to be very similar. The use of the two internal standards was validated appropriate for the absolute quantification of NQO1, as evidenced by satisfactory validation results over a concentration range of 1.62–162 fmol μL⁻¹. This method has been successfully applied to the absolute quantification of NQO1 expression in various tumor cell lines and tissues. NQO1 expression in human tumor tissues is much higher than that in the neighboring normal tissues in both the cases of lung and colon cancer. The quantitative results obtained from the isotopic and non-isotopic methods are quite similar, further supporting that the use of non-isotopic analog peptide as internal standard is appropriate and feasible for the quantification of NQO1. By comparing with a classical isotopic IS, the present study indicates that the use of a non-isotopic peptide analog to the proteotypic peptide as the internal standard can get equal accuracy and preciseness in measuring NQO1. The universal applicability of the non-isotopic IS approach for the quantification of proteins warrants further research.     

The influence of non-rubber constituents on performance of silica reinforced natural rubber compounds

An in-rubber study of the interaction of silica with proteins present in natural rubber show that the latter compete with the silane coupling agent during the silanisation reaction; the presence of proteins makes the silane less efficient for improving dispersion and filler–polymer coupling, and thus influences the final properties of the rubber negatively. Furthermore, the protein content influences the rheological properties as well as filler–filler and filler–polymer interactions. Stress strain properties also vary with protein content, as do dynamic properties. With high amounts of proteins present in natural rubber, the interactions between proteins and silica are able to disrupt the silica–silica network and improve silica dispersion. High amounts of proteins reduce the thermal sensitivity of the filler–polymer network formation. The effect of proteins is most pronounced when no silane is used, but they are not able to replace a coupling agent.     

Advances in polymer and polymeric nanostructures for protein conjugation

Linear polymers have been considered the best molecular structures for the formation of efficient protein conjugates due to their biological advantages, synthetic convenience and ease of functionalization. In recent years, much attention has been dedicated to develop synthetic strategies that produce the most control over protein conjugation utilizing linear polymers as scaffolds. As a result, different conjugate models, such as semitelechelic, homotelechelic, heterotelechelic and branched or star polymer conjugates, have been obtained that take advantage of these well-controlled synthetic strategies. Development of protein conjugates using nanostructures and the formation of said nanostructures from protein–polymer bioconjugates are other areas in the protein bioconjugation field. Although several polymer–protein technologies have been developed from these discoveries, few review articles have focused on the design and function of these polymers and nanostructures. This review will highlight some recent advances in protein-linear polymer technologies that employ protein covalent conjugation and successful protein-nanostructure bioconjugates (covalent conjugation as well) that have shown great potential for biological applications.     

A Practical Manufacturing Synthesis of 1-(R)-Hydroxymethyl-Dtpa: An Important Intermediate in the Synthesis of MRI Contrast Agents

An efficient synthesis of alcohol 2 is described from L-Serine (OMe) in four synthetic steps. The process uses readily available reagents and is suitable for manufacturing.     

Uncertainty Quantification for Modern High-Dimensional Regression via Scalable Bayesian Methods

Tremendous progress has been made in the last two decades in the area of high-dimensional regression, especially in the “large p, small n” setting. Such sample starved settings inevitably lead to models which are potentially very unstable and hence quite unreliable. To this end, Bayesian shrinkage methods have generated a lot of recent interest in the modern high-dimensional regression and model selection context. Such methods span the wide spectrum of modern regression approaches and include among others, spike-and-slab priors, the Bayesian lasso, ridge regression, and global-local shrinkage priors such as the Horseshoe prior and the Dirichlet–Laplace prior. These methods naturally facilitate tractable uncertainty quantification and have thus been used extensively across diverse applications. A common unifying feature of these models is that the corresponding priors on the regression coefficients can be expressed as a scale mixture of normals. This property has been leveraged extensively to develop various three-step Gibbs samplers to explore the corresponding intractable posteriors. The convergence of such samplers however is very slow in high dimensions settings, making them disconnected to the very setting that they are intended to work in. To address this challenge, we propose a comprehensive and unifying framework to draw from the same family of posteriors via a class of tractable and scalable two-step blocked Gibbs samplers. We demonstrate that our proposed class of two-step blocked samplers exhibits vastly superior convergence behavior compared to the original three-step sampler in high-dimensional regimes on simulated data as well as data from a variety of applications including gene expression data, infrared spectroscopy data, and socio-economic/law enforcement data. We also provide a detailed theoretical underpinning to the new method by deriving explicit upper bounds for the (geometric) rate of convergence, and by proving that the proposed two-step sampler has superior spectral properties. Supplementary material for this article is available online.     

Explicit solvent molecular dynamics simulations of chaperonin-assisted rhodanese folding

Chaperonins are known to facilitate the productive folding of numerous misfolded proteins, Despite their established importance, the mechanism of chaperonin-assisted protein folding remains unknown. In the present article, all-atom explicit solvent molecular dynamics (MD) simulations have been performed for the first time on rhodanese folding in a series of cavity-size and cavity-charge chaperonin mutants. A compromise between stability and flexibility of chaperonin structure during the substrate folding has been observed and the key factors affecting this dynamic process are discussed.