Protein precipitation and denaturation by dimethyl sulfoxide

Directly Quantifiable Biotinylation Using a Water-Soluble Isatoic Anhydride Platform

Isatoic anhydride (IA) has been shown to be a useful platform for quantifiable bioconjugation. The elaboration of a water-soluble isatoic anhydride-based platform with biotin offers readily quantifiable biotinylation reagents through nondestructive methods of quantification. The incorporation of functionality is directly quantified using the reagent's unique absorbance or fluorescence signature, located outside the biological window. Several biotinylation reagents are prepared with various linker lengths, and the quantification of biotinylated proteins is demonstrated and compared to results from the traditional HABA assay.

Bio-inspired Ag nanovilli-based sandwich-type SERS aptasensor for ultrasensitive and selective detection of 25-hydroxy vitamin D3

Vitamin D has been identified as an essential biomarker for various diseases such as rheumatoid arthritis, cancer, and cardiovascular diseases. Recently, many reports have demonstrated a potential link between vitamin D and systemic infections, including coronavirus disease 2019. The villi of the small intestine increase the surface area of the intestinal walls, demonstrating exceptionally efficient absorption of nutrients in the lumen and adding digestive secretions. In this study, based on the villi structure, we developed a bio-inspired silver nanovilli-based sandwich-type surface enhanced Raman scattering aptasensor for the ultrasensitive and selective detection of 25-hydroxy vitamin D₃. The densely packed nanovilli structure enhanced the Raman signal, forming hotspots owing to its large surface area. Using experiments and electromagnetic simulations, we optimized the nanovilli structure as a SERS sensor. The sandwich-type aptasensor was designed using an aptamer and 4-Phenyl-1,2,4-triazoline-3,5-dione-methylene blue complex. The nanovilli-based aptasensor could sensitively detect various concentrations of 25-hydroxy vitamin D₃, ranging from those found in deficient to excess conditions. The detection limit of the nanovilli-based sandwich-type aptasensor for 25-hydroxy vitamin D₃ was 0.001 ng/mL, which is much lower than the deficiency concentration, and was detectable even in the human serum. In addition, our proposed sensor exhibited good repeatability (17.76%) and reproducibility (7.47%). Moreover, the nanovilli-based sandwich-type SERS aptasensor could selectively distinguish 25-hydroxy vitamin D₃ from other vitamins. The silver nanovilli-based sandwich-type surface enhanced Raman scattering aptasensor opens a new avenue for the development of a bio-inspired vitamin-sensing platform.

Dimethyl Sulfoxide-Free and Water-Soluble Fluorescent Probe for Detection of Bovine Serum Albumin Prepared by Ionic Co-assembly of Amphiphiles

Detection of bovine serum albumin (BSA) is an important issue in the sense of medical applications and enzymatic reactions; however, the recently developed fluorescent probes require the involvement of dimethyl sulfoxide (DMSO), which may be detrimental to proteins. In this study, we demonstrated a DMSO-free and water-soluble fluorescent probe prepared by ionic co-assembly of amphiphiles. The cationic amphiphile is a newly designed molecule (denoted by DPP-12) bearing a conjugated diketopyrrolopyrrole (DPP) and two tetraphenylethylene groups. It turns out that the fluorescence emission of DPP-12 depends on the amount of anionic amphiphilic sodium dodecyl benzene sulfonate (SDBS). The fluorescence intensity first increases and then decreases with the concentration of SDBS, and each branch presents a linear relationship. BSA consumes SDBS by the formation of complexes, thus leading to an increase of fluorescence intensity of the mixed solution of DPP-12 and SDBS. Therefore, the mixed solution of DPP-12 and SDBS was applied as a fluorescent probe to detect the low concentration of BSA by back-titration. This fluorescent probe does not require DMSO and has good tolerance to metal ions in blood and good photostability. The limit of detection is as low as 940 nM, almost 3 orders of magnitude lower than the content in organisms.

Thermodynamic Evaluation of the Interactions between Anticancer Pt(II) Complexes and Model Proteins

In this work, we have analysed the binding of the Pt(II) complexes ([PtCl(4′-phenyl-2,2′:6′,2″-terpyridine)](CF₃SO₃) (1), [PtI(4′-phenyl-2,2′:6′,2″-terpyridine)](CF₃SO₃) (2) and [PtCl(1,3-di(2-pyridyl)benzene) (3)] with selected model proteins (hen egg-white lysozyme, HEWL, and ribonuclease A, RNase A). Platinum coordination compounds are intensively studied to develop improved anticancer agents. In this regard, a critical issue is the possible role of Pt-protein interactions in their mechanisms of action. Multiple techniques such as differential scanning calorimetry (DSC), electrospray ionization mass spectrometry (ESI-MS) and UV-Vis absorbance titrations were used to enlighten the details of the binding to the different biosubstrates. On the one hand, it may be concluded that the affinity of 3 for the proteins is low. On the other hand, 1 and 2 strongly bind them, but with major binding mode differences when switching from HEWL to RNase A. Both 1 and 2 bind to HEWL with a non-specific (DSC) and non-covalent (ESI-MS) binding mode, dominated by a 1:1 binding stoichiometry (UV-Vis). ESI-MS data indicate a protein-driven chloride loss that does not convert into a covalent bond, likely due to the unfavourable complexes’ geometries and steric hindrance. This result, together with the significant changes of the absorbance profiles of the complex upon interaction, suggest an electrostatic binding mode supported by some stacking interaction of the aromatic ligand. Very differently, in the case of RNase A, slow formation of covalent adducts occurs (DSC, ESI-MS). The reactivity is higher for the iodo-compound 2, in agreement with iodine lability higher than chlorine.

The pursuit of resin-dentin bond durability: Simultaneous enhancement of collagen structure and polymer network formation in hybrid layers

OBJECTIVE

Imperfect polymer formation as well as collagen's susceptibility to enzymatic degradation increase the vulnerability of hybrid layers over time. This study investigated the effect of new dimethyl sulfoxide (DMSO)-containing pretreatments on long-term bond strength, hybrid layer quality, monomer conversion and collagen structure.

METHODS

H₃PO₄-etched mid-coronal dentin surfaces from extracted human molars (n = 8) were randomly treated with aqueous and ethanolic DMSO solutions or following the ethanol-wet bonding technique. Dentin bonding was performed with a three-step etch-and-rinse adhesive. Resin-dentin beams (0.8 mm²) were stored in artificial saliva at 37 °C for 24 h and 2.5 years, submitted to microtensile bond strength testing at 0.5 mm/min and semi-quantitative SEM nanoleakage analysis (n = 8). Micro-Raman spectroscopy was used to determine the degree of conversion at different depths in the hybrid layer (n = 6). Changes in the apparent modulus of elasticity of demineralized collagen beams measuring 0.5 × 1.7 × 7 mm (n = 10) and loss of dry mass (n = 10) after 30 days were calculated via three-point bending and precision weighing, respectively.

RESULTS

DMSO-containing pretreatments produced higher bond strengths, which did not change significantly over time presenting lower incidence of water-filled zones. Higher uniformity in monomer conversion across the hybrid layer occurred for all pretreatments. DMSO-induced collagen stiffening was reversible in water, but with lower peptide solubilization.

SIGNIFICANCE

Improved polymer formation and higher stability of the collagen-structure can be attributed to DMSO's unique ability to simultaneously modify both biological and resin components within the hybrid layer. Pretreatments composed of DMSO/ethanol may be a viable-effective alternative to extend the longevity of resin-dentin bonds.

Mechanistic insight into esterase-catalyzed hydrolysis of phthalate esters (PAEs) based on integrated multi-spectroscopic analyses and docking simulation

A novel PAE-hydrolyzing esterase (named Hyd) gene was screened from the genomic library of Rhodococcus sp. 2G and was successfully expressed in heterologous E. coli, which was defined as a new family of esterolytic enzymes. The purified Hyd could efficiently degrade various PAEs, displaying high activity and stability with a broad range of pH (4-10) and temperature (20-60 °C). Interaction mechanism of Hyd with dibutyl phthalate (DBP) was investigated by integrated multi-spectroscopic and docking simulation methods. Fluorescence and UV-vis spectra revealed that DBP could quench the fluorescence of Hyd through a static quenching mechanism. The results from synchronous fluorescence and CD spectra confirmed that the DBP binding to Hyd triggered conformational and micro-environmental changes of Hyd, which were characterized by increased stretching extent and random coil, and decreased α-helix and β-sheet. Molecular docking study showed that DBP could be bound to the cavity of Hyd with hydrogen bonding and hydrophobic interaction. A novel and distinctive catalytic mechanism was proposed: two key residues Thr¹⁹⁰ and Ser¹⁹¹ might catalyze the hydrolysis of DBP, instead of the conserved catalytic triad (Ser-His-Asp) reported elsewhere, which was confirmed by site-directed mutagenesis.

Development of Water Solubility of 2-Phenylsulfanylhydroquinone Dimer Dye

With the aim of developing a new fluorescence dye with enhanced photophysical properties, this study describes the modification of the 2-phenylsulfanylhydroquinone dimer to realize a new bioimaging molecule. The characteristics of the dimer were advanced by introducing tetraethylene glycol side chains to provide sufficient water solubility and a tether consisting of an N-hydroxysuccinimide-terminated C6-carbon chain to attach bioactive molecules. Two derivatives containing two or three tetraethylene glycol side chains were designed and prepared, and the latter showed sufficient water solubility for biochemical applications. Both compounds exhibited similar photophysical properties and blue fluorescence under UV light irradiation. The dye containing three tetraethylene glycol units reacted with bovine serum albumin in water to give fluorescent derivatives.

Discovery, biological evaluation and molecular dynamic simulations of butyrylcholinesterase inhibitors through structure-based pharmacophore virtual screening

Aim: Butyrylcholinesterase (BChE) is a crucial therapeutic target because it is associated with multiple pathological elements of Alzheimer's disease (AD). An integrated computational strategy was employed to exploit effective BChE inhibitors. Methods & results: Ten compounds derived from the Enamine database by structure-based pharmacophore virtual screening were further evaluated for biological activity; out of the ten, only five had an IC₅₀ of less than 100 μM. Among these five compounds, a new molecule, 970180, presented the most potency against BChE, with an IC₅₀ of 4.24 ± 0.16 μM, and acted as a mixed-type inhibitor. Molecular dynamic simulations and absorption, distribution, metabolism and excretion prediction further confirmed its high potential as a good candidate of BChE inhibitor. Furthermore, cytotoxicity of molecule 970180 was not observed at concentrations up to 50 μM, and the molecule also showed a prominent neuroprotective effect compared with tacrine at 25 and 50 μM. Conclusion: This study provides an effective structure-based pharmacophore virtual screening method to discover BChE inhibitors and provide new choices for the development of BChE inhibitors, which may be beneficial for AD patients.

Winter is coming: the future of cryopreservation

The preservative effects of low temperature on biological materials have been long recognised, and cryopreservation is now widely used in biomedicine, including in organ transplantation, regenerative medicine and drug discovery. The lack of organs for transplantation constitutes a major medical challenge, stemming largely from the inability to preserve donated organs until a suitable recipient is found. Here, we review the latest cryopreservation methods and applications. We describe the main challenges-scaling up to large volumes and complex tissues, preventing ice formation and mitigating cryoprotectant toxicity-discuss advantages and disadvantages of current methods and outline prospects for the future of the field.

Principles of Ice-Free Cryopreservation by Vitrification

Vitrification is an alternative to cryopreservation by freezing that enables hydrated living cells to be cooled to cryogenic temperatures in the absence of ice. Vitrification simplifies and frequently improves cryopreservation because it eliminates mechanical injury from ice, eliminates the need to find optimal cooling and warming rates, eliminates the importance of differing optimal cooling and warming rates for cells in mixed cell type populations, eliminates the need to find a frequently imperfect compromise between solution effects injury and intracellular ice formation, and can enable chilling injury to be "outrun" by using rapid cooling without a risk of intracellular ice formation. On the other hand, vitrification requires much higher concentrations of cryoprotectants than cryopreservation by freezing, which introduces greater risks of both osmotic damage and cryoprotectant toxicity. Fortunately, a large number of remedies for the latter problem have been discovered over the past 35 years, and osmotic damage can in most cases be eliminated or adequately controlled by paying careful attention to cryoprotectant introduction and washout techniques. Vitrification therefore has the potential to enable the superior and convenient cryopreservation of a wide range of biological systems (including molecules, cells, tissues, organs, and even some whole organisms), and it is also increasingly recognized as a successful strategy for surviving harsh environmental conditions in nature. But the potential of vitrification is sometimes limited by an insufficient understanding of the complex physical and biological principles involved, and therefore a better understanding may not only help to improve present outcomes but may also point the way to new strategies that may be yet more successful in the future. This chapter accordingly describes the basic principles of vitrification and indicates the broad potential biological relevance of this alternative method of cryopreservation.

The dynamic changes of glycogen molecular structure in Escherichia coli BL21(DE3)

Diurnal alteration of glycogen molecular structure has been identified in healthy mice. Recently, both fragile (disintegration in dimethyl sulfoxide) and stable (not disintegrating in DMSO) glycogen particles were found in Escherichia coli. However, how glycogen structure changes dynamically in E. coli is not clear. The question examined here is whether fragile, stable glycogen α particles occur in bacteria, following a similar pattern as in mice. In this study, we examine the dynamic changes of glycogen molecular structure over 24-h in E. coli BL21(DE3), using transmission electron microscopy, size exclusion chromatography and fluorophore-assisted carbohydrate electrophoresis at representative time points. It was found that glycogen structure was mainly fragile at the synthesis stage and largely stable during the degradation stage. qRT-PCR results indicated that balance of anabolic and catabolic gene expression levels in glycogen metabolism could be a key factor affecting the fragility of glycogen α particles in bacteria.

Molecular diagnostic of toxigenic Corynebacterium diphtheriae strain by DNA sensor potentially suitable for electrochemical point-of-care diagnostic

The presented study is focused on the development of electrochemical genosensor for detection of tox gene fragment of toxigenic Corynebacterium diphtheriae strain. Together with our previous studies it fulfils the whole procedure for fast and accurate diagnostic of diphtheria at its early stage of infection with the use of electrochemical methods. The developed DNA sensor potentially can be used in more sophisticated portable device. After the electrochemical stem-loop probe structure optimization the conditions for real asymmetric PCR (aPCR) product detection were selected. As was shown it was crucial to optimize the magnesium and organic solvent concentrations in detection buffer. Under optimal conditions it was possible to selectively detect as low as 20.8 nM of complementary stand in 5 min or 0.5 nM in 30 min with sensitivity of 12.81 and 0.24 1⋅μM^-1 respectively. The unspecific biosensor response was elucidated with the use of new electrode blocking agent, diethyldithiocarbamate. Its application in electrochemical genosensors lead to significant higher current values and the biosensor response even in conditions with magnesium ion depletion. The developed biosensor selectivity was examined using samples containing genetic material originated from a number of non-target bacterial species which potentially can be present in the human upper respiratory tract.

Cholesteryl-Conjugated Ribonuclease A Exhibits Enzyme Activity in Aqueous Solution and Resistance to Dimethyl Sulfoxide

Using bovine pancreatic ribonuclease A (RNase A) and cholesterol, we synthesized cholesteryl-conjugated ribonuclease A (CHRNase A) to evaluate the influence of a conjugated hydrophobic moiety on protein function. Nuclear magnetic resonance and matrix-assisted laser desorption/ionization time-of-flight spectrometry suggested that one cholesteryl group was conjugated to RNase A. Differential scanning calorimetry indicated that CHRNase A was denatured in the solid state but was folded in phosphate buffer (0.05 mol/L, pH 6.5). CHRNase A resembled RNase A in its secondary structure, but circular dichroism (CD) spectra revealed that the helical content of CHRNase A was decreased and the tertiary structure of CHRNase A differed from that of RNase A. Furthermore, fluorescence measurements, CD spectra, an 8-anilino-1-naphthalenesulfonic acid ammonium salt-based assay, and surface tension measurements suggested that cholesterol was conjugated to a tyrosine residue on the protein surface. The relative activity of CHRNase A to RNase A was 79 ± 7%, and the enzyme activity of CHRNase A by adding β-cyclodextrin (β-CyD) increased to 129 ± 7%. Therefore, we considered that the cholesteryl group interacted with substrate (cytidine 2'3'-cyclic monophosphate monosodium salt) to inhibit the enzyme reaction. Finally, the environment around tyrosine residues in CHRNase A in dimethyl sulfoxide was similar to that of native RNase A in phosphate buffer (0.05 mol/L, pH 6.5). These results suggest that cholesterol conjugation to RNase A altered RNase A functionality, including improvement of RNase A resistance to dimethyl sulfoxide and modulation of the ability of β-CyD to control RNase A enzymatic activity.

Me2SO perfusion time for whole-organ cryopreservation can be shortened: Results of micro-computed tomography monitoring during Me2SO perfusion of rat hearts

Cryopreservation of whole organs and specific tissues is an important and continually expanding field of medicine. The protocols currently used for organ preservation do not ensure survivability and functionality; the protocols for ovarian tissue lead to acceptable outcomes, but these are still capable of further improvement. In general, cryopreservation protocols need to be optimized. One important approach to improving cryopreservation protocols in general involves reducing exposure to cytotoxic cryoprotective agents prior to freezing. This study, therefore, evaluated the real-time tissue penetration of dimethyl sulfoxide, a cryoprotective agent that is widely used in cryopreservation. Dimethyl sulfoxide penetration in rat hearts perfused with a 15% (v/v) dimethyl sulfoxide solution was examined in real-time using dynamic contrast-enhanced micro-computed tomography imaging. Viability of cardiomyocytes was not significantly affected by the dimethyl sulfoxide perfusion procedure. Two different perfusion rates were evaluated and compared with perfusion using a common iodine-based contrast agent (iomeprol). The dynamic contrast-enhanced micro-computed tomography imaging data showed that dimethyl sulfoxide flushes both the extracellular and intracellular spaces in rat heart tissue to 95% equilibration after ≈ 35 s via perfusion. Subsequent wash-out via perfusion is completed to 95% within ≈ 49 s. The equilibration duration routinely used in dimethyl sulfoxide–based protocols for cryopreservation should therefore be questioned. Shorter incubation duration would perhaps be sufficient, as well as being beneficial in relation to cell survivability. It would be helpful to have techniques for non-invasive real-time monitoring of the penetration of cryoprotective agents and such techniques should be used to revise cryopreservation protocols. Switching to perfusion-based equilibration procedures might be beneficial, if feasible.

γ-Glutamyltranspeptidase from Bacillus amyloliquefaciens: transpeptidation activity enhancement and L-theanine production

L-theanine, a unique amino acid in green tea with health benefits, can be enzymatically synthesized by γ-glutamyltranspeptidase (γ-GT; EC 2.3.2.2). Here, a salt-tolerant γ-glutamyltranspeptidase from a marine bacterium Bacillus amyloliquefaciens was expressed in Escherichia. coli BL21 (DE3) and was shown to be optimally active at 55 °C, pH 8.5 and alkali stable. A mutant, with higher transpeptidation activity, was obtained following two rounds of directed evolution using error-prone PCR and site-saturation mutagenesis. The mutation increased the ratio of transpeptidation to hydrolysis from 1.6 to 35.6. Additionally, Kinetic analysis exhibited 17.5% decrease of K_m, 13.0-fold increase of K_cat, and 16.3-fold increase of K_cat/K_m in mutant V319A/S437 G versus the wild-type. The 3-D modelling analysis revealed a tighter binding pocket in mutant V319A/S437 G. The frequency of hydrogen bond between donor substrate and two residues in the catalytic pocket (Gly437 and Thr375) was enhanced, which stabilized the ligand binding and thus improved the catalytic efficiency. The optimal conditions for the biocatalytic synthesis were determined as pH 10.0, 20 μg mL^-1BaGT, 200 mM L-glutamine, 2 M ethylamine, and a reaction time of 5 h. The V319A/S437 G mutant was shown to increase the percentage yield of L-theanine from 58% to 83%. These results indicate the great potential of V319A/S437 G in L-theanine production after further study.

Sustainable production, biochemical and molecular characterization of thermo-and-solvent stable alkaline serine keratinase from novel Bacillus pumilus AR57 for promising poultry solid waste management

The increasing amount of recalcitrant keratinous wastes generated from the poultry industry poses a serious threat to the environment. Keratinase have gained much attention to convert these wastes into valuable products. Ever since primitive feathers first appeared on dinosaurs, microorganisms have evolved to degrade this most recalcitrant keratin. In this study, we identified a promising keratinolytic bacterial strain for bioconversion of poultry solid wastes. A true keratinolytic bacterium was isolated from the slaughterhouse soil and was identified and designated as Bacillus pumilus AR57 by 16S rRNA sequencing. For enhanced keratinase production and rapid keratin degradation, the media components and substrate concentration were optimized through shake flask culture. White chicken feather (1% w/v) was found to be the good substrate concentration for high keratinase production when supplemented with simple medium ingredients. The biochemical characterization reveals astounding results which makes the B. pumilus AR57 keratinase as a novel and unique protease. Optimum activity of the crude enzyme was exhibited at pH 9 and 45 °C. The crude extracellular keratinase was characterized as thermo-and-solvent (DMSO) stable serine keratinase. Bacillus pumilus AR57 showed complete degradation (100%) of white chicken feather (1% w/v) within 18 h when incubated in modified minimal medium supplemented with DMSO (1% v/v) at 150 rpm at 37 °C. Keratinase from modified minimal medium supplemented with DMSO exhibits a half-life of 4 days. Whereas, keratinase from the modified minimal medium fortified with white chicken feather (1% w/v) was stable for 3 h only. Feather meal produced by B. pumilus AR57 was found to be rich in essential amino acids. Hence, we proposed B. pumilus AR57 as a potential candidate for the future application in eco-friendly bioconversion of poultry waste and the keratinase could play a pivotal role in the detergent industry. While feather meal may serve as an alternative to produce animal feed and biofertilizers.

The multifaceted effects of DMSO and high hydrostatic pressure on the kinetic constants of hydrolysis reactions catalyzed by α-chymotrypsin

The cosolvent DMSO and high pressure have antagonistic effects on the kinetic constants of α-chymotrypsin-catalyzed hydrolysis reactions.

Synthesis and biological evaluation of thiazole derivatives as LbSOD inhibitors

Leishmaniasis is considered as one of the major neglected tropical diseases due to its magnitude and wide geographic distribution. Leishmania braziliensis, responsible for cutaneous leishmaniasis, is the most prevalent species in Brazil. Superoxide dismutase (SOD) belongs to the antioxidant pathway of the parasites and human host. Despite the differences between SOD of Leishmania braziliensis and human make this enzyme a promising target for drug development efforts. No medicinal chemistry effort has been made to identify LbSOD inhibitors. Herein, we show that thermal shift assays (TSA) and fluorescent protein-labeled assays (FPLA) can be employed as primary and secondary screens to achieve this goal. Moreover, we show that thiazole derivatives bind to LbSOD with micromolar affinity.

A Novel Long-Range n to π* Interaction Secures the Smallest known α-Helix in Water

The introduction of an amide bond linking side chains of the first and fifth amino acids forms a cyclic pentapeptide that optimally stabilizes the smallest known α-helix in water. The origin of the stabilization is unclear. The observed dependence of α-helicity on the solvent and cyclization linker led us to discover a novel long-range n to π* interaction between a main-chain amide oxygen and a uniquely positioned carbonyl group in the linker of cyclic pentapeptides. CD and NMR spectra, NMR and X-ray structures, modelling, and MD simulations reveal that this first example of a synthetically incorporated long-range n to π* CO⋅⋅⋅C^γ =Ο interaction uniquely enforces an almost perfect and remarkably stable peptide α-helix in water but not in DMSO. This unusual interaction with a covalent amide bond outside the helical backbone suggests new approaches to synthetically stabilize peptide structures in water.

Technical Capabilities and Limitations of Optical Spectroscopy and Calorimetry Using Water-Miscible Solvents: The Case of Dimethyl Sulfoxide, Acetonitrile, and 1,4-Dioxane

In drug development, water-miscible solvents are commonly used to dissolve drug substances. Typical routine procedures in drug development include dilution of the stock drug solution into an aqueous solution containing target macromolecules for drug binding assays. However, water-miscible solvents impose some technical limitations on the assays on account of their light absorption and heat capacity. Here, we examined the effects of the dilution of 3 water-miscible solvents, that is, dimethyl sulfoxide, acetonitrile, and 1,4-dioxane, on the baseline stability and signal/noise ratio in circular dichroism spectroscopy, isothermal titration calorimetry, and differential scanning calorimetry. Dimethyl sulfoxide and 1,4-dioxane affect the signal/noise ratio of circular dichroism spectra at typically used concentrations due to their light absorbance. The water-miscible solvents generate interfering signals in the isothermal titration calorimetry due to their mixing heat. They show negative or positive slope in the differential scanning calorimetry. Such interfering effects of the solvents are reduced by appropriate dilution according to the analytical techniques. Because the water-miscible solvents have solubilization capacity for alkyl chain moieties and aromatic moieties of chemicals, drug substances containing these moieties can be dissolved into the solvents and then subjected to the analyses to examine their interactions with target proteins after appropriate dilution of the drug solutions.

Electrochemical characterization of natural organic matter by direct voltammetry in an aprotic solvent

The complex and indeterminant composition of NOM makes characterization of its redox properties challenging. Approaches that have been taken to address this challenge include chemical probe reactions, potentiometric titrations, chronocoulometry, and voltammetry. In this study, we revisit the use of direct voltammetric methods in aprotic solvents by applying an expanded and refined suite of methods to a large set of NOM samples and model compounds (54 NOM samples from 10 different sources, 7 NOM model compounds, and 2 fresh extracts of plant materials that are high in redox-active quinonoid model compounds dissolved in DMSO). Refinements in the methods of fitting the data obtained by staircase cyclic voltammetry (SCV) provided improved definition of peaks, and square wave voltammetry (SWV), performed under the same conditions as SCV, provided even more reliable identification and quantitation of peaks. Further evidence is provided that DMSO improves the electrode response by unfolding some of the tertiary structure of NOM polymers, thereby allowing greater contact between redox active functional groups and the electrode surface. We averaged experimental peak potentials for all NOM compounds and calculated potentials in water. Average values for Epa1, Epc1, and Ep1 in DMSO were -0.866 ± 0.069, -1.35 ± 0.071, and -0.831 ± 0.051 V vs. Ag/Ag+, and -0.128, -0.613, and -0.0930 V vs. SHE in water. In addition to peak potentials, the breadth of SCV peaks was quantified as a way to characterize the degree to which the redox activity of NOM is due to a continuum of contributing functional groups. The average breadth values were 1.63 ± 0.24, 1.28 ± 0.34, and 0.648 ± 0.15 V for Epa1, Epc1, and Ep1 respectively. Comparative analysis of the overall dataset-from SCV and SWV on all NOMs and model compounds-revealed that NOM redox properties vary over a narrower range than expected based on model compound properties. This lack of diversity in redox properties of NOM is similar to conclusions from other recent work on the molecular structure of NOM, all of which could be the result of selectivity in the common extraction methods used to obtain the materials.

Conspecific and allospecific larval extracts entice mosquitoes to lay eggs and may be used in attract-and-kill control strategy

One of the strategies of integrated vector management is to lure gravid mosquitoes for surveillance purposes or to entice them to lay eggs in water containing toxins that kill the offspring (attract-and-kill or trap-and-kill). Typically, the major challenge of this approach is the development of a lure that stimulates oviposition plus a toxin with no deterrent effect. Bacillus thuringiensis var. israelensis (Bti) satisfies the latter criterion, but lures for these autocidal gravid traps are sorely needed. We observed that gravid Aedes aegypti, Ae. albopictus, and Culex quinquefasciatus laid significantly more eggs in cups with extracts from 4th-stage larvae (4 L) of the same or different species. No activity was found when 4 L were extracted with hexane, diethyl ether, methanol, or butanol, but activity was observed with dimethyl sulfoxide extracts. Larval extracts contained both oviposition stimulant(s)/attractant(s) and deterrent(s), which partitioned in the water and hexane phases, respectively. Lyophilized larval extracts were active after a month, but activity was reduced by keeping the sample at 4 °C. In the tested range of 0.1 to 1 larvae-equivalent per milliliter, oviposition activity increased in a dose-dependent manner. In field experiments, Ae. aegpti laid significantly more eggs in traps loaded with larval extracts plus Bti than in control traps with water plus Bti.

Control of Solvent Dynamics around the B12-Dependent Ethanolamine Ammonia-Lyase Enzyme in Frozen Aqueous Solution by Using Dimethyl Sulfoxide Modulation of Mesodomain Volume

The temperature-dependent structure and dynamics of two concentric solvent phases, the protein-associated domain (PAD) and the mesodomain, that surround the ethanolamine ammonia-lyase (EAL) protein from Salmonella typhimurium in frozen polycrystalline aqueous solution are addressed by using electron paramagnetic resonance spectroscopy of the paramagnetic nitroxide spin probe, TEMPOL, over the temperature ( T) range 190-265 K. Dimethyl sulfoxide (DMSO), added at 0.5, 2.0, and 4.0% v/v and present at the maximum freeze concentration at T ≤ 245 K, varies the volume of the interstitial aqueous DMSO mesodomain ( V_meso) relative to a fixed PAD volume ( V_PAD). The increase in V_meso/ V_PAD from 0.8 to 6.0 is quantified by the partitioning of TEMPOL between the two phases. As V_meso/ V_PAD is increased, the Arrhenius parameters for activated TEMPOL rotational motion in the mesodomain remain uniform, whereas the parameters for TEMPOL in the PAD show a progressive transformation toward the mesodomain values (higher mobility). An order-disorder transition (ODT) in the PAD is detected by the exclusion of TEMPOL from the PAD into the mesodomain. The ODT T value is systematically lowered by increased V_meso/ V_PAD (from 215 to 200 K), and PAD ordering kinks the mesodomain Arrhenius dependence. Thus there is reciprocity in PAD-mesodomain solvent coupling. The results are interpreted as a dominant influence of ice-boundary confinement on the PAD solvent structure and dynamics, which is transmitted through the mesodomain and which decreases with mesodomain volume at increased added DMSO. The systematic tuning of PAD and mesodomain solvent dynamics by the variation of added DMSO is an incisive approach for the resolution of contributions of protein-solvent dynamical coupling to EAL catalysis.

Protein-Templated Dynamic Combinatorial Chemistry: Brief Overview and Experimental Protocol

Dynamic combinatorial chemistry (DCC) is a powerful tool to identify bioactive compounds. This efficient technique allows the target to select its own binders and circumvents the need for synthesis and biochemical evaluation of all individual derivatives. An ever-increasing number of publications report the use of DCC on biologically relevant target proteins. This minireview complements previous reviews by focusing on the experimental protocol and giving detailed examples of essential steps and factors that need to be considered, such as protein stability, buffer composition and cosolvents.

Functionalised bicyclic tetramates derived from cysteine as antibacterial agents

Routes to bicyclic tetramates derived from cysteine permitting ready incorporation of functionality at two different points around the periphery of a heterocyclic skeleton are reported. This has enabled the identification of systems active against Gram-positive bacteria, some of which show gyrase and RNA polymerase inhibitory activity. In particular, tetramates substituted with glycosyl side chains, chosen to impart polarity and aqueous solubility, show high antibacterial activity coupled with modest gyrase/polymerase activity in two cases. An analysis of physicochemical properties indicates that the antibacterially active tetramates generally occupy physicochemical space with MW of 300-600, clog D7.4 of -2.5 to 4 and rel. PSA of 11-22%. This work demonstrates that biologically active 3D libraries are readily available by manipulation of a tetramate skeleton.

Lessons we can learn from neurons to make cancer cells quiescent

Cancer is a major concern for contemporary societies. However, the incidence of cancer is unevenly distributed among tissues and cell types. In particular, the evidence indicates that neurons are absolutely resistant to cancer and this is commonly explained on the basis of the known postmitotic state of neurons. The dominant paradigm on cancer understands this problem as a disease caused by mutations in cellular genes that result in unrestrained cell proliferation and eventually in tissue invasion and metastasis. However, the evidence also shows that mutations and gross chromosomal anomalies are common in functional neurons that nevertheless do not become neoplastic. This fact suggests that in the real nonexperimental setting mutations per se are not enough for inducing carcinogenesis but also that the postmitotic state of neurons is not genetically controlled or determined, otherwise there should be reports of spontaneously transformed neurons. Here we discuss the evidence that the postmitotic state of neurons has a structural basis on the high stability of their nuclear higher order structure that performs like an absolute tumor suppressor. We also discuss evidence that it is possible to induce a similar structural postmitotic state in nonneural cell types as a practical strategy for stopping or reducing the progression of cancer.

Conformational perturbation of peptides in presence of polar organic solvents

The critical role played by solvent environment in maintaining the conformational integrity of peptides and proteins is accepted without question. Numerous experiments have suggested that perturbing the solvent environment of peptides and proteins by the addition of polar organic solvents have important consequences for the conformation of these molecules. However, experimental studies of such perturbations often report different kinds of effects depending on the solvent used and/or the sequence/structure of the molecule under study. In this work we report a simulation based comparative study on the effects of adding two common organic solvents viz. Dimethyl sulfoxide (DMSO) and Acetonitrile (MeCN) on the dynamical conformation of a test peptide Ace-Gly-X-Gly-Nme where X is any amino acid. Our studies identify important differences in peptide solvation by these two solvents, which we attempt to correlate with the kinetic stability of the conformation, as well as the identity of the central 'X' residue in the test peptide.

Exchangeable deuterons introduce artifacts in amide 15N CEST experiments used to study protein conformational exchange

Protein molecules sample different conformations in solution and characterizing these conformations is crucial to understanding protein function. ¹⁵N CEST experiments are now routinely used to study slow conformational exchange of protein molecules between a 'visible' major state and 'invisible' minor states. These experiments have also been adapted to measure the solvent exchange rates of amide protons by exploiting the one bond deuterium isotope effect on the amide ¹⁵N chemical shifts. However at moderately high temperatures (~ 50 °C) that are sometimes required to populate protein minor conformers to levels (~ 1%) that can be detected by CEST experiments solvent H/D exchange can lead to 'dips' in low B₁¹⁵N CEST profiles that can be wrongly assigned to the conformational exchange process being characterized. This is demonstrated in the case of ~ 18 kDa T4 Lysozyme (T4L) at 50 °C and the ~ 11 kDa E. coli hibernation promoting factor (HPF) at 52 °C. This problem is trivially solved by eliminating the exchangeable deuterons in the solvent by using either an external D₂O lock or by using a small amount (~ 1-3%) of a molecule like d6-DMSO that does not contain exchangeable deuterons to lock the spectrometer.

Minute Additions of DMSO Affect Protein Dynamics Measurements by NMR Relaxation Experiments through Significant Changes in Solvent Viscosity

Studies of protein-ligand binding often rely on dissolving the ligand in dimethyl sulfoxide (DMSO) to achieve sufficient solubility, and then titrating the ligand solution into the protein solution. As a result, the final protein-ligand solution contains small amounts of DMSO in the buffer. Here we report how the addition of DMSO impacts studies of protein conformational dynamics. We used 15 N NMR relaxation to compare the rotational diffusion correlation time (τC ) of proteins in aqueous buffer with and without DMSO. We found that τC scales with the viscosity of the water-DMSO mixture, which depends sensitively on the amount of DMSO and varies by a factor of 2 across the relevant concentration range. NMR relaxation studies of side chains dynamics are commonly interpreted using τC as a fixed parameter, obtained from backbone 15 N relaxation data acquired on a separate sample. Model-free calculations show that errors in τC , arising from mismatched DMSO concentration between samples, lead to significant errors in order parameters. Our results highlight the importance of determining τC for each sample or carefully matching the DMSO concentrations between samples.

Screening of Some Essential Oil Constituents as Potential Inhibitors of the ATP Synthase of Escherichia coli

Many novel bacterial targets and natural inhibitors of enzymes are currently being considered to overcome antibiotic resistance of Escherichia coli. Hence, in this study, 20 essential oil constituents were screened for their potential inhibitory effect on E. coli ATP synthase. This enzyme is involved in the hydrolysis of ATP into ADP and inorganic phosphate (Pi). First, E. coli membrane ATP synthase was isolated via cell lysis. A spectrophotometric method was optimized to quantify the released phosphate from ATP hydrolysis in order to follow the enzymatic activity. The method was validated by determining the kinetic parameters of this reaction (K_m = 144.66 μM and V_max = 270.27 μM/min), and through the inhibition assays of ATP synthase using three reference inhibitors, thymoquinone (half maximal inhibitory concentration [IC₅₀ ] = 50.93 μM), resveratrol (maximum inhibition of 40%), and quercetin (IC₅₀ = 29.01 μM). Among the studied essential oil components, α-terpinene was the most potent inhibitor (IC₅₀ = 19.74 μM) followed by β-pinene, isoeugenol, eugenol, and estragole.

Gold-nanostar-based SERS substrates for studying protein aggregation processes

Aggregation of proteins has been related to some neurodegenerative diseases such as Alzheimer's and Parkinson's among others. Raman spectroscopy is a useful technique for the investigation of protein conformation and of changes in their secondary structure. In this study, a surface enhanced Raman spectroscopy (SERS) substrate based on the immobilization of plasmonic gold nanostars on a glass slide via silanization of the surface has been prepared and characterized. Gold nanostars were synthesized via a seed-growth method using gold nanoparticles as seeds obtained via stainless steel as the reducing agent. The plasmonic substrate provided an enhancement of 5.7 × 102 fold, as shown for the Raman signal of crystal violet. Using this SERS-active substrate, the investigation of aggregation processes of bovine serum albumin (BSA) and myoglobin proteins upon temperature and solvent modification has been enabled with enhanced sensitivity. Both curve fitting and deconvolution of the amide I band, as well as 2D correlation analysis, were employed for the evaluation of the changes in the SERS spectra of the protein samples. The amide I band within the SERS spectra of the BSA protein revealed a decrease in the α-helix structures within the secondary structure of the protein while the presence of β-sheet structures increased with temperature and solvent concentration.

Protein Solvent Interaction: Transition of Protein-solvent Interaction Concept from Basic Research into Solvent Manipulation of Chromatography

Previously, we have reviewed in this journal (Arakawa, T., Kita, Y., Curr. Protein Pept. Sci., 15, 608-620, 2014) the interaction of arginine with proteins and various applications of this solvent additive in the area of protein formulations and downstream processes. In this special issue, we expand the concept of protein-solvent interaction into the analysis of the effects of solvent additives on various column chromatography, including mixed-mode chromatography. Earlier in our research, we have studied the interactions of such a variety of solvent additives as sugars, salts, amino acids, polymers and organic solvents with a variety of proteins, which resulted in mechanistic understanding on their protein stabilization and precipitation effects, the latter known as Hofmeister series. While such a study was then a pure academic research, rapid development of genetic engineering technologies and resultant biotechnologies made it a valuable knowledge in fully utilizing solvent additives in manipulation of protein solution, including column chromatography.

A novel dry-bonding approach to reduce collagen degradation and optimize resin-dentin interfaces

In dentistry, the wet-bonding approach relies on water to maintain demineralized collagen expanded for proper resin infiltration; nevertheless, hydrolytic instability of the resin-dentin interface is inevitable with current bonding techniques. Considering dimethyl sulfoxide’s (DMSO) ability to “biomodify” collagen and precipitate enzymes, the aim was to test whether the use of DMSO would permit adequate resin bonding to H₃PO₄-etched dehydrated dentin and assess its impact on collagen degradation by host-derived enzymes. Etched dentin surfaces from extracted sound human molars were randomly bonded in wet or dry conditions using aqueous or ethanolic DMSO solutions as pretreatments and bonding resins with or without DMSO. Bonded teeth were sectioned into resin-dentin slabs for confocal in situ zymography and beams for microtensile bond strength test. Demineralized powdered dentin was incubated in the tested DMSO -media and a hydroxyproline assay evaluated dissolution of collagen peptides. Zymography was performed on protein extracts obtained from dry and wet H₃PO₄-ecthed dentin powder treated with the DMSO- media. The correlative biochemical analysis demonstrated that reduction of water content during dentin hybridization by the innovative dry-bonding approaches with DMSO is effective to inactivate host-derived MMP-2 and MMP-9 and thus reduce collagen degradation while simultaneously optimizing resin-dentin bonding.

3D Printing Bioactive PLGA Scaffolds Using DMSO as a Removable Solvent

Present bioprinting techniques lack the methodology to print with bioactive materials that retain their biological functionalities. This constraint is due to the fact that extrusion-based printing of synthetic polymers is commonly performed at very high temperatures in order to achieve desired mechanical properties and printing resolutions. Consequently, current methodology prevents printing scaffolds embedded with bioactive molecules, such as growth factors. With the wide use of mesenchymal stem cells (MSCs) in regenerative medicine research, the integration of growth factors into 3D printed scaffolds is critical because it can allow for inducible MSC differentiation. We have successfully incorporated growth factors into extrusion printed poly (lactic-co-glycolic acid) (PLGA) scaffolds by introducing dimethyl sulfoxide (DMSO) for low temperature printing. Mechanical testing results demonstrated significantly different compressive and tensile properties for PLGA scaffold printed with or without DMSO. In particular, the PLGA-DMSO scaffold displayed a highly stretchable feature compared to the regular PLGA scaffold. The cellular response of growth factor introduction was evaluated in vitro using human mesenchymal stem cells (hMSCs). By evaporating the DMSO after printing, we ensured that there was no cytotoxic effect on seeded hMSCs. The addition of lineage specific growth factors led to increased expression of corresponding genetic markers for chondrogenesis, osteogenesis, and adipogenesis. We concluded that the use of DMSO for 3D printed scaffold fabrication with bioactive items is a revolutionary methodology in advancing regenerative medicine. The incorporation of bioactive molecules opens pathways to more therapeutic uses for 3D printing in treating damaged or deteriorating native tissue.

High-level expression and molecular characterization of a recombinant prolidase from Escherichia coli NovaBlue

Long-term use of organophosphorus (OP) compounds has become an increasing global problem and a major threat to sustainability and human health. Prolidase is a proline-specific metallopeptidase that can offer an efficient option for the degradation of OP compounds. In this study, a full-length gene from Escherichia coli NovaBlue encoding a prolidase (EcPepQ) was amplified and cloned into the commercially-available vector pQE-30 to yield pQE-EcPepQ. The overexpressed enzyme was purified from the cell-free extract of isopropyl thio-β-D-galactoside IPTG-induced E. coli M15 (pQE-EcPepQ) cells by nickel-chelate chromatography. The molecular mass of EcPepQ was determined to be about 57 kDa by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and the result of size-exclusion chromatography demonstrated that the enzyme was mainly present in 25 mM Tris–HCl buffer (pH 8.0) as a dimeric form. The optimal conditions for EcPepQ activity were 60 °C, pH 8.0, and 0.1 mM Mn²⁺ ion. Kinetic analysis with Ala-Pro as the substrate showed that the K_m and k_cat values of EcPepQ were 8.8 mM and 926.5 ± 2.0 s⁻¹, respectively. The thermal unfolding of EcPepQ followed a two-state process with one well-defined unfolding transition of 64.2 °C. Analysis of guanidine hydrochloride (GdnHCl)-induced denaturation by tryptophan emission fluorescence spectroscopy revealed that the enzyme had a [GdnHCl]_0.5,N-U value of 1.98 M. The purified enzyme also exhibited some degree of tolerance to various water/organic co-solvents. Isopropanol and tetrahydrofuran were very detrimental to the enzymatic activity of EcPepQ; however, other more hydrophilic co-solvents, such as formamide, methanol, and ethylene glycol, were better tolerated. Eventually, the non-negative influence of some co-solvents on both catalytic activity and structural stability of EcPepQ allows to adjust the reaction conditions more suitable for EcPepQ-catalyzed bioprocess.