The Application of Microsampling Disks in Circular Dichroism Spectroscopy for Peptide and Nucleic Acid Drugs.

In recent years, there has been a growing focus on the development of medium-sized drugs based on peptides or nucleic acids owing to their potential therapeutic benefits. As some of these medium-sized drugs exert their therapeutic effects by adopting specific secondary structures, evaluating their conformational states is crucial to ensure the efficacy, quality, and safety of the drug products. It is important to assess the structural integrity of biomolecular therapeutics to guarantee their intended pharmacological activity and maintain the required standards for drug development and manufacturing. One widely utilized technique for quality evaluation is secondary structural analysis using circular dichroism (CD) spectroscopy. Given the higher production and quality control costs associated with medium-sized drugs compared with small-molecule drugs, developing analytical techniques that enable CD analysis with reduced sample volumes is highly desirable. Herein, we focused on a microsampling disk-type cell as a potential solution for reducing the required sample volume. We investigated whether CD spectral analysis using a microsampling disk could provide equivalent spectra compared with the standard cell (sample volume: approx. 300 µL). Our findings demonstrated that the microsampling disk (sample volume: 2-10 µL) could be successfully applied to CD spectral analysis of peptide and nucleic acid drugs, paving the way for more efficient and cost-effective quality evaluation processes.

Effect of Fluorine Substitution on Absorption and Emission Properties of Figure-eight-shaped [5]Helicene Dimer: A Computational Study at RI-MP2/RI-ADC(2) Level.

Chirality is a very important characteristic of optically active molecules and polyaromatics with helical structures, and plays a vital role in various applications in material science. In the present work, we show the effects of fluorine substitution at various positions in a figure-8-shaped [5]helicene dimer on the ground and excited state g-factors. Calculations for the ground and excited states are performed at the MP2 and ADC(2) levels of theory, respectively. The results reveal that fluorination has a large effect on the excited state structures. The values of the excited state dissymmetry factors for the molecules with fluorinations at both ends of the figure-8 systems are smaller than that of the parent system. On the other hand, fluorinations only in the stacked-phenyl region results in an increase in the value of g cpl ${\left| {g_{{\rm{cpl}}} } \right|}$ . The perfluorinated system shows the smallest g cpl ${\left| {g_{{\rm{cpl}}} } \right|}$ .

Loop2 Size Modification Reveals Significant Impacts on the Potency of α-Conotoxin TxID.

α4/6-conotoxin TxID, which was identified from Conus textile, simultaneously blocks rat (r) α3ß4 and rα6/α3ß4 nicotinic acetylcholine receptors (nAChRs) with IC50 values of 3.6 nM and 33.9 nM, respectively. In order to identify the effects of loop2 size on the potency of TxID, alanine (Ala) insertion and truncation mutants were designed and synthesized in this study. An electrophysiological assay was used to evaluate the activity of TxID and its loop2-modified mutants. The results showed that the inhibition of 4/7-subfamily mutants [+9A]TxID, [+10A]TxID, [+14A]TxID, and all the 4/5-subfamily mutants against rα3ß4 and rα6/α3ß4 nAChRs decreased. Overall, ala-insertion or truncation of the 9th, 10th, and 11th amino acid results in a loss of inhibition and the truncation of loop2 has more obvious impacts on its functions. Our findings have strengthened the understanding of α-conotoxin, provided guidance for further modifications, and offered a perspective for future studies on the molecular mechanism of the interaction between α-conotoxins and nAChRs.

New Tricholomalides D-G from the Mushroom Tricholoma ustaloides Grown in an Italian Beech Wood.

Four novel seconeodolastane diterpenoids, named tricholomalides D-G, were isolated, together with the known tricholomalide C, from the fruiting bodies of Tricholoma ustaloides Romagn., a species belonging to the large Tricholoma genus of higher mushrooms (Basidiomycota, family Tricholomataceae). They were isolated through multiple chromatographic separations, and the structures, including the absolute configuration, were established through a detailed analysis of MS, NMR, and CD spectral data and comparison with related compounds reported in the literature, which has been thoroughly revised.

Identification and characterization of a hydrophobin Vmh3 from Pleurotus ostreatus.

Hydrophobins (HPs) are relatively small surface-active proteins of fungal origin. Being an industrially important protein, isolation of new molecules from GRAS (Generally Regarded as Safe) strains like mushrooms is the need of the time. In the present work, hydrophobin Vmh3-1 is isolated, purified, and identified from a culture broth and vegetative mycelia of Pleurotus ostreatus grown in a Potato dextrose broth (PDB) in static culture conditions. Purified proteins from the broth and the cell wall showed bands of 11 kDa and 17 kDa when analyzed on SDS-PAGE. Hydrophobin Vmh3-1 was identified in purified protein samples by the Orbitrap-HR-LC-MS/MS analysis with a maximum of 66% sequence coverage. The amphipathic nature of the protein was revealed by an increase in the water contact angle (WCA) of the hydrophilic surface of glass by 87% as well as a decrease in the WCA of the hydrophobic surface of Teflon by 19%. The emulsification property was tested with food-grade oils and Hexane. A maximum activity (EI 24) of 87.64% was recorded for Sunflower oil. In CD (Circular dichroism) spectra, Vmh3-1 showed the typical spectra of hydrophobin with a dominance of ß-sheets (51%) in the secondary structure and a minimum percentage of the α-helix (2%). The protein did not show a self-aggregating property on vigorous shaking making it suitable for numerous industrial applications. The identification of Vmh3-1 with detailed amino acid sequencing and the characterization of the protein to evaluate its potential in surface modifications for various industrial applications is demonstrated herein for the first time.

A new Pb2+-specific DNAzyme by revisiting the catalytic core of 10-23 DNAzyme.

10-23 DNAzyme is a catalytic DNA molecule from in vitro selection, the 15-mer catalytic core was investigated for more DNAzyme variants by block deletions. DNAzyme DZM01 was selected with metal ion dependence of Pb2+ â‰« Mn2+, with no activity in the presence of Mg2+ (20 mM), Ca2+ (20 mM), Zn2+ (20 mM, pH 6). The unique binding properties of Pb2+ with nucleic acids might be responsible for the formation of the catalytic core, which is different from that of other divalent metal ions. More DNAzyme variants are expected to be derived for specific metal ion dependence by various nucleobase sequences and modifications.

Methods for determining the absolute configurations of marine ladder-shaped polyethers.

Marine dinoflagellates produce a unique family of bioactive substances featuring multiple ether rings aligned in a ladder shape. These are large, complex molecules with potent bioactivity. Targeted chiral centers sit on either the skeletal ladders or on the side chains of these compounds. However, the laborious steps of isolation and purification severely diminish the amount of sample available for assigning these chiral centers via structural investigations. Three important methods were used to assign the stereochemistry of the molecules, (a) circular dichroism (CD) spectroscopy, (b) labeling with fluorescent chiral reagents for high-performance liquid chromatography (HPLC) analysis, and (c) derivatization with anisotropic reagents for nuclear magnetic resonance (NMR) analysis. The addition of fluorescent chiral reagents allowed for the use of much less material than typically required. In this review, we present examples of the determination of absolute configurations in ladder-shaped polyethers. The targeted compounds include ciguatoxins (CTXs), gymnocin-B, gambieric acids, prymnesin-2, maitotoxin, yessotoxins, gambierol, brevisamide, and brevisin.

Chemosensory proteins used as target for screening behaviourally active compounds in the rice pest Cnaphalocrocis medinalis (Lepidoptera: Pyralidae).

Reverse chemical ecology based on insect functional odorant binding proteins has been extensively studied to screen behaviourally active compounds, whereas chemosensory proteins (CSPs), which are reportedly involved in olfactory chemical reception and could serve as molecular targets remain unclear. In the present study, two behaviourally active compounds for Cnaphalocrocis medinalis, a serious pest of rice in Asia, were successfully screened via an antenna-biased CSP, CmedCSP33. Fluorescence competitive binding assays showed that CmedCSP33 could bind to seven out of 32 rice volatiles. Fluorescence quenching experiments revealed that CmedCSP33 forms a stable complex with nerolidol and ß-ionone, and circular dichroism (CD) spectra demonstrated that these two compounds cause conformational changes in CmedCSP33. Furthermore, H-tube olfactometer bioassays showed that C. medinalis displayed prominent attractant responses to nerolidol and prominent repellent responses to ß-ionone. Additionally, binding assays and CD spectra at different pH values implied that extensive conformational changes may be a general feature of CSPs for triggering the subsequent chemical transduction. Overall, our findings provide evidence for the involvement of CSPs in olfactory perception, and a protocol for effectively screening behaviourally active compounds.

Elevated growth temperature can enhance photosystem I trimer formation and affects xanthophyll biosynthesis in Cyanobacterium Synechocystis sp. PCC6803 cells.

In the thylakoid membranes of the mesophilic cyanobacterium Synechocystis PCC6803, PSI reaction centers (RCs) are organized as monomers and trimers. PsaL, a 16 kDa hydrophobic protein, a subunit of the PSI RC, was previously identified as crucial for the formation of PSI trimers. In this work, the physiological effects accompanied by PSI oligomerization were studied using a PsaL-deficient mutant (ΔpsaL), not able to form PSI trimers, grown at various temperatures. We demonstrate that in wild-type Synechocystis, the monomer to trimer ratio depends on the growth temperature. The inactivation of the psaL gene in Synechocystis grown phototropically at 30°C induces profound morphological changes, including the accumulation of glycogen granules localized in the cytoplasm, resulting in the separation of particular thylakoid layers. The carotenoid composition in ΔpsaL shows that PSI monomerization leads to an increased accumulation of myxoxantophyll, zeaxanthin and echinenone irrespective of the temperature conditions. These xanthophylls are formed at the expense of ß-carotene. The measured H2O→CO2 oxygen evolution rates in the ΔpsaL mutant are higher than those observed in the wild type, irrespective of the growth temperature. Moreover, circular dichroism spectroscopy in the visible range reveals that a peak attributable to long-wavelength-absorbing carotenoids is apparently enhanced in the trimer-accumulating wild-type cells. These results suggest that specific carotenoids are accompanied by the accumulation of PSI oligomers and play a role in the formation of PSI oligomer structure.

Characterization of recombinant pectate lyase refolded from inclusion bodies generated in E. coli BL21(DE3).

Pectate lyase (EC 4.2.2.2) gene from Bacillus subtilis RCK was cloned and expressed in Escherichia coli to maximize its production. In addition to soluble fraction, bioactive pectate lyase was also obtained from inclusion body aggregates by urea solubilization and refolding under in vitro conditions. Enzyme with specific activity ∼3194IU/mg and ∼1493IU/mg were obtained from soluble and inclusion bodies (IBs) fraction with recovery of 56% and 74% in terms of activity, respectively. The recombinant enzyme was moderately thermostable (t1/2 60min at 50°C) and optimally active in wider alkaline pH range (7.0-10.5). Interaction of protein with its cofactor CaCl2 was found to stimulate the change in tertiary structure as revealed by near UV CD spectra. Intrinsic tryptophan fluorescence spectra indicated that tryptophan is involved in substrate binding and there might be independent binding of Ca(2+) and polygalacturonic acid to the active site. The recombinant enzyme was found to be capable of degrading pectin and polygalacturonic acid. The work reports novel conditions for refolding to obtain active recombinant pectate lyase from inclusion bodies and elucidates the effect of ligand and substrate binding on protein conformation by circular dichroism (CD) and fluorescence spectrofluorometry.

An in situ generated achiral Cu(II)-containing polymer complex sensor for enantioselective recognition induced from L-/D-histidine enantiomers.

A novel achiral polymer P-1 is synthesized by the polymerization of (2,5-bis(octyloxy)-1,4-phenylene)diboronic acid (M-1) with pyridine-2,6-diylbis(methanylylidene)bis(4-iodoaniline) (M-2) via Pd-catalyzed Suzuki coupling reaction. The tridentate ligand in the main chain backbone can further coordinate with Cu(2+) to afford the corresponding achiral copper-containing polymer complex P-2, which selectively responds to L-/D-histidine with significant fluorescence enhancement over other amino acids. Interestingly, P-2 exhibits obvious CD response toward L- or D-histidine compared with its model compound MC, indicating that this kind Cu(II)-containing polymer complex sensor can be used as an effective chemosensor for enantioselective recognition of histidine enantiomers by means of CD spectroscopy.

High-pressure microfluidisation positively impacts structural properties and improves functional characteristics of almond proteins obtained from almond meal.

Almond protein isolate (API) obtained from almond meal was processed using dynamic high-pressure microfluidisation (0, 40, 80, 120, and 160 MPa pressure; single pass). Microfluidisation caused significant reductions in the particle size and increased absolute zeta potential. SDS-PAGE analysis indicated reduction in band intensity and the complete disappearance of bands beyond 80 MPa. Structural analysis (by circular dichroism, UV-Vis, and intrinsic-fluorescence spectra) of the API revealed disaggregation (up to 80 MPa) and then re-aggregation beyond 80 MPa. Significant increments in protein digestibility (1.16-fold) and the protein digestibility corrected amino acid score (PDCAAS; 1.15-fold) were observed for the API (80 MPa) than control. Furthermore, significant improvements (P < 0.05) in the functional properties were observed, viz., the antioxidant activity, protein solubility, and emulsifying properties. Overall, the results revealed that moderate microfluidisation treatment (80 MPa) is an effective and sustainable technique for enhancing physico-chemical and functional attributes of API, thus potentially enabling its functional food/nutraceuticals application.

Structural effects of inosine substitution in telomeric DNA quadruplex.

The telomeric DNA, a distal region of eukaryotic chromosome containing guanine-rich repetitive sequence of (TTAGGG)n, has been shown to adopt higher-order structures, specifically G-quadruplexes (G4s). Previous studies have demonstrated the implication of G4 in tumor inhibition through chromosome maintenance and manipulation of oncogene expression featuring their G-rich promoter regions. Besides higher order structures, several regulatory roles are attributed to DNA epigenetic markers. In this work, we investigated how the structural dynamics of a G-quadruplex, formed by the telomeric sequence, is affected by inosine, a prevalent modified nucleotide. We used the standard (TTAGGG)n telomere repeats with guanosine mutated to inosine at each G position. Sequences (GGG)4, (IGG)4, (GIG)4, (GGI)4, (IGI)4, (IIG)4, (GII)4, and (III)4, bridged by TTA linker, are studied using biophysical experiments and molecular modeling. The effects of metal cations in quadruplex folding were explored in both Na+ and K+ containing buffers using CD and UV-melting studies. Our results show that antiparallel quadruplex topology forms with the native sequence (GGG)4 and the terminal modified DNAs (IGG)4 and (GGI)4 in both Na+ and K+ containing buffers. Specifically, quadruplex hybrid was observed for (GGG)4 in K+ buffer. Among the other modified sequences, (GIG)4, (IGI)4 and (GII)4 show parallel features, while (IIG)4 and (III)4 show no detectable conformation in the presence of either Na+ or K+. Our studies indicate that terminal lesions (IGG)4 and (GGI)4 may induce certain unknown conformations. The folding dynamics become undetectable in the presence of more than one inosine substitution except (IGI)4 in both buffer ions. In addition, both UV melting and CD melting studies implied that in most cases the K+ cation confers more thermodynamic stability compared to Na+. Collectively, our conformational studies revealed the diverse structural polymorphisms of G4 with position dependent G-to-I mutations in different ion conditions.

Comprehensive insights into the structures and dynamics of plant telomeric G-quadruplexes.

Telomeres, which are located at the ends of eukaryotic chromosomes, are crucial for genomic maintenance. Most telomeric DNA is composed of tandemly repeated guanine (G)-rich sequences, which form G-quadruplexes (G4s). The structures and dynamics of telomeric G4s are essential for telomere functioning and helpful for G4-based biosensing. However, they are far from being understood, especially for plants. In this contribution, the folding, environment-induced G4 dynamics, and protein-catalyzed unfolding of plant telomeric G4s were comprehensively studied. It was found that diverse plant telomeric sequences from land plants to green algae could fold into G4 structures. In addition, 5'-proximal ssDNA but not 3'-proximal ssDNA drove conversion of anti-parallel G4 structures to parallel structures, and both 5' and 3' ssDNA decreased the stability of G4s in dilute solution. Furthermore, molecular crowding promoted the formation of parallel structures for three-layer but not for two-layer G4s, and increased the stability of all selected G4s. Finally, AtRecQ2 helicase resolved the stable parallel structure of typical plant telomeric G4 in crowded solution, but ssDNA binding protein AtRPA did not. Furthermore, AtRecQ2 unwound the structure more efficiently in the presence of AtRPA. The results may expand our understanding on the structures and dynamics of plant telomeric G4s.

A new cycloheptane derivative from the fungus Penicillium crustosum JT-8.

A new highly oxygenated cycloheptane derivative crustane (1), along with fourteen known compounds (2-15) were isolated from Penicillium crustosum JT-8. The structure of compound 1 was determined by extensive spectroscopic data, DP4+ probability analyses and dimolybdenum CD method. Compound 1 exhibited moderate antibacterial activity against Staphylococcus aureus with MIC of 4.0 µg/mL.

Ultrasonication Induced Alterations in Physicochemical and Functional Properties of Myosin.

BACKGROUND: Several reports have indicated that ultrasonication can change the solubility of muscle proteins and improves the functional properties of meat and isolated muscle proteins. Moreover, available literature suggests that ultrasonication can significantly improve the gelling properties of muscle proteins. OBJECTIVES: The present study was carried out to investigate the effect of low-frequency ultrasonication on the secondary structure of myosin and the impact of these structural changes on solubility and gelling ability. METHODS: Myosin from breast muscles (Pectoralis major) of broiler chicken was extracted and exposed to low-frequency ultrasonication for 30 min. Four aliquots collected at the interval of 5, 10, 20, and 30 min were analysed for change in ATPase activity, sulfhydryl content, surface hydrophobicity, alpha-helicity. The possible impact of these changes on heat-induced gelation was observed through electron micrographs. RESULTS: Ultrasonication reduced the enzymatic activity of myosin and increased the reactive sulfhydryl content. Decreased α-helicity and increased intrinsic fluorescence displayed significant structural changes at the secondary and tertiary levels. Myosin aggregation, as indicated by electron micrographs, showed a marked decrease. The microstructure of myosin gels displayed a distinct correlation with ultrasonication-induced structural changes. Furthermore, improved microstructure led to a significant increase in the water retention capacity of myosin gels. CONCLUSION: In conclusion, ultrasonication of myosin caused a marked change in structure at the tertiary and secondary levels. Structural changes apparently confined within the globular head region and rod portion of myosin were displayed by reduced enzymatic activity and improved gelation/solubility. Results of our study convincingly showed that ultrasonication improved the microstructure of myosin gels resulting in increased WHC.

Circular dichroism spectroscopic assessment of structural changes upon protein thermal unfolding at contrasting pH: Comparison with molecular dynamics simulations.

In most instances, the usual fastness of protein unfolding events hinders determining changes in secondary structures associated with this process because these determinations rely on the recording of high-resolution circular dichroism (CD) spectra. In this work, far-UV CD spectra, recorded at ten-minute intervals, were used to evaluate the time course followed by four classes of secondary structures in the slow temperature-induced unfolding of yeast triosephosphate isomerase (yTIM) under distinct pH conditions. CONTIN-LL and SELCON3 algorithms were used for the deconvolution of spectra. Both algorithms furnished helix and unordered structure contents that changed according to first-order kinetics, agreeing with the behavior shown by CD data at specific wavelengths. Analyses of unfolded yTIM spectra, using a dataset that includes spectra of unfolded proteins and either one of the two algorithms, clearly showed a more unordered protein structure at high pH; this finding was corroborated with analysis of the difference spectra. Molecular dynamics (MD) simulations performed with AMBER and OPLS force fields resulted in more extensive loss of helices and gain in coils at high pH, in agreement with spectroscopic results. However, structural differences between low- and high-pH unfolded yTIM were relatively small. Comparison of results from CD and MD thus point to the need of fine-tuning of MD procedures.

H101G Mutation in Rat Lens αB-Crystallin Alters Chaperone Activity and Divalent Metal Ion Binding.

BACKGROUND: The molecular chaperone function of αB-crystallins is heavily involved in maintaining lens transparency and the development of cataracts. OBJECTIVES: The aim of the study was to investigate whether divalent metal ion binding improves the stability and αB-crystallin chaperone activity. METHODS: In this study, we have developed an H101G αB-crystallin mutant and compared the surface hydrophobicity, chaperone activity, and secondary and tertiary structure with the wild type in the presence and absence of metal ions. RESULTS: Substitution of His101 with glycine resulted in structural and functional changes. Spectral analysis and chaperone-like activity assays showed that substitution of glycine resulted in a higher percentage of random coils, increased hydrophobicity, and 22±2% higher chaperone-like activity. Whereas in the presence of the Cu2+ ion, H101G exhibited 32±1% less chaperone-like activity compared to the wild type. CONCLUSION: Cu2+ has been reported to enhance the chaperone-like activity of lens α-crystallin. Our results indicate that H101 is the predominant Cu2+ binding site, and the mutation resulted in a partial unfolding that impaired the binding of Cu2+ to H101 residue. In conclusion, this study further helps to understand the important binding site for Cu2+ to αB-crystallin.

B.1.1.7 (Alpha) variant is the most antigenic compared to Wuhan strain, B.1.351, B.1.1.28/triple mutant and B.1.429 variants.

The rapid spread of the SARS-CoV-2 virus and its variants has created a catastrophic impact worldwide. Several variants have emerged, including B.1.351 (Beta), B.1.1.28/triple mutant (P.1), B.1.1.7 (Alpha), and B.1.429 (Epsilon). We performed comparative and comprehensive antigenicity mapping of the total S-glycoprotein using the Wuhan strain and the other variants and identified 9-mer, 15-mer, and 20-mer CTL epitopes through in silico analysis. The study found that 9-mer CTL epitope regions in the B.1.1.7 variant had the highest antigenicity and an average of the three epitope types. Cluster analysis of the 9-mer CTL epitopes depicted one significant cluster at the 70% level with two nodes (KGFNCYFPL and EGFNCYFPL). The phage-displayed peptides showed mimic 9-mer CTL epitopes with three clusters. CD spectra analysis showed the same band pattern of S-glycoprotein of Wuhan strain and all variants other than B.1.429. The developed 3D model of the superantigen (SAg)-like regions found an interaction pattern with the human TCR, indicating that the SAg-like component might interact with the TCR beta chain. The present study identified another partial SAg-like region (ANQFNSAIGKI) from the S-glycoprotein. Future research should examine the molecular mechanism of antigen processing for CD8+ T cells, especially all the variants' antigens of S-glycoprotein.

Discovery of behaviorally active semiochemicals in Aenasius bambawalei using a reverse chemical ecology approach.

BACKGROUND: The invasive mealybug, Phenacoccus solenopsis, has caused serious damage to cotton crops throughout the world. Aenasius bambawalei is a dominant endoparasitoid of P. solenopsis. Exploration of behaviorally active semiochemicals may promote the efficacy of parasitoids used in biological control. Reverse chemical ecology, based on the physiological function of odorant-binding proteins (OBPs), provides an effective approach to screen behaviorally active compounds to target insect pests. Determination of the binding mechanisms and specificity towards different odorants in A. bambawalei may facilitate the development of more-efficient biological control strategies. RESULTS: We characterized the expression profile and analyzed the binding affinity of OBP28 in A. bambawalei. AbamOBP28 showed high expression in the wings and antennae of both male and female A. bambawalei. A fluorescence competitive binding assay indicated that AbamOBP28 displayed strong binding affinity to most candidate ligands. Circular dichroism spectra demonstrated that 1-octen-3-one, myrcene, dodecane, 2,4,4-trimethyl-2-pentene, nonanal, and limonene elicited conformational changes in AbamOBP28. Electrophysiological and behavioral bioassays revealed that diethyl sebacate, 2,4,4-trimethyl-2-pentene, and 1-octen-3-one evoked significant electroantennography responses and functioned as attractants in A. bambawalei at specific concentrations. Furthermore, three-dimensional structure modeling and molecular docking showed that hydrogen bonds were formed by Glu1 and Ser75 of AbamOBP28 with diethyl sebacate, respectively. CONCLUSION: These results demonstrate that AbamOBP28 is involved in the chemoreception of A. bambawalei. The identified protein provides a potential target for efficient enemy utilization and pest control, and the overall results may help develop protocols for more effective screening of behaviorally active semiochemicals. © 2021 Society of Chemical Industry.