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…     

DeepNGlyPred: A Deep Neural Network-Based Approach for Human N-Linked Glycosylation Site Prediction

Protein N-linked glycosylation is a post-translational modification that plays an important role in a myriad of biological processes. Computational prediction approaches serve as complementary methods for the characterization of glycosylation sites. Most of the existing predictors for N-linked glycosylation utilize the information that the glycosylation site occurs at the N-X-[S/T] sequon, where X is any amino acid except proline. Not all N-X-[S/T] sequons are glycosylated, thus the N-X-[S/T] sequon is a necessary but not sufficient determinant for protein glycosylation. In that regard, computational prediction of N-linked glycosylation sites confined to N-X-[S/T] sequons is an important problem. Here, we report DeepNGlyPred a deep learning-based approach that encodes the positive and negative sequences in the human proteome dataset (extracted from N-GlycositeAtlas) using sequence-based features (gapped-dipeptide), predicted structural features, and evolutionary information. DeepNGlyPred produces SN, SP, MCC, and ACC of 88.62%, 73.92%, 0.60, and 79.41%, respectively on N-GlyDE independent test set, which is better than the compared approaches. These results demonstrate that DeepNGlyPred is a robust computational technique to predict N-Linked glycosylation sites confined to N-X-[S/T] sequon. DeepNGlyPred will be a useful resource for the glycobiology community.     

A Novel Approach for the Surface Modification of Polymeric Membrane with Phospholipid Polymer

A new economic and convenient method to modify the surface of microporous polypropylene (PP) membranes with phospholipid polymer was given. The process included the photo-irradiated graft polymerization of N,N-dimethylaminoethyl methacrylate (DMAEMA) and the ring-opening reaction of the grafted polyDMAEMA with 2-alkyloxy-2-oxide-1,3,2-dioxo-phospholanes (AOP). Four AOPs, whose alkyloxy groups consisted of dodecyl, tetradecyl,hexadecyl and octadecyl moieties, were used to convert the grafted polyDMAEMA to phospholipidpolymers. FT-IR spectra confirmed the chemical change of membrane surface. Platelets adhesion experiment indicated that PP membrane with excellent blood compatible surface could be fabricated by this method.     

Site Covalent Modification of Methionyl Peptides for the Production of FRET Complexes

Flax cyclic peptides (orbitides, linusorbs (LOs)) [1–8‐NαC],[1‐MetO₂]‐linusorb B1 ([MetO₂]‐LO1) and [1–9‐NαC],[1‐MetO₂]‐linusorb B2 ([MetO₂]‐LO2) are biologically active. These LOs lack active nuclei commonly used in peptide modification. We have developed reactions to activate methionine methyl sulphide to produce stable derivatives. In these reactions, LOs are converted to sulfonium intermediates and subsequently to derivatives containing active nuclei while preserving their fundamental structures. The reaction conditions preserved cyclic peptide fundamental structure and organic solvent solubility. [Met]‐LO1 and [Met]‐LO2 analogues containing activated groups (?CN, ?COOEt, and ?NH₂) in the form of methionine, methionine (S)‐oxide, and methionine (S,S)‐dioxide amino acids were synthesized and characterized by LCMS and 1D and 2D NMR spectroscopy. Coumarin orbitide complexes produced in this manner bind Eu³⁺ yielding FRET compounds that absorb energy through coumarin antennae and emit photons at lanthanide wavelengths.     

A Practical Approach for the Detection of Protein Tau with a Portable Potentiostat

Along with many factors, the change in protein tau isoforms, which has an obvious role in the function of microtubules, is an important biomarker of Alzheimer's disease. The aim of this study is to determine the protein Tau-441 with a portable potentiostat using a practical approach. For this purpose, screen printed electrodes (SPCEs) were first hydroxylated and then functional self-assembled monolayers were formed on the surface with 3-aminopropyltriethoxysilane (APTES). Evidence of anti-Tau being immobilized on to the surface was followed by techniques such as cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS) and Fourier transform infrared spectroscopy (FTIR). The constructed immunosensor showed a linear response within the concentration range of 0.0064–0.8 ng/mL for the target analyte Tau-441 and the limit of detection was found to be 0.0053 ng/mL. In addition, analytical behaviors such as reproducible measurements and storage life of the developed immunosensor with a portable potentiostat were also investigated. It has been demonstrated that Tau-441 can be captured with the help of portable device with sensitivity in CSF environment.     

Deciphering the Selectivity of Bombyx mori Pheromone Binding Protein for Bombykol over Bombykal: A Theoretical Approach

In this article we report calculations dedicated to estimate the selectivity of the Bombyx mori pheromone binding protein towards the two closely related pheromonal components Bombykol and Bombykal. The selectivity is quantified by the binding free‐energy difference, obtained either by the thermodynamic integration or by the MM‐GBSA approach. In the latter, the selectivity is decomposed on a per‐residue basis, which identifies the residues considered crucial for the selectivity of the protein for Bombykol over Bombykal. A discussion on the role of Bombyx mori pheromone binding protein is provided on the basis of these results.     

A Systematic Approach for the Evaluation of Triethanolamine as a Possible Sulfur Dioxide Sorption Detector Coating

Abstract

A change in the vibrating frequency of a quartz crystal can be an accurate measurement of the mass change on the surface of the crystal. When coated with an absorbing compound, the subsequent frequency change indicates the sorption of a chemical species by the coating. An approach is proposed for evaluating potential crystal coatings and is. applied to the evaluation of Triethanolamine as a possible sulfur dioxide sorption detector coating.     

Theranostic Approach for the Protein Corona of Polysaccharide Nanoparticles

Polysaccharide nanoparticles are promising materials in the wide range of disciplines such as medicine, nutrition, food production, agriculture, material science and others. They excel not only in their non‐toxicity and biodegradability but also in their easy preparation. As well as inorganic particles, a protein corona (PC) around polysaccharide nanoparticles is formed in biofluids. Moreover, it has been considered that the overall response of the organism to nanoparticles presence depends on the PC. This review summarises scientific publications about the structural chemistry of polysaccharide nanoparticles and their impact on theranostic applications. Three strategies of implementation of the PC in theranostics have been discussed: I) Utilisation of the PC in therapy; II) How the composition of the PC is analysed for specific disease markers; III) How the formed PC can interact with the immune system and enhances the immunomodulation or immunoelimination. Thus, the findings from this review can contribute to improve the design of drug delivery systems. However, it is still necessary to elucidate the mechanisms of nano‐bio interactions and discover new connections in nanoscale research.     

Targeted Bottom–Up Mass Spectrometry Approach for the Relative Quantification of Post-Translational Modification of Bovine κ-Casein during Milk Fermentation

κ-casein (κ-CN) is one of the key components in bovine milk, playing a unique role in the structuration of casein micelles. It contains in its chemical structure up to sixteen amino acid residues (mainly serine and threonine) susceptible to modifications, including glycosylation and phosphorylation, which may further be formed during milk processing. In this study, changes in post-translational modification (PTM) of κ-CN during bovine milk fermentation were investigated. One-to-five-day fermented milk samples were produced. A traditional bottom–up proteomics approach was used to establish a multiple-reaction monitoring (MRM) method for relative quantification of κ-CN PTM. Endoproteinase Glu-C was found to efficiently digest the κ-CN molecule. The developed LC-MS method was validated by performing assessments of linearity, precision, repeatability, reproducibility, limit of detection (LOD), and limit of quantification (LOQ). Among the yielded peptides, four of them containing serine and threonine residues were identified and the unmodified as well as the modified variants of each of them were relatively quantified. These peptides were (1) IPTINTIASGEPTSTTE _{[140, 158]}, (2) STVATLE _{[162, 168]}, (3) DSPE _{[169, 172]}, and (4) INTVQVTSTAV _{[180, 190]}. Distribution analysis between unmodified and modified peptides revealed that over 50% of κ-CN was found in one of its modified forms in milk. The fermentation process further significantly altered the composition between unmodified/modified κ-CN, with glycoslaytion being predominant compared to phosphorylation (p < 0.01). Further method development towards α and β-CN fractions and their PTM behavior would be an asset to better understand the changes undergone by milk proteins and the micellar structure during fermentation.     

Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence

Ultrafast excited‐state deactivation dynamics of small cytosine (Cy) and 1‐methylcytosine (1mCy) microhydrates, Cy?(H₂O)_1‐3 and 1mCy?(H₂O)_1,2, produced in a supersonic expansion have been studied by mass‐selected femtosecond pump–probe photoionization spectroscopy at about 267 nm excitation. The seeded supersonic expansion of Ar/H₂O gas mixtures allowed an extensive structural relaxation of Cy and 1mCy microhydrates to low‐energy isomers. With the aid of electronic structure calculations, we assigned the observed ultrafast dynamics to the dominant microhydrate isomers of the amino‐keto tautomer of Cy and 1mCy. Excited‐state lifetimes of Cy?(H₂O)_1‐3 measured here are 0.2–0.5 ps. Comparisons of the Cy?H₂O and 1mCy?H₂O transients suggest that monohydration at the amino Watson–Crick site induces a substantially stronger effect than at the sugar‐edge site in accelerating excited‐state deactivation of Cy.     

Modification of Amorphous Mesoporous Zirconia Nanoparticles with Bisphosphonic Acids: A Straightforward Approach for Tailoring the Surface Properties of the Nanoparticles

The use of readily prepared bisphosphonic acids obtained in few steps through a thio-Michael addition of commercially available thiols on tetraethyl vinylidenebisphosphonate enables the straightforward surface modification of amorphous mesoporous zirconia nanoparticles. Simple stirring of the zirconia nanoparticles in a buffered aqueous solution of the proper bisphosphonic acid leads to the surface functionalization of the nanoparticles with different kinds of functional groups, charge and hydrophobic properties. Formation of both chemisorbed and physisorbed layers of the bisphosphonic acid take place, observing after extensive washing a grafting density of 1.1 molecules/nm² with negligible release in neutral or acidic pH conditions, demonstrating stronger loading compared to monophosphonate derivatives. The modified nanoparticles were characterized by IR, XPS, ζ-potential analysis to investigate the loading of the bisphosphonic acid, FE-SEM to investigate the size and morphologies of the nanoparticles and ³¹P and ¹H MAS NMR to investigate the coordination motif of the phosphonate units on the surface. All these analytical techniques demonstrated the strong affinity of the bisphosphonic moiety for the Zr(IV) metal centers. The functionalization with bisphosphonic acids represents a straightforward covalent approach for tailoring the superficial properties of zirconia nanoparticles, much straightforward compared the classic use of trisalkoxysilane or trichlorosilane reagents typically employed for the functionalization of silica and metal oxide nanoparticles. Extension of the use of bisphosphonates to other metal oxide nanoparticles is advisable.     

A Robust Analytical Approach for the Identification of Specific Protein Carbonylation Sites: Metal-Catalyzed Oxidations of Human Serum Albumin

The formation of protein carbonyls in the metal-catalyzed oxidation of human serum albumin (HSA) is characterized using a new analytical approach that involves tagging the modification site with multiple hydrazide reagents. Protein carbonyl formation at lysine and arginine residues was catalyzed with copper and iron ions, and the resulting oxidation patterns in HSA are contrasted. A total of 18 modification sites were identified with iron-ion catalysis and 14 with copper-ion catalysis. However, with the more stringent requirement of identification with at least two tagging reagents, the number of validated modification sites drops to 10 for iron and nine for copper. Of the 14 total validated sites, there were only five in common for the two metal ions. The results illustrate the value of using multiple tagging agents and highlight the selective and specific nature of metal-catalyzed protein oxidations.     

Heavy Metals and Human Health: Possible Exposure Pathways and the Competition for Protein Binding Sites

Heavy metals enter the human body through the gastrointestinal tract, skin, or via inhalation. Toxic metals have proven to be a major threat to human health, mostly because of their ability to cause membrane and DNA damage, and to perturb protein function and enzyme activity. These metals disturb native proteins’ functions by binding to free thiols or other functional groups, catalyzing the oxidation of amino acid side chains, perturbing protein folding, and/or displacing essential metal ions in enzymes. The review shows the physiological and biochemical effects of selected toxic metals interactions with proteins and enzymes. As environmental contamination by heavy metals is one of the most significant global problems, some detoxification strategies are also mentioned.     

PHRONESIS: A One-Shot Approach for Sequential Assignment of Protein Resonances by Ultrafast MAS Solid-State NMR Spectroscopy

Solid-state NMR (ssNMR) spectroscopy has emerged as the method of choice to analyze the structural dynamics of fibrillar, membrane-bound, and crystalline proteins that are recalcitrant to other structural techniques. Recently, ¹H detection under fast magic angle spinning and multiple acquisition ssNMR techniques have propelled the structural analysis of complex biomacromolecules. However, data acquisition and resonance-specific assignments remain a bottleneck for this technique. Here, we present a comprehensive multi-acquisition experiment (PHRONESIS) that simultaneously generates up to ten 3D ¹H-detected ssNMR spectra. PHRONESIS utilizes broadband transfer and selective pulses to drive multiple independent polarization pathways. High selectivity excitation and de-excitation of specific resonances were achieved by high-fidelity selective pulses that were designed using a combination of an evolutionary algorithm and artificial intelligence. We demonstrated the power of this approach with microcrystalline U-¹³C,¹⁵N GB1 protein, reaching 100 % of the resonance assignments using one data set of ten 3D experiments. The strategy outlined in this work opens up new avenues for implementing novel ¹H-detected multi-acquisition ssNMR experiments to speed up and expand the application to larger biomolecular systems.     

Rate and Extent of Carbon Dioxide Uptake In Room Temperature Ionic Liquids: A New Approach Using Microdisc Electrode Voltammetry

A simple method is introduced which enables the simultaneous determination of both the maximum CO₂ concentration and kinetics of CO₂ uptake and release by a room temperature ionic liquid. This method is based upon the analysis of chronoamperometry recorded in bulk ionic liquid at intervals during exposure to CO₂ and subsequent exposure to vacuum to remove the dissolved CO₂. Comparing experimental data with a numerical model reveals the rate‐limiting factors for both uptake and release of CO₂.     

An Approach for Visualization of the Active Site of Enzymes with Unknown Three-Dimensional Structures

Abstract

A new approach for virtual characterization of the active site structure of enzymes with unknown three-dimensional (3D) structure has been proposed. It includes analysis of data on enzyme interaction with reversible competitive inhibitors, their 3D structures and moulding of the substrate-binding region. The superposition of ligands in biologically active conformations allows to determine the shape and dimension of the active site cavity accommodating these compounds. Monoamine oxidase A (MAO-A), a “typical” enzyme with unknown spatial organisation, was used to test this method. The correctness of such approach was validated by the analysis of HIV protease interaction with its inhibitors using 3D structures of their complexes. Mould of the substrate/inhibitor binding site can be used for the visualization of this binding site and for searching new ligands in molecular databases.     

Role of Tryptophan in the Active Site of Plant Esterase: Chemical Modification and Fluorometric Studies

Plant esterase extracted from wheat flour play key roles in the spectrophotometric detection of organophosphorus compounds (OPs) for food safety and human health. The purpose of the present study was to investigate the role of tryptophan residues in the activity and structure of plant esterase by chemical modification and fluorometric studies. Active site characterization of purified plant esterase showed the involvement of tryptophan in the catalytic activity. Only one was essential for the enzyme activity by the Tsou’s analysis. Substrate protection experiments further confirmed that the tryptophan residue was located at the substrate-binding site. Fluorescence quenching studies elucidated that the tryptophan residues were largely exposed to the solvent, and a smaller fraction of the surface tryptophan residues had electropositively charged amino acids around them. Experimental results obtained here are expected to promote the applications of plant esterase in OPs detection. Further confirmation of the existence of other critical residues and detailed explanation of their functions were also required for the elucidation of the mechanism involved in the detection of OPs.     

Modification of Soy Protein for Wood Adhesives using Mussel Protein as a Model: The Influence of a Mercapto Group

Summary: Mussel protein can serve as a strong and water‐resistant adhesive, but is expensive and not readily available. Soy protein is inexpensive, abundant, and readily available, but is a poor adhesive. Mussel protein contains a high amount of mercapto‐containing cysteine. This study revealed that increasing the free mercapto group content in soy protein could greatly increase the strength and water‐resistance of wood composites bonded with the modified soy protein.

Preparation of the modified SPIs.