PKA17—A Coarse-Grain Grid-Based Methodology and Web-Based Software for Predicting Protein pKa Shifts

We have developed and tested PKA17, a coarse-grain grid-based model for predicting protein pK _a shifts. Our pK _a predictor is currently deployed via a website interface. We have carried out parameter fitting using 442 Asp, Glu, His, Lys, and Arg residues for which experimental results are available in the literature. PROPKA software has been used for benchmarking. The average unsigned error and root-mean-square deviation (RMSD) have been found to be 0.628 and 0.831 pH units, respectively, for PKA17. The corresponding results with PROPKA are 0.761 and 1.063 units. We have assessed the robustness of the developed PKA17 methodology with a number of tests and have also explored the possibility of using a combination of PROPKA and PKA17 calculations in order to improve the accuracy of predicted pK _a values for protein residues. We have also once again confirmed that protein acidity constants are influenced almost entirely by residues in the immediate spatial proximity of the ionizable amino acids. The resulting PKA17 software has been deployed online with a web-based interface at http://users.wpi.edu/~jpcvitkovic/pka_calc.html . © 2019 Wiley Periodicals, Inc.     

Nutraceutical Products—State-of-the-Art for Sample Preparation in Pesticide Residues Analysis

Nutraceutical products are plant-based materials primarily valued for their possible medicinal or therapeutic properties. According to their “natural” origin they are often perceived as being safe; however, for the prevention of economic losses, pesticides may be used against pest, mold and insects causing plant damage. Bearing in mind that a nutraceutical is a concentrated form of the plant, pesticides could be found in the final product in possibly worrying concentration. Nutraceutical products and dried herb materials typically represent very complex matrices for pesticide residue analysis, therefore a proper sample preparation protocol with appropriate clean-up steps is necessary prior to the analysis. Hence, this article gives an overview of pesticide residue analyses in nutraceuticals and provides the state of the art for sample preparation techniques applied for different types of nutraceuticals.     

CNDO Studies on the Intermolecular Coulomb Interaction in TCNQ-Stack

The coulomb interaction among TCNQ- molecules in different stack structures was calculated by quantum chemistry CNDO method. The results of the calculation would be used to explain the change rule of the electricity property of the TCNQ complex very well.     

Mirion—A Software Package for Automatic Processing of Mass Spectrometric Images

Mass spectrometric imaging (MSI) techniques are of growing interest for the Life Sciences. In recent years, the development of new instruments employing ion sources that are tailored for spatial scanning allowed the acquisition of large data sets. A subsequent data processing, however, is still a bottleneck in the analytical process, as a manual data interpretation is impossible within a reasonable time frame. The transformation of mass spectrometric data into spatial distribution images of detected compounds turned out to be the most appropriate method to visualize the results of such scans, as humans are able to interpret images faster and easier than plain numbers. Image generation, thus, is a time-consuming and complex yet very efficient task. The free software package “Mirion,” presented in this paper, allows the handling and analysis of data sets acquired by mass spectrometry imaging. Mirion can be used for image processing of MSI data obtained from many different sources, as it uses the HUPO-PSI-based standard data format imzML, which is implemented in the proprietary software of most of the mass spectrometer companies. Different graphical representations of the recorded data are available. Furthermore, automatic calculation and overlay of mass spectrometric images promotes direct comparison of different analytes for data evaluation. The program also includes tools for image processing and image analysis.

Entrapment of Humic Acid in a Sol-Gel Matrix—A New Tool for Sorption Studies

Humic substances are natural complexed mixtures of organic compounds originated from the decomposition of plant and animal residues. These compounds are ubiquitous in soils, sediments, surface waters and groundwaters. They contain both hydrophobic and hydrophilic moieties, able to interact with hydrophobic organic contaminants and with heavy metals. These sorption interactions play a crucial role in contaminants fate and transport and their understanding and quantification are essential for modeling and predictions. However, sorption analyses frequently suffer from experimental problems. A novel idea presented in this study is to use sol-gel as an inert matrix to immobilize (entrap) specific, well defined, humic molecules which then be used in sorption studies. We developed a successful procedure for the immobilization of humic acid (HA) in a sol-gel matrix. After gelation and drying, the doped gel was crushed and washed several times, yielding a very stable product. It was then used in a series of batch experiments, studying the sorption of several polycyclic aromatic hydrocarbons (PAHs) with Aldrich HA. The sorption coefficients (K _oc) obtained with the immobilized HA were highly correlated with the values expected based on the hydrophobicity of the contaminants. We concluded that the entrapped HA retained its original properties and that it was accessible to the external contaminants through the pore network.     

Exposed Body Surface Area—A Determinate for UV Radiant Energy in Human UV Exposure Studies

Solar ultraviolet (UV) exposure of people and related health risk is mainly examined by estimating the received UV radiant exposure. However, for several effects such as DNA damage, vitamin D photosynthesis or the probability of developing skin cancer, UV radiant energy is important and with that the size of exposed skin area. There is also a complex interaction between body shape and behavior like sun exposure habits, so that careful analysis is necessary when estimating health effects from UV exposure. In this paper, knowledge on body shape and methods of calculating the total body surface area (BSA) are summarized. BSA depends mainly on the height and weight of a person as well as on gender, ethnicity and body shape. BSA and body shape differ significantly between different populations and both change during life. This paper proposes formulas for BSA that consider height, weight, gender, ethnicity and body shape. As the exposed BSA depends on clothing, finally an approach is presented which aims to calculate the size of body parts released by real garments. In summary, this paper will enable future researchers to quantify the exposed BSA by best matching their study population and consequently investigate risks caused by solar UV exposure.     

Isoentropic and Isoenthalpic Temperatures of Protein Unfolding in Hydrophobic Interaction Chromatography

Hydrophobic interaction chromatography (HIC) is widely used for the separation and purification of biopolymers in their native state, and now also becomes a new method to refold the denatured proteins1. The effect of salt or water concentration2 on the pr…     

A pH Switch for β-Sheet Protein Folding

Protein design advancements have led to biotechnological strategies based on more stable and more specific structures. Herein we present a 6-residue sequence (HPATGK) that acts as a stable structure-nucleating turn at physiological and higher pH but is notably unfavorable for chain direction reversal at low pH. When placed into the turn of a β-sheet, this leads to a pH switch of folding. Using a standard 3-stranded β-sheet model, the WW domain, it was found that the pH switch sequence insertion caused minimal change at pH 8 but a ca. 50 °C drop in the melting temperature (T_m) was observed at pH 2.5: ΔΔG_F ≥11.3 kJ mol⁻¹. Using the strategies demonstrated in this article, the redesign of β-sheets to contain a global, or local, pH-dependent conformational switch should be possible.     

A Novel Model for Protein Immobilization on Microspheres

The immobilization of proteins, especially receptor proteins commonly used in high through-put screening of drugs (HTS), have received great attention in recent years. There are many successful isothermal models for describing the adsorption of protein onto solid surface, such as Langmuir model, Bi-Langmuir model, Fowler model, Freundlich model,Freundlich–Langmuir model and Tekmin model etc. In all these models, Langmuir model was the most favorable one model accepted by many researchers,…     

Interaction parameter for hydrogen-containing mixtures in the Peng—Robinson equation of state

A new correlation for the Peng—Robinson interaction parameter δ_ij of hydrogen-containing mixtures is proposed here. Values of δ_ij obtained from literature vapour—liquid equilibrium data are represented by a cubic polynomial in terms of the temperature. The correlation predicts better values than other correlations proposed in the literature for the same systems, and is applicable to wider ranges of temperature. Applications of the proposed equations to VLE are presented.     

Simultaneous Multi-Wavelength UV-Visible Detection for HPLC Using a Diode-Array Spectrophotometer—A Versatile Software Package

Abstract

A BASIC program was developed to monitor absorbance simultaneously at various wavelengths using an HP8451A Diode Array Spectrophotometer linked to a HPLC system and equipped with a flow cell. The program measures a maximum of ten wavelengths and takes a maximum of 240 measurements for each wavelength, using only 16K of memory and a dual disc drive. The program includes the options of replotting using a different ordinate scale and saving the numerical data on disc.     

Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com      

A Novel Protein Found in Selenium-rich Silkworm Pupas

Selenium(Se)is well known for its cancer-preventive function1.In our previous work,silkworm pupas from Ziyang county of Shanxi Province,one of the two largest Se-rich areas in China,was found to have Se content215times higher than that from Luoyang which is a normal region in China2.Meanwhile,Se-rich amino acids extracted from Ziyang pupas could efficiently induce the apoptosis of human hepatoma cells SMMC-7721.In order to find out the effective component responsible for this carcinostat…     

Crosslinked penicillin acylase aggregates for synthesis of β-lactam antibiotics in organic medium

Crosslinked enzyme aggregates (CLEAs) of a partially purified penicillin acylase from a recombinant Escherichia coli strain have been produced as a novel type of biocatalysts well endowed to perform in organic media. Different protein precipitants were studied and glutaraldehyde was used as the crosslinking agent. Precipitation curves were obtained for all precipitants to determine the concentrations at which all the protein precipitated out of the solution. The effect of the glutaraldehyde-to-protein ratio was studied with respect to process recovery and the specific activity and stability of the biocatalyst. Recovery of penicillin acylase activity was moderately high, about 50%; major losses of enzyme activity were produced at the precipitation step. Specific activities of all CLEAs were very high, which is one of the advantages of using nonsupported biocatalysts. Ammonium sulfate and tert-butyl alcohol were the best precipitants at a glutaraldehyde-protein mass ratio of 2 and were selected to perform the kinetically controlled synthesis of ampicillin in 60% (v/v) ethylene glycol medium. At comparable conversion yields, volumetric and specific antibiotic productivity were much higher for CLEAs than for carrier-bound penicillin acylases.     

A Cooperative Approach for the Extraction of Protein Motifs

Many problems in chemistry depend on the ability to identify the global solution of a function, which can be a minimum or a maximum. Because the number of local optima grows exponentially with the complexity of the problems, finding the global optimum tur…     

TReNDS—Software for reaction monitoring with time-resolved non-uniform sampling

NMR spectroscopy, used routinely for structure elucidation, has also become a widely applied tool for process and reaction monitoring. However, the most informative of NMR methods—correlation experiments—are often useless in this kind of applications. The traditional sampling of a multidimensional FID is usually time-consuming, and thus, the reaction-monitoring toolbox was practically limited to 1D experiments (with rare exceptions, e.g., single-scan or fast-sampling experiments). Recently, the technique of time-resolved non-uniform sampling (TR-NUS) has been proposed, which allows to use standard multidimensional pulse sequences preserving the temporal resolution close to that achievable in 1D experiments. However, the method existed only as a prototype and did not allow on-the-fly processing during the reaction. In this paper, we introduce TReNDS: free, user-friendly software kit for acquisition and processing of TR-NUS data. The program works on Bruker, Agilent, and Magritek spectrometers, allowing to carry out up to four experiments with interleaved TR-NUS. The performance of the program is demonstrated on the example of enzymatic hydrolysis of sucrose.     

Evaluation of Drug Interaction in Binding to Protein by High Performance Liquid Chromatography

Drugs in the body are bound to metabolizing enzymes, targets/receptors and transport proteins in certain extent. The binding of drugs to targets or receptors is mainly specific and responsible for its pharmacological and therapeutic effects. The metabolizing of drugs by enzyme involves both     

Studies in inorganic polyelectrolytes — Part II

Viscosity behaviour of several samples ofGraham's salt with varying molecular weight has been studied. Reduced viscosity (η _sp /c) versus concentration curves were found to be characteristic of polyelectrolytes. They are dependent on the molecular weight and can be reduced to straight lines by plotting the reciprocal of the reduced viscosity against the square root of concentration. The intrinsic viscosities obtained by extrapolation were found to be proportional to the square of molecular weights. The value of reduced viscosity at any particular concentration in the concentration range between 0.25% and 4.0% was linearly related to the molecular weight. Reduced viscosities were found to decrease considerably on addition of electrolytes. Reduced viscosity versus added salt concentration curves were remarkably molecular weight dependent. The p_H of the medium seemed to have no effect at all. Bivalent salts reduce the viscosity to a much greater extent than monovalent ones. By keeping the concentration of the added salt constant and varying that ofGraham's salt, curves showing hump which disappeared at higher concentration of the added salt, were obtained. In the action of electrolytes the more important factor is the valency of cation rather than the ionic strength of the medium. Most observations confirm the already well-establishedFolding-Chain Theory of polyelectrolytes developed byKatchalsky, Fuoss and others.     

Stable Isotope Labeling Strategy for Protein–Ligand Binding Analysis in Multi-Component Protein Mixtures

Described here is a stable isotope labeling protocol that can be used with a chemical modification- and mass spectrometry-based protein–ligand binding assay for detecting and quantifying both the direct and indirect binding events that result from protein–ligand binding interactions. The protocol utilizes an H₂¹⁶O₂ and H₂¹⁸O₂ labeling strategy to evaluate the chemical denaturant dependence of methionine oxidation in proteins both in the presence and absence of a target ligand. The differential denaturant dependence to the oxidation reactions performed in the presence and absence of ligand provides a measure of the protein stability changes that occur as a result of direct interactions of proteins with the target ligand and/or as a result of indirect interactions involving other protein–ligand interactions that are either induced or disrupted by the ligand. The described protocol utilizes the ¹⁸O/¹⁶O ratio in the oxidized protein samples to quantify the ligand-induced protein stability changes. The ratio is determined using the isotopic distributions observed for the methionine-containing peptides used for protein identification in the LC-MS-based proteomics readout. The strategy is applied to a multi-component protein mixture in this proof-of-principle experiment, which was designed to evaluate the technique’s ability to detect and quantify the direct binding interaction between cyclosporin A and cyclophilin A and to detect the indirect binding interaction between cyclosporin A and calcineurin (i.e., the protein–protein interaction between cyclophilin A and calcineurin that is induced by cyclosporin A binding to cyclophilin A).     

A Novel Method for Diminishing Protein Aggregation during Denatuaration Process

Many experimental results show that aggregation is the main side reaction in the renaturation process of proteins and once the proteins aggregate, it is rather difficult to be renatured again. Therefore, the renaturation efficiency can be highly enhanced,…