Thermal Plasma Technology: Where Do We Stand and Where Are We Going?

In this overview, an attempt is made to assess the present and future research and development in thermal plasma processing of materials restricted to (1) thermal plasma coating technologies, (2) thermal plasma synthesis of fine powders, (3) thermal plasma waste destruction, and (4) thermal plasma spheroidization and densification. Since thermal plasma processing is, in general, governed by a large number of parameters, implementation of controls becomes mandatory. The lack of sufficient controls combined with economic drawbacks in some cases has been the main obstacle for the growth of thermal plasma technology. Present R&D efforts, however, address these problems.     

Updates on Dengue Vaccine and Antiviral: Where Are We Heading?

Approximately 100–400 million people from more than 100 countries in the tropical and subtropical world are affected by dengue infections. Recent scientific breakthroughs have brought new insights into novel strategies for the production of dengue antivirals and vaccines. The search for specific dengue inhibitors is expanding, and the mechanisms for evaluating the efficacy of novel drugs are currently established, allowing for expedited translation into human trials. Furthermore, in the aftermath of the only FDA-approved vaccine, Dengvaxia, a safer and more effective dengue vaccine candidate is making its way through the clinical trials. Until an effective antiviral therapy and licensed vaccine are available, disease monitoring and vector population control will be the mainstays of dengue prevention. In this article, we highlighted recent advances made in the perspectives of efforts made recently, in dengue vaccine development and dengue antiviral drug.     

Hairy Core–Shell Nanoparticles via RAFT: Where are the Opportunities and Where are the Problems and Challenges?

The preparation of hairy core–shell nanoparticles including (crosslinked) micelles, unimolecular micelles such as star polymers with block structures in each arm and surface grafted nanoparticles such as inorganic particles via the RAFT process are discussed. The RAFT process is certainly a highly versatile process. However, it should not be forgotten that RAFT polymerization is a process, i.e., superimposed on a conventional free radical process. Furthermore, the livingness of the process is dependent on the accessibility of the RAFT group, which can be hampered in certain approaches such as star synthesis and surface grafting from nanoparticles. Nevertheless, the RAFT process is a versatile toolbox that offers good solutions to a range of problems in the preparation of hairy nanoparticles.

     

Modeling the Dynamics of Protein–Protein Interfaces,How and Why?

Protein–protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein–protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein–protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein–protein interface.     

Ion spectroscopy: Where did it come from; where is it now; and where is it going?

The ASMS conference on ion spectroscopy brought together at Asilomar on October 16–20, 2009 a large group of mass spectrometrists working in the area of ion spectroscopy. In this introduction to the field, we provide a brief history, its current state, and where it is going. Ion spectroscopy of intermediate size molecules began with photoelectron spectroscopy in the 1960s, while electronic spectroscopy of ions using the photodissociation “action spectroscopic” mode became active in the next decade. These approaches remained for many years the main source of information about ionization energies, electronic states, and electronic transitions of ions. In recent years, high-resolution laser techniques coupled with pulsed field ionization and sample cooling in molecular beams have provided high precision ionization energies and vibrational frequencies of small to intermediate sized molecules, including a number of radicals. More recently, optical parametric oscillator (OPO) IR lasers and free electron lasers have been developed and employed to record the IR spectra of molecular ions in either molecular beams or ion traps. These results, in combination with theoretical ab initio molecular orbital (MO) methods, are providing unprecedented structural and energetic information about gas-phase ions.     

The Physics and Radiochemistry of Solar Neutrino Detectors: What Have We Learned and What Can We Expect?

The situation in solar neutrino science has changed drastically in the past decade, with results now available from five neutrino experiments that use different methods to look at different regions of the solar-neutrino energy-spectrum. While the goal of all of these experiments is physics, they all rely heavily on chemistry and radiochemistry. Three of these experiments are radiochemical, the ³⁷Cl detector and the two different forms of ⁷¹Ga detectors used in GALLEX and SAGE are based on the chemical isolation and counting of the radioactive products of neutrino interactions. The other two, Kamiokande and its improved successor, Super- Kamiokande, detect neutrinos in real time; however, they also depend sensitively on radiochemistry in that (as in all the solar neutrino detectors) radioactive contaminants must be controlled at very low levels. It is noteworthy that all of these experiments (a) have detected solar neutrinos, but (b) all report deficits of the observed neutrinos relative to the predictions of standard solar models — the so-called "solar neutrino problem". In this paper, I review the basic principles of operation of these neutrino detectors, report their recent results, and discuss some of the interpretations that are now in vogue. I then describe some of the new neutrino detectors that are under construction or being developed, and discuss the kinds of new results we might expect to see in the early years of the new millennium.     

Purification and Characterization of PRL Protein Tyrosine Phosphatases

PRLs constitute a subfamily of protein tyrosine phosphatases(PTPs). In the present paper are reported the molecular cloning, expression, purification, and characterization of all the three members of the PRL enzymes in human and the only PRL in C. elegans. These enzymes were expressed as glutathione S-transferase (GST) fusion proteins in DE3pLysS E. coil cells, and the recombinant fusion proteins were purified on glutathione-Sepharose affinity columns. Having been cleaved with thrombin, GST-free enzymes were further purified on an S-100 Sepharose gel filtration column. The purified proteins show single polypeptide bands on SDS-polyacrylamide gel electrophoresis. With para-nitrophenyl phosphate(p-NPP) as a substrate, PRLs exhibit classical Michaelis-Menten kinetics with Vmax values two orders of magnitude smaller than those of classic PTPs. The responses of PRLs to ionic strength, metal ions and phosphatase inhibitors are similar to those of other characterized PTPs, but their optimal pH values are different. These data thus reveal distinct common biochemical properties of PRL subfamily PTPs as well.     

N-Phospho-α-Amino Acids and Co-Evolution of Nucleic Acid and Protein

N-phospho-α -amino acids obtainable from aqueous condition were different from their corresponding β -analogues intrinsically. As the self-reproduction unites, N-phospho-α -amino acids were capable to produce non-random oligopeptides. As the phosphoryl donor, they were able to phosphorylate the nucleosides much faster than the deoxynucleosides.     

The Coordination of NiII and CuII Ions to the Polyhistidyl Motif of Hpn Protein: Is It as Strong as We Think?

Hpn, one of Helicobacter pylori′s nickel‐accessory proteins, is an amazingly peculiar protein: Almost half of its sequence consists of polyhistidyl (poly‐His) residues. Herein, we try to understand the origin of this naturally occurring sequence, thereby shedding some light on the bioinorganic chemistry of Hpn′s numerous poly‐His repeats. By using potentiometric, mass spectrometric, and various spectroscopic techniques, we studied the Ni^II‐ and Cu^II complexes of the wild‐type Ac‐THHHHYHGG‐NH₂ fragment of Hpn and of its six analogues, in which consecutive residues (His or Tyr) were replaced by Ala (Ala‐substitution or Ala‐scan approaches), thereby resulting in Ac‐TAHHHYHGG‐NH₂, Ac‐THAHHYHGG‐NH₂, Ac‐THHAHYHGG‐NH₂, Ac‐THHHAYHGG‐NH₂, Ac‐THHHHAHGG‐NH₂, and Ac‐THHHHYAGG‐NH₂ peptides. We found that the His4 residue is critical for both Ni^II‐ and Cu^II‐ion binding and the effectiveness of binding varies even if the substituted amino acid does not take part in the direct binding interactions.     

Protein–polysaccharide interactions and aggregates in food formulations

The protein–polysaccharide combinations that lead to electrostatic complex and coacervate formation are the object of extensive research using both layer-by-layer and mixed emulsion approaches. The protein–polysaccharide conjugates demonstrated interesting physicochemical properties as stabilizers and emulsifiers, as well as texture modifiers in food products. Furthermore, they are potential optimal nutrient delivery systems. Their complex behavior due to several factors such as pH, ionic strength, concentration, heat, and mechanical treatments is the main reason behind the continuous growth of the research field. The review is reporting some recent advances on the topic, along with an overview of the possible interactions between protein and polysaccharide, from Maillard reaction to enzymatic cross-linking passing through coacervates.     

Ultraviolet Light,Unfolded Protein Response and Autophagy†

The endoplasmic reticulum (ER) plays an important role in the regulation of protein synthesis. Alterations in the folding capacity of the ER induce stress, which activates three ER sensors that mediate the unfolded protein response (UPR). Components of the pathways regulated by these sensors have been shown to regulate autophagy. The last corresponds to a mechanism of self-eating and recycling important for proper cell maintenance. Ultraviolet radiation (UV) is an external damaging stimulus that is known for inducing oxidative stress, and DNA, lipid and protein damage. Many controversies exist regarding the role of UV-inducing ER stress or autophagy. However, a connection between the three of them has not been addressed. In this review, we will discuss the contradictory theories regarding the relationships between UV radiation with the induction of ER stress and autophagy, as well as hypothetic connections between UV, ER stress and autophagy.     

A Bioorthogonal Click Chemistry Toolbox for Targeted Synthesis of Branched and Well-Defined Protein–Protein Conjugates

Bioorthogonal chemistry holds great potential to generate difficult-to-access protein–protein conjugate architectures. Current applications are hampered by challenging protein expression systems, slow conjugation chemistry, use of undesirable catalysts, or often do not result in quantitative product formation. Here we present a highly efficient technology for protein functionalization with commonly used bioorthogonal motifs for Diels–Alder cycloaddition with inverse electron demand (DA_inv). With the aim of precisely generating branched protein chimeras, we systematically assessed the reactivity, stability and side product formation of various bioorthogonal chemistries directly at the protein level. We demonstrate the efficiency and versatility of our conjugation platform using different functional proteins and the therapeutic antibody trastuzumab. This technology enables fast and routine access to tailored and hitherto inaccessible protein chimeras useful for a variety of scientific disciplines. We expect our work to substantially enhance antibody applications such as immunodetection and protein toxin-based targeted cancer therapies.     

Detecting Protein–Glycolipid Interactions Using Glycomicelles and CaR-ESI-MS

This study reports on the use of the catch-and-release electrospray ionization mass spectrometry (CaR-ESI-MS) assay, combined with glycomicelles, as a method for detecting specific interactions between water-soluble proteins and glycolipids (GLs) in aqueous solution. The B subunit homopentamers of cholera toxin (CTB₅) and Shiga toxin type 1 B (Stx1B₅) and the gangliosides GM1, GM2, GM3, GD1a, GD1b, GT1b, and GD2 served as model systems for this study. The CTB₅ exhibits broad specificity for gangliosides and binds to GM1, GM2, GM3, GD1a, GD1b, and GT1b; Stx1B₅ does not recognize gangliosides. The CaR-ESI-MS assay was used to analyze solutions of CTB₅ or Stx1B₅ and individual gangliosides (GM1, GM2, GM3, GD1a, GD1b, GT1b, and GD2) or mixtures thereof. The high affinity interaction of CTB₅ with GM1 was successfully detected. However, the apparent affinity, as determined from the mass spectra, is significantly lower than that of the corresponding pentasaccharide or when GM1 is presented in model membranes such as nanodiscs. Interactions between CTB₅ and the low affinity gangliosides GD1a, GD1b, and GT1b, as well as GD2, which served as a negative control, were detected; no binding of CTB₅ to GM2 or GM3 was observed. The CaR-ESI-MS results obtained for Stx1B₅ reveal that nonspecific protein-ganglioside binding can occur during the ESI process, although the extent of binding varies between gangliosides. Consequently, interactions detected for CTB₅ with GD1a, GD1b, and GT1b are likely nonspecific in origin. Taken together, these results reveal that the CaR-ESI-MS/glycomicelle approach for detecting protein–GL interactions is prone to false positives and false negatives and must be used with caution.

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Isolation and Identification of α-Glucosidase and Protein Glycation Inhibitors from Stereospermum colais

Stereospermum colais (family Bignoniaceae) is a well-known pharmacologically potent medicinal plant reported in traditional systems of medicine. Phytochemical investigation of the roots of S. colais resulted in the isolation of seven compounds, and the metabolites were screened for its α-glucosidase enzyme inhibition and anti-glycation property. The compounds identified were β-sitosterol (1), 2-(4′-hydroxyphenyl) ethyl undecanoate (2), 2-(4′-hydroxyphenyl)ethyl pentadecanoate (3), 5α-ergosta-7,22-dien-3β-ol (4), ursolic acid (5), lapachol (6), and pinoresinol (7). Ursolic acid, lapachol, and pinoresinol possessed IC₅₀ values of 119.01, 130.29, and 125.62 nM, respectively, compared to standard ascorbic acid with an IC₅₀ value of 201.01 nM. The other compounds failed to show the activity. Results of the current study showcased the possible exploration of this medicinal plant for the treatment of type 2 diabetes in line with the development of phytopharmaceutical industry.     

Probing the Selectivity and Protein⋅Protein Interactions of a Nonreducing Fungal Polyketide Synthase Using Mechanism-Based Crosslinkers

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Delineating Protein–Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple-Walker Umbrella Sampling Simulations

The protein–protein interaction energetics can be obtained by calculating the potential of mean force (PMF) from umbrella sampling (US) simulations, in which samplings are often enhanced along a predefined vector as the reaction coordinate. However, any slight change in the vector may significantly vary the calculated PMF, and therefore the energetics using a random choice of vector may mislead. A non-predefined curve path-based sampling enhancement approach is a natural alternative, but was relatively less explored for protein–protein systems. In this work, dissociation of the barnase–barstar complex is simulated by implementing non-predefined curvilinear pathways in US simulations. A simple variational principle is applied to determine the lower bound PMF, which could be used to derive the standard free energy of binding. Two major dissociation pathways, which include interactions with the RNA-binding loop and the Val 36 to Gly 40 loop, are observed. Further, the proposed approach was used to discriminate the decoys from protein–protein docking studies. © 2019 Wiley Periodicals, Inc.     

Reliable Determinations of Protein–Ligand Interactions by Direct ESI-MS Measurements. Are We There Yet?

The association-dissociation of noncovalent interactions between protein and ligands, such as other proteins, carbohydrates, lipids, DNA, or small molecules, are critical events in many biological processes. The discovery and characterization of these interactions is essential to a complete understanding of biochemical reactions and pathways and to the design of novel therapeutic agents that may be used to treat a variety of diseases and infections. Over the last 20 y, electrospray ionization mass spectrometry (ESI-MS) has emerged as a versatile tool for the identification and quantification of protein–ligand interactions in vitro. Here, we describe the implementation of the direct ESI-MS assay for the determination of protein–ligand binding stoichiometry and affinity. Additionally, we outline common sources of error encountered with these measurements and various strategies to overcome them. Finally, we comment on some of the outstanding challenges associated with the implementation of the assay and highlight new areas where direct ESI-MS measurements are expected to make significant contributions in the future.     

Protein recognition by bivalent, ‘turn-on’ fluorescent molecular probes

We show that the conversion of a known intercalating dye (i.e., thiazole orange) into a bivalent protein binder could lead to the realization of a novel class of ‘turn-on’ fluorescent molecular probes that detect proteins with high affinity, selectivity, and a high signal-to-noise (S/N) ratio. The feasibility of the approach is demonstrated with monomolecular probes that light-up in the presence of three different proteins: acetylcholinesterase (AChE), glutathione-s-transferase (GST), or avidin (Av) at low concentrations and with minimal background signal. The way by which such probes can be used to detect individual protein isoforms and be applied in inhibitor screening, cell imaging, and biomarker detection is described.     

Protein—Protein Interactions in Aqueous Ammonium Sulfate Solutions. Lysozyme and Bovine Serum Albumin (BSA)

Osmotic pressures have been measured to determine lysozyme—lysozyme,BSA—BSA, and lysosyme—BSA interactions for protein concentrations to 100 g-L^–1in an aqueous solution of ammonium sulfate at ambient temperature, as a functionof ionic strength and pH. Osmotic second virial coefficients for lysozyme, forBSA, and for a mixture of BSA and lysozyme were calculated from theosmotic-pressure data for protein concentrations to 40 g-L^–1. The osmotic second virialcoefficient of lysozyme is slightly negative and becomes more negative withrising ionic strength and pH. The osmotic second virial coefficient for BSA isslightly positive, increasing with ionic strength and pH. The osmotic second virialcross coefficient of the mixture lies between the coefficients for lysozyme andBSA, indicating that the attractive forces for a lysozyme—BSA pair areintermediate between those for the lysozyme—lysozyme and BSA—BSA pairs. For proteinconcentrations less than 100 g-L^–1, experimental osmotic-pressure data comparefavorably with results from an adhesive hard-sphere model, which has previouslybeen shown to fit osmotic compressibilities of lysozyme solutions.