Circular Dichroism Techniques: Biomolecular and Nanostructural Analyses- A Review

Analytical considerations for characterization of generic peptide product: A regulatory insight

The Peptide therapeutics market was evaluated to be around USD 45.67 BN in 2023 and is projected to witness massive growth at a CAGR of around 5.63 % from 2024 to 2032 (USD 80.4 BN). Generic peptides are expected to reach USD 27.1 billion by 2032 after the patent monopoly of the pioneer peptides expires, and generic peptides become accessible. The generic manufacturers are venturing into peptide-based therapeutics for the aforementioned reasons. There is an abundance of material accessible regarding the characterization of peptides, which can be quite confusing for researchers. The FDA believes that an ANDA applicant may now demonstrate that the active component in a proposed generic synthetic peptide drug product is the "same" as the active ingredient in a peptide of rDNA origin that has previously been approved. To ensure the efficacy, safety, and quality of peptide therapies during development, regulatory bodies demand comprehensive characterization utilizing several orthogonal methodologies. This article elaborates the peptide characterization by segmenting into different segments as per the critical quality attribute from identification of the peptide to the physicochemical property of the peptide therapeutics which will be required to demonstrate the sameness with reference product based on the size of the peptide chain and molecular weight of the peptides. Article insights briefly on each individual technique and the orthogonal techniques for each test were explained. The impurities requirements in the generic peptides as per the regulatory requirement were also discussed.

Preparation, design, identification and application of self-assembly peptides from seafood: A review

Hydrogels formed by self-assembling peptides with low toxicity and high biocompatibility have been widely used in food and biomedical fields. Seafood contains rich protein resources and is also one of the important sources of natural bioactive peptides. The self-assembled peptides in seafood have good functional activity and are very beneficial to human health. In this review, the sequence of seafood self-assembly peptide was introduced, and the preparation, screening, identification and characterization. The rule of self-assembled peptides was elucidated from amino acid sequence composition, amino acid properties (hydrophilic, hydrophobic and electric), secondary structure, interaction and peptide properties (hydrophilic and hydrophobic). It was introduced that the application of hydrogels formed by self-assembled peptides, which lays a theoretical foundation for the development of seafood self-assembled peptides in functional foods and the application of biological materials.

Experimental and theoretical aspects of magnetic circular dichroism and magnetic circularly polarized luminescence in the UV, visible and IR ranges: A review

A historical sketch of the MCD (magnetic circular dichroism) spectroscopy is reported in its experimental and theoretical aspects. MCPL (magnetic circularly polarized luminescence) is also considered. The main studies are presented encompassing porphyrinoid systems, aggregates and materials, as well as simple organic molecules useful for the advancement of the interpretation. The MCD of chiral systems is discussed with special attention to new studies of natural products with potential pharmaceutical valence, including Amaryllidaceae alkaloids and related isocarbostyrils. Finally, the vibrational form of MCD, called MVCD, which is recorded in the IR part of the spectrum is also discussed. A final brief note on perspectives is given.

Understanding selective sensing of human serum albumin using a D-π-A probe: a photophysical and computational approach

The human serum albumin (HSA) level is a valuable indicator of an individual's health status. Therefore, its detection/estimation can be used to diagnose several diseases. In this work, we have developed a series of donor-π-acceptor probes, which were found to selectively detect HSA over BSA (bovine serum albumin). Among these probes, A4, which bears the trifluoroacetyl group, showed the highest selectivity for HSA, with limits of detection and quantification being 1.36 nM and 2.59 nM, respectively. CD spectroscopy of the HSA-A4 ensemble indicated an increase in the α-helicity of the protein, while the displacement assays revealed the localization of the probe in the hemin site of HSA. The probe works on the principle of excited state intramolecular charge transfer (ICT). Its selectivity was also validated computationally. Docking experiments confirmed the preference of the probe for the hemin binding IB site of HSA, as observed from the fluorescence displacement assay results, and a comparison of docking scores demonstrated the greater preference of A4 for HSA compared to BSA. Computational experiments also showed a change in preference for HSA amino acid residues exhibited by the excited state of probe A4 (Tyr161, Met123, Pro118, and Leu115) when compared to its ground state (Arg186 and His146). Hydrophobic interactions dominated the excited state protein-probe ensemble, whereas there was significant involvement of the water bridges along with the hydrophobic interactions in the ground state ensemble. Probe A4 was also assessed for its practical utility and found to successfully sense HSA in urine at extremely low concentrations. Moreover, the A4-HSA ensemble was employed for hemin sensing with a detection limit of 0.23 μM.

Oxidative refolding by Copper-catalyzed air oxidation consistently increases the homogeneity and activity of a Novel Interleukin-2 mutein

Interleukin-2 (IL-2) has been used in cancer treatment for over 30 years. However, due to its high toxicity, new mutant variants have been developed. These variants retain some of the biological properties of the original molecule but offer other therapeutic advantages. At the Center of Molecular Immunology, the IL-2 no-alpha mutein, an IL-2 agonist with lower toxicity than wtIL-2, has been designed, produced, and is currently being evaluated in a Phase I/II clinical trial. The mutein is produced in E. coli as an insoluble material that must be refolded in vitro to yield a fully active protein. Controlled oxidation steps are essential in the purification process of recombinant proteins produced in E. coli to ensure the proper formation of the disulfide bonds in the molecules. In this case, the new purification process includes a copper-catalyzed air oxidation step to induce disulfide bond establishment. The optimal conditions of pH, copper, protein and detergent concentration for this step were determined through screening. The produced protein demonstrated a conserved 3D structure, higher purity, and greater biological activity than the obtained by established process without the oxidation step. Four batches were produced and evaluated, demonstrating the consistency of the new process.

Collagen-targeted protein nanomicelles for the imaging of non-alcoholic steatohepatitis

In vivo molecular imaging tools hold immense potential to drive transformative breakthroughs by enabling researchers to visualize cellular and molecular interactions in real-time and/or at high resolution. These advancements will facilitate a deeper understanding of fundamental biological processes and their dysregulation in disease states. Here, we develop and characterize a self-assembling protein nanomicelle called collagen type I binding - thermoresponsive assembled protein (Col1-TRAP) that binds tightly to type I collagen in vitro with nanomolar affinity. For ex vivo visualization, Col1-TRAP is labeled with a near-infrared fluorescent dye (NIR-Col1-TRAP). Both Col1-TRAP and NIR-Col1-TRAP display approximately a 3.8-fold greater binding to type I collagen compared to TRAP when measured by surface plasmon resonance (SPR). We present a proof-of-concept study using NIR-Col1-TRAP to detect fibrotic type I collagen deposition ex vivo in the livers of mice with non-alcoholic steatohepatitis (NASH). We show that NIR-Col1-TRAP demonstrates significantly decreased plasma recirculation time as well as increased liver accumulation in the NASH mice compared to mice without disease over 4 hours. As a result, NIR-Col1-TRAP shows potential as an imaging probe for NASH with in vivo targeting performance after injection in mice. STATEMENT OF SIGNIFICANCE: Direct molecular imaging of fibrosis in NASH patients enables the diagnosis and monitoring of disease progression with greater specificity and resolution than do elastography-based methods or blood tests. In addition, protein-based imaging probes are more advantageous than alternatives due to their biodegradability and scalable biosynthesis. With the aid of computational modeling, we have designed a self-assembled protein micelle that binds to fibrillar and monomeric collagen in vitro. After the protein was labeled with near-infrared fluorescent dye, we injected the compound into mice fed on a NASH diet. NIR-Col1-TRAP clears from the serum faster in these mice compared to control mice, and accumulates significantly more in fibrotic livers.This work advances the development of targeted protein probes for in vivo fibrosis imaging.

Proof of ssDNA degraded from dsDNA for ET recombination

The widely used ET recombination requires an ssDNA product degraded by Rac phage protein E588 from dsDNA for strand invasion. However, proof of the ssDNA product is still elusive. The study provided three levels of proof sequentially. The probable ssDNAs degraded by E588 from the fluorescent plus-, minus-, or double-stranded dsDNA pET28a-xylanase exhibited a half fluorescence intensity of the corresponding dsDNAs, equivalent to the E588 degradation nucleotides half that of the total nucleotides degraded from the corresponding dsDNA. The ssDNA product degraded by E588 from the fluorescent minus-stranded dsDNA was confirmed by gradient gel-electrophoresis and two nuclease degradation reactions. Degraded by E588 from the dsDNA pET28a-xylanase that had a phosphorothioated plus-stranded 5'-terminus, the plus-stranded ssDNA product was separated via gel electrophoresis and recovered via a DNAclean kit. The recovered ssDNA product was proven to have intact 5'- and 3'-ends by DNA sequencing analysis. This study provides a solid foundation for the mechanism of ssDNA invasion.

The effect of salinity on trimethoprim adsorption by activated sludge extracellular polymeric substances at trace concentration

The saline wastewater produced in industrial activities and seawater use would flow into wastewater treatment plants and affect the characteristic of extracellular polymeric substance (EPS) of activated sludge, which could potentially impact the removal of antibiotics via adsorption. Nonetheless, the effect of salinity on trimethoprim adsorption by activated sludge extracellular polymeric substances at trace concentration and the underlying mechanism remain largely unknown. In this study, the effect of salinity on the adsorption removal of a typical antibiotic, i.e., trimethoprim (TMP) at trace concentration (25.0 μg/L) was evaluated. The results showed the content of EPS was decreased significantly from 56.36 to 21.70 mg/g VSS when the salinity was increased from 0 to 10 g/L. Protein fractions occupied the predominant component of EPS, whose concentration was decreased from 38.17 to 12.83 mg/g VSS. The equilibrium adsorption capacity of activated sludge for TMP was decreased by 49.70% (from 4.97 to 2.50 μg/g VSS). The fluorescence quenching results indicated the fluorescence intensity of tryptophan-like substances was decreased by 30% and the adsorption sites of EPS were decreased from 0.51 to 0.21 when the salinity was increased. The infrared spectrum and XPS results showed that the nitrogen-containing groups from protein were decreased significantly. The circular dichroic analysis showed α helix structure of protein in EPS was decreased with the increase of salinity, which was responsible for the decrease of adsorption capacity for TMP.

A comprehensive review on the enantiomeric separation of chiral drugs using metal-organic frameworks

Chiral drugs play an important role in modern medicine, but obtaining pure enantiomers from racemic mixtures can pose challenges. When a drug is chiral, only one enantiomer (eutomer) typically exhibits the desired pharmacological activity, while the other (distomer) may be biologically inactive or even toxic. Racemic drug formulations introduce additional health risks, as the body must still process the inactive or detrimental enantiomer. Some distomers have also been linked to teratogenic effects and unwanted side effects. Therefore, developing efficient and scalable methods for separating chiral drugs into their pure enantiomers is critically important for improving patient safety and outcomes. Metal-organic frameworks (MOFs) show promise as novel materials for chiral separation due to their highly tunable structures and interactions. This review summarizes recent advancements in using MOFs for chromatographic and spectroscopic resolution of drug enantiomers. Both the opportunities and limitations of MOF-based separation techniques are discussed. A thorough understanding of these methods could aid the continued development of pure enantiomer formulations and help reduce health risks posed by racemic drug mixtures.

Poly(l-proline)-Stabilized Polypeptide Nanostructures via Ring-Opening Polymerization-Induced Self-Assembly (ROPISA)

Poly(proline) II helical motifs located at the protein-water interface stabilize the three-dimensional structures of natural proteins. Reported here is the first example of synthetic biomimetic poly(proline)-stabilized polypeptide nanostructures obtained by a straightforward ring-opening polymerization-induced self-assembly (ROPISA) process through consecutive N-carboxyanhydride (NCA) polymerization. It was found that the use of multifunctional 8-arm initiators is critical for the formation of nanoparticles. Worm-like micelles as well as spherical morphologies were obtained as confirmed by dynamic light scattering (DLS), transmission electron microscopy (TEM), and small angle X-ray scattering (SAXS). The loading of the nanostructures with dyes is demonstrated. This fast and open-vessel procedure gives access to amino acids-based nanomaterials with potential for applications in nanomedicine.

Circular dichroism of relativistically-moving chiral molecules

Understanding the impact of the relativistic motion of a chiral molecule on its optical response is a prime challenge for fundamental science, but it also has a direct practical relevance in our search for extraterrestrial life. To contribute to these significant developments, we describe a multi-scale computational framework that combines quantum chemistry calculations and full-wave optical simulations to predict the chiral optical response from molecules moving at relativistic speeds. Specifically, the effect of a relativistic motion on the transmission circular dichroism (TCD) of three life-essential biomolecules, namely, B-DNA, chlorophyll a, and chlorophyll b, is investigated. Inspired by previous experiments to detect interstellar chiral molecules, we assume that the molecules move between a stationary observer and a light source, and we study the rotationally averaged TCD as a function of the speed of the molecule.We find that the TCD spectrum that contains the signatures of the molecules shifts with increasing speed to shorter wavelengths, with the effects already being visible for moderate velocities.

Synthesis, Characterization, and Study of the Antimicrobial Potential of Dimeric Peptides Derived from the C-Terminal Region of Lys49 Phospholipase A2 Homologs

Currently, the search for new alternatives to conventional antibiotics to combat bacterial resistance is an urgent task, as many microorganisms threaten human health due to increasing bacterial resistance to traditional medicines. Thus, new molecules such as antimicrobial peptides have emerged as promising alternatives because of their low induction of resistance and broad spectrum of action. In this context, in the past few years, our research group has synthesized and characterized a peptide derived from the C-terminal region of the Lys49 PLA2-like BthTX-I, named p-BthTX-I. After several studies, the peptide (p-BthTX-I)2K was proposed as the molecule with the most considerable biotechnological potential. As such, the present work aimed to evaluate whether the modifications made on the peptide (p-BthTX-I)2K can be applied to other molecules originating from the C-terminal region of PLA2-like Lys49 from snake venoms. The peptides were obtained through the solid-phase peptide synthesis technique, and biochemical and functional characterization was carried out using dichroism techniques, mass spectrometry, antimicrobial activity against ESKAPE strains, hemolytic activity, and permeabilization of lipid vesicles. The antimicrobial activity of the peptides was promising, especially for the peptides (p-AppK)2K and (p-ACL)2K, which demonstrated activity against all strains that were tested, surpassing the model molecule (p-BthTX-I)2K in most cases and maintaining low hemolytic activity. The modifications initially proposed for the (p-BthTX-I)2K peptide were shown to apply to other peptides derived from Lys49 PLA2-like from snake venoms, showing promising results for antimicrobial activity. Future assays comparing the activity of the dimers obtained through this strategy with the monomers of these peptides should be carried out.

Unraveling the impact of the p.R107L mutation on the structure and function of human αB-Crystallin: Implications for cataract formation

To date, several pathogenic mutations have been identified in the primary structure of human α-Crystallin, frequently involving the substitution of arginine with a different amino acid. These mutations can lead to the incidence of cataracts and myopathy. Recently, an important cataract-associated mutation has been reported in the functional α-Crystallin domain (ACD) of human αB-Crystallin protein, where arginine 107 (R107) is replaced by a leucine. In this study, we investigated the structure, chaperone function, stability, oligomerization, and amyloidogenic properties of the p.R107L human αB-Crystallin using a number of different techniques. Our results suggest that the p.R107L mutation can cause significant changes in the secondary, tertiary, and quaternary structures of αB-Crystallin. This cataractogenic mutation led to the formation of protein oligomers with larger sizes than the wild-type protein and reduced the chemical and thermal stability of the mutant chaperone. Both fluorescence and microscopic assessments indicated that this mutation significantly altered the amyloidogenic properties of human αB-Crystallin. Furthermore, the mutant protein indicated an attenuated in vitro chaperone activity. The molecular dynamics (MD) simulation confirmed the experimental results and indicated that p.R107L mutation could alter the proper conformation of human αB-Crystallin dimers. In summary, our results indicated that the p.R107L mutation could promote the formation of larger oligomers, diminish the stability and chaperone activity of human αB-Crystallin, and these changes, in turn, can play a crucial role in the development of cataract disorder.

Evaluation of miR-155 silencing using a molecular beacon in human lung adenocarcinoma cell line

Lung cancer (LC) is a leading cause of global cancer-related deaths, highlighting the development of innovative methods for biomarker detection improving the early diagnostics. microRNAs (miRs) alterations are known to be involved in the initiation and progression of human cancers and can act as biomarkers for diagnostics and treatment. Herein, we develop the application of molecular beacon (MB) technology to monitor miR-155-3p expression in human lung adenocarcinoma A549 cells without complementary DNA synthesis, amplification, or expensive reagents. Furthermore, we produced gold nanoparticles (AuNPs) for delivering antisense oligonucleotides into A549 cells to reduce miR-155-3p expression, which was subsequently detectable using the MB. The MB was designed and structural characterized by Förster Resonance Energy Transfer (FRET)-melting, Circular Dichroism (CD), Nuclear magnetic resonance (NMR), and fluorometric experiments, and then the hybridization conditions were optimized for an in vitro approach involving the detection of miR-155-3p in total RNA extracted from A549 cell line. The expression profile of miR-155-3p was obtained by RT-qPCR. The results demonstrated that MB was properly designed and showed efficacy in targeting miR-155-3p. Furthermore, a limit of detection down to nanomolar concentration was achieved and the specificity of the biosensor was proved. Moreover, the self-assembly of ASOs with AuNPs exhibited exceptional target specificity, effectively silencing miR-155-3p. Notably, compared to lipid-based transfection agent, AuNPs displayed superior silencing efficiency. We highlighted the ability of MB to detect changes in the target gene expression after gene silencing. Overall, this innovative approach represents a promising tool for detecting various biomarkers at the same time, with potential applications in clinical settings.

Elucidating the interaction mechanism of rice glutelin and soybean 11S globulin using multi-spectroscopy and molecular dynamics simulation methods

Rice gluten, as the hydrophobic protein, exhibits restricted application value in hydrophilic food, which may be enhanced through interaction with soybean 11S globulin, characterized by favorable functional properties. This study aims at revealing their interaction mechanism via multi-spectroscopy and molecular dynamics simulation. The formation and structural change of rice glutelin-soybean 11S globulin complexes were detected using fluorescence, ultra-violet and circular dichroism spectra. The addition of 11S globulin increased the contents of α-helix, β-turn and random coil, but decreased β-sheet content, and the change in secondary structure was correlated with particle size. Moreover, exposure of hydrophobic groups and formation of disulfide bonds occurred in the complexes. Molecular dynamics simulation verified these experimental results through analyses of root mean square deviation and fluctuation, hydrogen bond, secondary structure, and binding free energy analysis. This study contributes to expounding the interaction mechanism of protein and protein from the molecular level.

Trimeric and Tetrameric Cationic Styryl Dyes as Novel Fluorescence and CD Probes for ds-DNA and ds-RNA

The wide use of mono- or bis-styryl fluorophores in biomedical applications prompted the presented design and study of a series of trimeric and tetrameric homo-analogues, styryl moieties arranged around a central aromatic core. The interactions with the most common biorelevant targets, ds-DNA and ds-RNA, were studied by a set of spectrophotometric methods (UV-VIS, fluorescence, circular dichroism, thermal denaturation). All studied dyes showed strong light absorption in the 350-420 nm range and strongly Stokes-shifted (+100-160 nm) emission with quantum yields (Φf) up to 0.57, whereby the mentioned properties were finely tuned by the type of the terminal cationic substituent and number of styryl components (tetramers being red-shifted in respect to trimers). All studied dyes strongly interacted with ds-DNA and ds-RNA with 1-10 nM-1 affinity, with dye emission being strongly quenched. The tetrameric analogues did not show any particular selectivity between ds-DNA or ds-RNA due to large size and consequent partial, non-selective insertion into DNA/RNA grooves. However, smaller trimeric styryl series showed size-dependent selective stabilization of ds-DNA vs. ds-RNA against thermal denaturation and highly selective or even specific recognition of several particular ds-DNA or ds-RNA structures by induced circular dichroism (ICD) bands. The chiral (ICD) selectivity was controlled by the size of a terminal cationic substituent. All dyes entered efficiently live human cells with negligible cytotoxic activity. Further prospects in the transfer of ICD-based selectivity into fluorescence-chiral methods (FDCD and CPL) is proposed, along with the development of new analogues with red-shifted absorbance properties.

Nonlinear Optical Activity of a Chiral Organic-Inorganic ([(NH3CH2CH2)3NH])2[MnBr5]Br5 Photoluminescent and Piezoelectric Crystal

The family of Mn-based organic-inorganic hybrids has greatly expanded due to their advantages in applications. They also show superior bright and size-tunable photoluminescence and can be considered a perfect alternative to toxic lead-based compounds. In this work, we present the detailed structural, optical, and electrical characterization of ([(NH3CH2CH2)3NH])2[MnBr5]Br5. The title compound exhibits a unique type of inorganic arrangement created by the trigonal bipyramids. It crystallizes in noncentrosymmetric space group R32, indicating its optical activity, piezoelectricity, and second-order optical nonlinearity proven by the second harmonic of light measurements. The studied crystals exhibit intense photoluminescence originating from the Mn(II) ion 4T1(G) → 6A1 transition. The measured lifetime of the photoluminescence emission is ≤1.5 ms, while the measured quantum yield for both powder and crystal samples reaches ∼70%.

Interaction of 3,9-disubstituted acridine with single stranded poly(rA), double stranded poly(rAU) and triple stranded poly(rUAU): molecular docking - A spectroscopic tandem study

RNA plays an important role in many biological processes which are crucial for cell survival, and it has been suggested that it may be possible to inhibit individual processes involved in many diseases by targeting specific sequences of RNA. The aim of this work is to determine the affinity of novel 3,9-disubstited acridine derivative 1 with three different RNA molecules, namely single stranded poly(rA), double stranded homopolymer poly(rAU) and triple stranded poly(rUAU). The results of the absorption titration assays show that the binding constant of the novel derivative to the RNA molecules was in the range of 1.7-6.2 × 104 mol dm-3. The fluorescence and circular dichroism titration assays revealed considerable changes. The most significant results in terms of interpreting the nature of the interactions were the melting temperatures of the RNA samples in complexes with the 1. In the case of poly(rA), denaturation resulted in a self-structure formation; increased stabilization was observed for poly(rAU), while the melting points of the ligand-poly(rUAU) complex showed significant destabilization as a result of the interaction. The principles of molecular mechanics were applied to propose the non-bonded interactions within the binding complex, pentariboadenylic acid and acridine ligand as the study model. Initial molecular docking provided the input structure for advanced simulation techniques. Molecular dynamics simulation and cluster analysis reveal π - π stacking and the hydrogen bonds formation as the main forces that can stabilize the binding complex. Subsequent MM-GBSA calculations showed negative binding enthalpy accompanied the complex formation and proposed the most preferred conformation of the interaction complex.

Integrating Enzymes with Supramolecular Polymers for Recyclable Photobiocatalytic Catalysis

Chemical modifications of enzymes excel in the realm of enzyme engineering due to its directness, robustness, and efficiency; however, challenges persist in devising versatile and effective strategies. In this study, we introduce a supramolecular modification methodology that amalgamates a supramolecular polymer with Candida antarctica lipase B (CalB) to create supramolecular enzymes (SupEnzyme). This approach features the straightforward preparation of a supramolecular amphiphilic polymer (β-CD@SMA), which was subsequently conjugated to the enzyme, resulting in a SupEnzyme capable of self-assembly into supramolecular nanoparticles. The resulting SupEnzyme nanoparticles can form micron-scale supramolecular aggregates through supramolecular and electrostatic interactions with guest entities, thus enhancing catalyst recycling. Remarkably, these aggregates maintain 80 % activity after seven cycles, outperforming Novozym 435. Additionally, they can effectively initiate photobiocatalytic cascade reactions using guest photocatalysts. As a consequence, our SupEnzyme methodology exhibits noteworthy adaptability in enzyme modification, presenting a versatile platform for various polymer, enzyme, and biocompatible catalyst pairings, with potential applications in the fields of chemistry and biology.

Structural polymorphism of the nucleic acids in pentanucleotide repeats associated with the neurological disorder CANVAS

Short tandem repeats are inherently unstable during DNA replication depending on repeat length, and the expansion of the repeat length in the human genome is responsible for repeat expansion disorders. Pentanucleotide AAGGG and ACAGG repeat expansions in intron 2 of the gene encoding replication factor C subunit 1 (RFC1) cause cerebellar ataxia, neuropathy, vestibular areflexia syndrome (CANVAS) and other phenotypes of late-onset cerebellar ataxia. Herein, we reveal the structural polymorphism of the RFC1 repeats associated with CANVAS in vitro. Single-stranded AAGGG repeat DNA formed a hybrid-type G-quadruplex, whereas its RNA formed a parallel-type G-quadruplex with three layers. The RNA of the ACAGG repeat formed hairpin structure comprising C-G and G-C base pairs with A:A and GA:AG mismatched repeats. Furthermore, both pathogenic repeat RNAs formed more rigid structures than those of the nonpathogenic repeat RNAs. These findings provide novel insights into the structural polymorphism of the RFC1 repeats, which may be closely related to the disease mechanism of CANVAS.

Tertiary Plasticity Drives the Efficiency of Enterocin 7B Interactions with Lipid Membranes

The ability of antimicrobial peptides to efficiently kill their bacterial targets depends on the efficiency of their binding to the microbial membrane. In the case of enterocins, there is a three-part interaction: initial binding, unpacking of helices on the membrane surface, and permeation of the lipid bilayer. Helical unpacking is driven by disruption of the peptide hydrophobic core when in contact with membranes. Enterocin 7B is a leaderless enterocin antimicrobial peptide produced from Enterococcus faecalis that functions alone, or with its cognate partner enterocin 7A, to efficiently kill a wide variety of Gram-stain positive bacteria. To better characterize the role that tertiary structural plasticity plays in the ability of enterocin 7B to interact with the membranes, a series of arginine single-site mutants were constructed that destabilize the hydrophobic core to varying degrees. A series of experimental measures of structure, stability, and function, including CD spectra, far UV CD melting profiles, minimal inhibitory concentrations analysis, and release kinetics of calcein, show that decreased stabilization of the hydrophobic core is correlated with increased efficiency of a peptide to permeate membranes and in killing bacteria. Finally, using the computational technique of adaptive steered molecular dynamics, we found that the atomistic/energetic landscape of peptide mechanical unfolding leads to free energy differences between the wild type and its mutants, whose trends correlate well with our experiment.

HSA over BSA: Selective detection of Human Serum Albumin via a naphtho [2,1-b] furan-based system

Human serum albumin (HSA) is an important biomarker that can be used for the early diagnosis of many diseases. In this work, a TICT probe bearing fused naphtho-furan scaffold (NPNF) was developed and employed in the selective turn-on sensing of HSA. The probe's selectivity towards HSA was observed using steady-state fluorescence experiments, with limit of quantitation in micromolar levels. NPNF's capability to exclusively detect HSA over BSA was further studied/rationalized using anisotropy and time-resolved studies. Molecular docking was used to shed light on the location of NPNF in the subdomain IB of HSA. The practical application of the probe was also demonstrated by the detection of HSA in urine and the HSA-assisted detection of cerium.

Chiral plasmonic sensing: From the perspective of light-matter interaction

Molecular chirality is represented as broken mirror symmetry in the structural orientation of constituent atoms and plays a pivotal role at every scale of nature. Since the discovery of the chiroptic property of chiral molecules, the characterization of molecular chirality is important in the fields of biology, physics, and chemistry. Over the centuries, the field of optical chiral sensing was based on chiral light-matter interactions between chiral molecules and polarized light. Starting from simple optics-based sensing, the utilization of plasmonic materials that could control local chiral light-matter interactions by squeezing light into molecules successfully facilitated chiral sensing into noninvasive, ultrasensitive, and accurate detection. In this Review, the importance of plasmonic materials and their engineering in chiral sensing are discussed based on the principle of chiral light-matter interactions and the theory of optical chirality and chiral perturbation; thus, this Review can serve as a milestone for the proper design and utilization of plasmonic nanostructures for improved chiral sensing.

Synthesis and biophysical evaluation of carbosilane dendrimers as therapeutic siRNA carriers

Gene therapy presents an innovative approach to the treatment of previously incurable diseases. The advancement of research in the field of nanotechnology has the potential to overcome the current limitations and challenges of conventional therapy methods, and therefore to unlocking the full potential of dendrimers for use in the gene therapy of neurodegenerative disorders. The blood-brain barrier (BBB) poses a significant challenge when delivering therapeutic agents to the central nervous system. In this study, we investigated the biophysical properties of dendrimers and their complexes with siRNA directed against the apolipoprotein E (APOE) gene to identify an appropriate nanocarrier capable of safely delivering the cargo across the BBB. Our study yielded valuable insights into the complexation process, stability over time, the mechanisms of interaction, the influence of dendrimers on the oligonucleotide's spatial structure, and the potential cytotoxic effects on human cerebral microvascular endothelium cells. Based on our findings, we identified that the dendrimer G3Si PEG6000 was an optimal candidate for further research, potentially serving as a nanocarrier capable of safely delivering therapeutic agents across the BBB for the treatment of neurodegenerative disorders.

Changes in Secondary Structure and Properties of Bovine Serum Albumin as a Result of Interactions with Gold Surface

Proteins can alter their shape when interacting with a surface. This study explores how bovine serum albumin (BSA) modifies structurally when it adheres to a gold surface, depending on the protein concentration and pH. We verified that the gold surface induces significant structural modifications to the BSA molecule using circular dichroism, infrared spectroscopy, and atomic force microscopy. Specifically, adsorbed molecules displayed increased levels of disordered structures and β-turns, with fewer α-helices than the native structure. MP-SPR spectroscopy demonstrated that the protein molecules preferred a planar orientation during adsorption. Molecular dynamics simulations revealed that the interaction between cysteines exposed to the outside of the molecule and the gold surface was vital, especially at pH=3.5. The macroscopic properties of the protein film observed by AFM and contact angles confirm the flexible nature of the protein itself. Notably, structural transformation is joined with the degree of hydration of protein layers.

Diosmin: A Daboia russelii venom PLA2s inhibitor- purified, and characterized from Oxalis corniculata L medicinal plant

ETHNOPHARMACOLOGICAL RELEVANCE

Oxalis corniculata L is a medicinal plant that belongs to the Oxalidaceae family. It is a little, slow-growing plant with a frail appearance typically found in mild temperate and tropical areas like Pakistan and India. This plant also includes many other bioactive substances, including alkaloids, flavonoids, terpenoids, cardiac glycosides, saponins, phlobatannins, and steroids.

AIM OF THE STUDY

To investigate the anti-inflammatory effects of Compound diosmin, which is derived from Oxalis corniculata L, on VRV-PL-5 and VRV-PL-8a isolated from Vipera russelli.

MATERIALS AND METHODS

Extraction, purification, and characterization of bioactive by TLC, HPTLC, FT-IR analysis, UV-Vis spectrophotometer, LC-MS/MS Analysis, NMR, XRD Analysis, In vitro evaluation, Circular dichroism spectroscopy, in vivo, and in silico studies.

RESULTS

In this study, the extract of Oxalis corniculata was evaluated for its in vitro and in vivo anti-inflammatory effect against PLA2. The methanolic extract decreased hemolytic activity by about 60% at 1:75 w/w and neutralized the hemolytic activity completely at 1:100 w/w concentration. Diosmin inhibited VRV-PL-5 and VRV-PL-8a in a dose-dependent manner, with the extent of inhibition being about 56% for VRV-PL-5120 μM and VRV-PL-8a by 62% at the same concentration with IC50 concentrations of 87.08 μM for VRV-PL-5 and 82.08 μM for VRV-PL-8a, while at 75 μM. Diosmin inhibited the hemolytic activity of VRV-PL-5 by about 85%, and at the same concentration, VRV-PL-8a inhibited by about 75%. UV-CD spectra at the IC50 concentration of diosmin disrupted the secondary structure of VRV-PL-5 &VRV-PL-8a. In vivo, studies showed decreased myotoxicity and cardiotoxicity of the VRV-PL-5 &VRV-PL-8a, which was seen in the decrease in cytoplasmic markers LDH and CPK levels in the serum when incubated with diosmin. Furthermore, Histopathological studies of Muscles and lungs revealed that diosmin considerably protects against cellular abnormality caused by VRV-PL-5 & VRV-PL-8a. Molecular docking, MM/GBSA, and molecular dynamics simulation studies show that the diosmin is a potent inhibitor for VRV-PL-5 and VRV-PL-8a.

CONCLUSION

This study shows that diosmin is a potentially effective VRV-PL-5 and VRV-PL-8a.

Chiral Plasmonic Hybrid Nanostructures: A Gateway to Advanced Chiroptical Materials

Chirality introduces a new dimension of functionality to materials, unlocking new possibilities across various fields. When integrated with plasmonic hybrid nanostructures, this attribute synergizes with plasmonic and other functionalities, resulting in unprecedented chiroptical materials that push the boundaries of the system's capabilities. Recent advancements have illuminated the remarkable chiral light-matter interactions within chiral plasmonic hybrid nanomaterials, allowing for the harnessing of their tunable optical activity and hybrid components. These advancements have led to applications in areas such as chiral sensing, catalysis, and spin optics. Despite these promising developments, there remains a need for a comprehensive synthesis of the current state-of-the-art knowledge, as well as a thorough understanding of the construction techniques and practical applications in this field. This review begins with an exploration of the origins of plasmonic chirality and an overview of the latest advancements in the synthesis of chiral plasmonic hybrid nanostructures. Furthermore, representative emerging categories of hybrid nanomaterials are classified and summarized, elucidating their versatile applications. Finally, the review engages with the fundamental challenges associated with chiral plasmonic hybrid nanostructures and offer insights into the future prospects of this advanced field.

Comparative investigation on interaction between potent antimalarials and human serum albumin using multispectroscopic and computational approaches

This study performed a comparative investigation to explore the interaction mechanisms between two potential antimalarial compounds, JMI 346 and JMI 105, and human serum albumin (HSA), a vital carrier protein responsible for maintaining important biological functions. Our aim was to assess the pharmacological efficiency of these compounds while comprehensively analyzing their impact on the dynamic behavior and overall stability of the protein. A comprehensive array of multispectroscopic techniques, including UV-Vis. spectroscopy, steady-state fluorescence analysis, synchronous fluorescence spectroscopy, three-dimensional fluorescence and circular dichroism spectroscopy, docking studies, and molecular dynamics simulations, were performed to probe the intricate details of the interaction between the compounds and HSA. Our results revealed that both JMI 346 and JMI 105 exhibited promising pharmacological effectiveness within the context of malaria therapy. However, JMI 346 was found to exhibit a significantly higher affinity and only minor altered impact on HSA, suggesting a more favorable interaction with the protein on the dynamic behavior and overall stability of the protein in comparison to JMI 105. Further studies can build on these results to optimize the drug-protein interaction and enable the development of more potent and targeted antimalarial treatments.

Chiral Monitoring Across Both Enantiomeric Excess and Concentration Space: Leveraging Quantum Cascade Lasers for Sensitive Vibrational Circular Dichroism Spectroscopy

Recently, high-throughput quantum cascade laser-based vibrational circular dichroism (QCL-VCD) technology has reduced the measurement time for high-quality vibrational circular dichroism spectra from hours to a few minutes. This study evaluates QCL-VCD for chiral monitoring using flow-through measurement of a changing sample in a circulating loop. A balanced detection QCL-VCD system was applied to the enantiomeric pair R/S-1,1'-bi-2-naphthol in solution. Different mixtures of the two components were used to simulate a racemization process, collecting spectral data at a time resolution of 6 min, and over three concentration levels. The goal of this experimental setup was to evaluate QCL-VCD in terms of both molar and enantiomeric excess (EE) sensitivity at a time resolution relevant to chiral monitoring in chemical processes. Subsequent chemometric evaluation by partial least squares regression revealed a cross-validated prediction accuracy of 2.8% EE with a robust prediction also for the test data set (error = 3.5% EE). In addition, the data set was also treated with the least absolute shrinkage and selection operator (LASSO), which also achieved a robust prediction. Due to the operating principle of LASSO, the obtained coefficients constituted a few discrete spectral frequencies, which represent the most variance. This information can be used in the future for dedicated QCL-based instrument design, gaining a higher time resolution without sacrificing predictive capabilities.

Unwinding the SARS-CoV-2 Ribosomal Frameshifting Pseudoknot with LNA and G-Clamp-Modified Phosphorothioate Oligonucleotides Inhibits Viral Replication

Ribosomal frameshifting (RFS) at the slippery site of SARS-CoV-2 RNA is essential for the biosynthesis of the viral replication machinery. It requires the formation of a pseudoknot (PK) structure near the slippery site and can be inhibited by PK-disrupting oligonucleotide-based antivirals. We obtained and compared three types of such antiviral candidates, namely locked nucleic acids (LNA), LNA-DNA gapmers, and G-clamp-containing phosphorothioates (CPSs) complementary to PK stems. Using optical and electrophoretic methods, we showed that stem 2-targeting oligonucleotide analogs induced PK unfolding at nanomolar concentrations, and this effect was particularly pronounced in the case of LNA. For the leading PK-unfolding LNA and CPS oligonucleotide analogs, we also demonstrated dose-dependent RSF inhibition in dual luciferase assays (DLAs). Finally, we showed that the leading oligonucleotide analogs reduced SARS-CoV-2 replication at subtoxic concentrations in the nanomolar range in two human cell lines. Our findings highlight the promise of PK targeting, illustrate the advantages and limitations of various types of DNA modifications and may promote the future development of oligonucleotide-based antivirals.

Nature-Inspired Chiral Structures: Fabrication Methods and Multifaceted Applications

Diverse chiral structures observed in nature find applications across various domains, including engineering, chemistry, and medicine. Particularly notable is the optical activity inherent in chiral structures, which has emerged prominently in the field of optics. This phenomenon has led to a wide range of applications, encompassing optical components, catalysts, sensors, and therapeutic interventions. This review summarizes the imitations and applications of naturally occurring chiral structures. Methods for replicating chiral architectures found in nature have evolved with specific research goals. This review primarily focuses on a top-down approach and provides a summary of recent research advancements. In the latter part of this review, we will engage in discussions regarding the diverse array of applications resulting from imitating chiral structures, from the optical activity in photonic crystals to applications spanning light-emitting devices. Furthermore, we will delve into the applications of biorecognition and therapeutic methodologies, comprehensively examining and deliberating upon the multifaceted utility of chiral structures.

Regulating the surface topography of CpG nanoadjuvants via coordination-driven self-assembly for enhanced tumor immunotherapy

Immunoadjuvants play a key role in enhancing the efficacy of therapeutic tumor vaccines for treating malignant and recurrent cancers. However, due to the bottleneck in the rational design and mechanistic understanding of novel adjuvants, currently available immunoadjuvants in clinical practice are very limited. To boost adjuvant design and development, herein we propose a surface topography regulatory strategy for constructing novel adjuvants with improved adjuvant properties. One of the licensed adjuvants with a well-defined molecular mechanism of immune activation, cytosine-phosphate-guanine oligodeoxynucleotides (CpG ODNs), was used as the material framework. We constructed immunostimulatory CpG nanoparticles (CpG NPs) with different surface topographies by coordination-driven self-assembly between CpG ODNs and ferrous ions. These self-assembled CpG NPs combine the biological and physical activation abilities of innate immunity and can be used as adjuvants of tumor antigens for malignant tumor immunotherapy. The experimental results showed that these CpG NPs could rapidly enter innate immune cells and remold the tumor microenvironment (TME) to enhance anti-tumor immunotherapy via (i) inducing proinflammatory cytokine production; (ii) promoting the transformation of macrophages from immunosuppressed M2 types into immunoactivated M1 types; (iii) amplifying the antigen presentation of mature dendritic cells (DCs), and (iv) activating T cells in tumor sites. Among the prepared nanostructures, pompon-shaped nanoparticles (NPpo) showed the strongest adjuvant properties and anti-tumor immunotherapeutic effect as the adjuvant of ovalbumin in melanoma-bearing mice. Overall, this work provides an effective strategy for designing novel adjuvants for activating the immunosuppressed TME to enable better cancer immunotherapy.

Molecular profile of non-coding RNA-mediated glycolysis control in human cancers

The glycolysis is a common characteristic of cancer and it is responsible for providing enough energy to ensure growth. The glycolysis suppression is beneficial in tumor growth reduction. The stimulation/inhibition of glycolysis in cancer is tightly regulated by ncRNAs. The regulation of glycolysis by ncRNAs can influence proliferation and therapy response of tumor. The miRNAs are capable of inactivating enzymes responsible for glycolysis and suppressing signaling networks resulting in glycolysis induction. By regulation of glycolysis, miRNAs can affect therapy response. The lncRNAs and circRNAs follow a same pathway and by targeting glycolysis, they affect progression and therapy response of tumor. Noteworthy, lncRNAs and circRNAs sponge miRNAs in glycolysis mechanism control in tumor cells. Furthermore, ncRNA-mediated regulation of glycolysis mechanism can influence metastasis to organs of body. The ncRNAs regulating glycolysis are reliable biomarkers in cancer patients and more importantly, exosomal ncRNAs due to their presence in body fluids, are minimally-invasive biomarkers.

Hypoxia inducible factor-1α (HIF-1α) in breast cancer: The crosstalk with oncogenic and onco-suppressor factors in regulation of cancer hallmarks

Low oxygen level at tumor microenvironment leads to a condition, known as hypoxia that is implicated in cancer progression. Upon hypoxia, HIF-1α undergoes activation and due to its oncogenic function and interaction with other molecular pathways, promotes tumor progression. The HIF-1α role in regulating breast cancer progression is described, Overall, HIF-1α has upregulation in breast tumor and due to its tumor-promoting function, its upregulation is in favor of breast tumor progression. HIF-1α overexpression prevents apoptosis in breast tumor and it promotes cell cycle progression. Silencing HIF-1α triggers cycle arrest and decreases growth. Migration of breast tumor enhances by HIF-1α signaling and it mainly induces EMT in providing metastasis. HIF-1α upregulation stimulates drug resistance and radio-resistance in breast tumor. Furthermore, HIF-1α signaling induces immune evasion of breast cancer. Berberine and pharmacological intervention suppress HIF-1α signaling in breast tumor and regulation of HIF-1α by non-coding RNAs occurs. Furthermore, HIF-1α is a biomarker in clinic.

Evaluation of in vitro whey protein digestibility in a protein-catechins model system mimicking milk chocolate: Interaction with flavonoids does not hinder protein bioaccessibility

Flavonoids are largely present in plant food such as cocoa and derived products. These compounds can interact with proteins inherently contained in the food matrix and/or the proteolytic enzymes involved in gastrointestinal digestion. The flavonoid/protein interaction might hamper protein bioaccessibility and digestibility, affecting the nutritional quality. However, information on the digestion fate of proteins in food matrices containing both proteins and flavonoids is limited. The aim of this work was to evaluate the interaction between proteins and flavonoids and verify the potential effects of this interaction on protein digestibility. Taking milk chocolate as model, first a simple whey proteins/catechins mixed system was evaluated, and then the effects on digestibility were also verified in a real sample of commercial milk chocolate. The effects of the catechins/whey proteins interaction in the model system were evaluated by optical and chiro-optical spectroscopy, outlining a slight protein structure modification upon interaction with catechins. The digestibility of the protein fraction both in the model system, with and without catechins, and also in milk chocolate, was then determined by the application of INFOGEST in vitro digestion method: the bioaccessibility was evaluated in terms of protein hydrolysis and protein solubilisation, and major peptides generated by the digestion were also determined by LC/HR-MS. Despite the slight interaction with proteins, flavonoids were found to not hinder nor modify protein solubilization, protein hydrolysis and peptide profile by digestive enzymes. Also protein digestibility in milk chocolate, evaluated by SDS-PAGE, was found to be complete. The present data clearly indicate that the interaction of the proteins with the flavonoids present in the cocoa matrix does not to affect protein bioaccessibility during digestion.

High-performance circular polarization modulation using a dielectric metasurface

We demonstrate a chiral metasurface that exhibits a giant chiroptical response as well as functions as an optical diode due to geometrical asymmetry for circularly polarized light (CPL). Engineering the Mie-type multipole radiation using geometrical features led to performance values in terms of near-unity transmission and circular dichroism (CD) efficiency (about 0.96) and an extinction ratio of  ∼3.8×104 for 1550 nm wavelength. A continuous stopband of 1538-1556 nm is achieved for an unchosen component of CPL while keeping the transmission efficiency of the chosen CPL component larger than 0.9. Because of the high extinction ratio and CD efficiency, the proposed metasurface has the potential for chiroptical applications including high-contrast polarization imaging, precise Stokes parameters measurement, optical diodes, and polarization detection for CPL.

Spectroscopic fingerprints profiling the polysaccharide/protein/humic architecture of stratified extracellular polymeric substances (EPS) in activated sludge

Extracellular polymeric substances (EPS), with a stratified structure including tightly-bound EPS (TB-EPS), loosely-bound EPS (LB-EPS), and soluble EPS (S-EPS) surrounding the microbial cells, are known to vitally affect the physicochemical and biological functions of activated sludge in wastewater treatment. Polysaccharides (PS), proteins (PN), and humic acids (HA) are key components of EPS but their roles in constructing the multi-layer architecture are still unclear. This study explored the EPS characteristics in relation to the components using spectroscopic fingerprinting techniques. Ultraviolet-visible (UV-vis) spectra demonstrated stark difference between TB-EPS and other EPS. Fluorescence excitation-emission matrix (FEEM) and apparent quantum yield revealed further detailed differences. Fluorescence quotient analysis highlighted the dominance of TB-EPS, LB-EPS, and S-EPS in the excitation/emission wavelength (Ex/Em) region of Em = 350-400 nm, Em > 400 nm, and low-Stokes shift band (Em - Ex < 25 nm), respectively. Wavelength-wise prediction of the FEEM intensity was achieved through multiple linear regression against the chemical composition and variance partitioning analysis witnessed binary interactions of PS×HA and PS×PN in S-EPS, PN×HA and PS×PN in LB-EPS, and ternary interaction of PS×PN×HA in TB-EPS as well as the wavelength-specific fluorescence responses of these interactions. Further, X-ray photoelectron spectroscopy, infrared spectra, and circular dichroism spectra corroborated the differences in primary, secondary, and tertiary structures across the EPS layers. Ultrahigh-performance liquid chromatography-mass spectrometry detected molecular fragments confirming the multi-component hybridization among PS, PN, and HA. This study demonstrates a spectroscopic approach to sensitively fingerprint the fine structure of EPS, which has the potential for rapid monitoring of EPS and related sludge properties in wastewater treatment systems.

A class of peptides designed to replicate and enhance the Receptor for Hyaluronic Acid Mediated Motility binding domain

The extra-cellular matrix (ECM) is a complex and rich microenvironment that is exposed and over-expressed across several injury or disease pathologies. Biomaterial therapeutics are often enriched with peptide binders to target the ECM with greater specificity. Hyaluronic acid (HA) is a major component of the ECM, yet to date, few HA adherent peptides have been discovered. A class of HA binding peptides was designed using B(X₇)B hyaluronic acid binding domains inspired from the helical face of the Receptor for Hyaluronic Acid Mediated Motility (RHAMM). These peptides were bioengineered using a custom alpha helical net method, allowing for the enrichment of multiple B(X₇)B domains and the optimisation of contiguous and non-contiguous domain orientations. Unexpectedly, the molecules also exhibited the behaviour of nanofiber forming self-assembling peptides and were investigated for this characteristic. Ten 23-27 amino acid residue peptides were assessed. Simple molecular modelling was used to depict helical secondary structures. Binding assays were performed with varying concentrations (1-10 mg/mL) and extra-cellular matrices (HA, collagens I-IV, elastin, and Geltrex). Concentration mediated secondary structures were assessed using circular dichroism (CD), and higher order nanostructures were visualized using transmission electron microscopy (TEM). All peptides formed the initial apparent 3₁₀/alpha-helices, yet peptides 17x-3, 4, BHP3 and BHP4 were HA specific and potent (i.e., a significant effect) binders at increasing concentrations. These peptides shifted from apparent 3₁₀/alpha-helical structures at low concentration to beta-sheets at increasing concentration and also formed nanofibers which are noted as self-assembling structures. Several of the HA binding peptides outperformed our positive control (mPEP35) at 3-4 times higher concentrations, and were enhanced by self-assembly as each of these groups had observable nanofibers. STATEMENT OF SIGNIFICANCE: Specific biomolecules or peptides have played a crucial role in developing materials or systems to deliver key drugs and therapeutics to a broad spectrum of diseases and disorders. In these diseased tissues, cells build protein/sugar networks, which are uniquely exposed and great targets to deliver drugs to. Hyaluronic acid (HA) is involved in every stage of injury and is abundant in cancer. To date, only two HA specific peptides have been discovered. In our work, we have designed a way to model and trace binding regions as they appear on the face of a helical peptide. Using this method we have created a family of peptides enriched with HA binding domains that stick with 3-4 higher affinity than those previously discovered.

Prion Protein Octarepeat Domain Forms Transient β-Sheet Structures upon Residue-Specific Binding to Cu(II) and Zn(II) Ions

Misfolding of the cellular prion protein (PrP^C) is associated with the development of fatal neurodegenerative diseases called transmissible spongiform encephalopathies (TSEs). Metal ions appear to play a crucial role in PrP^C misfolding. PrP^C is a combined Cu(II) and Zn(II) metal-binding protein, where the main metal-binding site is located in the octarepeat (OR) region. Thus, the biological function of PrP^C may involve the transport of divalent metal ions across membranes or buffering concentrations of divalent metal ions in the synaptic cleft. Recent studies have shown that an excess of Cu(II) ions can result in PrP^C instability, oligomerization, and/or neuroinflammation. Here, we have used biophysical methods to characterize Cu(II) and Zn(II) binding to the isolated OR region of PrP^C. Circular dichroism (CD) spectroscopy data suggest that the OR domain binds up to four Cu(II) ions or two Zn(II) ions. Binding of the first metal ion results in a structural transition from the polyproline II helix to the β-turn structure, while the binding of additional metal ions induces the formation of β-sheet structures. Fluorescence spectroscopy data indicate that the OR region can bind both Cu(II) and Zn(II) ions at neutral pH, but under acidic conditions, it binds only Cu(II) ions. Molecular dynamics simulations suggest that binding of either metal ion to the OR region results in the formation of β-hairpin structures. As the formation of β-sheet structures can be a first step toward amyloid formation, we propose that high concentrations of either Cu(II) or Zn(II) ions may have a pro-amyloid effect in TSE diseases.

Conformational characterization of the mammalian-expressed SARS-CoV-2 recombinant receptor binding domain, a COVID-19 vaccine

The COVID-19 pandemic has caused a large number of diseases worldwide. There are few vaccines to constrain this disease and the value of them is high. In this sense, the antigens of the vaccine platform Soberana, the receptor binding domain from SARS-CoV-2 Spike protein, both the monomeric (mRBD) and dimeric (dRBD) forms, have been developed. This study encompassed several analyses by different techniques like circular dichroism (CD), fluorescence spectroscopy (FS) and Gel Filtration- High Performance Liquid ChLC of mRBD and dRBD. Monomer and dimer exhibited similar far-UV CD spectral characteristics with 54% of β-sheet content. Similar conformational features according to near-UV CD and FS studies were observed in both RBD. Stress stability studies by far-UV CD, FS, biological activity and GF-HPLC at 37 °C showed that mRBD is very stable. On the other hand, dRBD fluorescent emission showed a shift towards higher wavelengths as the incubation time increases, suggesting exposition of tryptophan residues, unlike what happens with mRBD. Biological activity outcome confirms these results. GF-HPLC profiles showed that in mRBD, the product of molecular stress are dimers and does not increase over time. However, dRBD showed dimer fragmentation as the main degradation species. This study reveals the usefulness of CD techniques for the analysis of degradation of RBD molecules as well as showed the difference in stability of both RBD molecules. Besides, our work provides useful insights into the production of a key protein used in diagnosis and therapeutics to fight COVID-19 pandemia.

Novel Casein-Derived Peptide-Zinc Chelate: Zinc Chelation and Transepithelial Transport Characteristics

Casein-derived peptides are recognized as promising candidates for improving zinc bioavailability through the form of a peptide-zinc chelate. In the present work, a novel 11-residue peptide TEDELQDKIHP identified from casein hydrolysate in our previous study was synthesized to investigate the zinc chelation characteristics. Meanwhile, the digestion stability and transepithelial transport of TEDELQDKIHP-Zn were also investigated. The obtained results indicated that the carboxyl groups (from Asp and Glu), amino groups (from Lys and His), pyrrole nitrogen group of Pro, and imidazole nitrogen group of His were responsible for zinc chelation. The complexation with zinc resulted in a more ordered structure of TEDELQDKIHP-Zn. In terms of digestion stability, the chelate of TEDELQDKIHP-Zn could remain stable to a large extent after gastric (78.54 ± 0.14%) and intestinal digestion (70.18 ± 0.17%). Moreover, TEDELQDKIHP-Zn was proven to be a well-absorbed biological particle with a P_app value higher than 1 × 10^-6 cm/s, and it could be transported across the intestine epithelium through transcytosis. TEDELQDKIHP-Zn exhibited more bioavailable effects on zinc absorption and ALP activity than inorganic zinc sulfate.

Vibrational circular dichroism spectra of natural products by means of the nuclear velocity perturbation theory

We present the application of the recently implemented nuclear velocity perturbation theory, using the combined Gaussian and plane waves approach in CP2K, to the vibrational circular dichroism (VCD) spectra of a set of natural products. Even though the calculations were carried out for isolated molecules in the gas-phase limit, neglecting inter-molecular interactions and anharmonic effects, the match between simulated and experimental spectra is reasonable. We also study the influence of different density functionals on the conformational search and the resulting VCD spectra via group coupling matrices (GCMs). The GCM analysis reveals that the VCD signal can in some cases arise from moieties which are close to each other and in other cases from moieties far from each other. Differences in spectra obtained using different exchange-correlation density functionals can be attributed to interaction terms between different moieties in the molecules changing their sign.

Detailing Protein-Bound Uremic Toxin Interaction Mechanisms with Human Serum Albumin in the Pursuit of Designing Competitive Binders

Chronic kidney disease is the gradual progression of kidney dysfunction and involves numerous co-morbidities, one of the leading causes of mortality. One of the primary complications of kidney dysfunction is the accumulation of toxins in the bloodstream, particularly protein-bound uremic toxins (PBUTs), which have a high affinity for plasma proteins. The buildup of PBUTs in the blood reduces the effectiveness of conventional treatments, such as hemodialysis. Moreover, PBUTs can bind to blood plasma proteins, such as human serum albumin, alter their conformational structure, block binding sites for other valuable endogenous or exogenous substances, and exacerbate the co-existing medical conditions associated with kidney disease. The inadequacy of hemodialysis in clearing PBUTs underscores the significance of researching the binding mechanisms of these toxins with blood proteins, with a critical analysis of the methods used to obtain this information. Here, we gathered the available data on the binding of indoxyl sulfate, p-cresyl sulfate, indole 3-acetic acid, hippuric acid, 3-carboxyl-4-methyl-5-propyl-2-furan propanoic acid, and phenylacetic acid to human serum albumin and reviewed the common techniques used to investigate the thermodynamics and structure of the PBUT-albumin interaction. These findings can be critical in investigating molecules that can displace toxins on HSA and improve their clearance by standard dialysis or designing adsorbents with greater affinity for PBUTs than HSA.

The comparison between zein-anthocyanins complex and nanoparticle systems: Stability enhancement, interaction mechanism, and in silico approaches

This research aimed to compare and characterize the physicochemical properties and interaction mechanism of zein and anthocyanins (ACNs) from experimental and theoretical perspectives. Zein-ACNs complex (ZACP) was prepared by mixing ACNs with different concentrations of zein, and zein-ACNs nanoparticles (ZANPs) were formed using ultrasound-assisted antisolvent precipitation method. The hydrated particle sizes of the two systems were 590.83 nm and 99.86 nm, respectively, and observed to be spherical under transmission electron microscopy (TEM). The multi-spectroscopy approaches confirmed hydrogen bonding and hydrophobic forces were the dominant forces for stabilizing ACNs. The retention of ACNs, color stability and antioxidant activities were also improved in both systems. Furthermore, molecular simulation results were consistent with the multi-spectroscopy findings, which clarified the contribution of van der Waals forces to the binding of zein and ACNs. This study provided a practical approach for stabilizing ACNs and expanding the utilization of plant proteins as stabilization systems.

Supramolecular self-assembly of glycosaminoglycan mimetic nanostructures for cell proliferation and 3D cell culture application

Glycosaminoglycans (GAGs), such as heparin, heparan sulfate and chondroitin sulfate, are playing important roles in various biological processes. Due to the laborious work of organic or enzymatic total synthesis of GAGs, different approaches, including glycopolymers, dendrimers, etc., have been developed to mimic the structures and bioactivities of GAGs, but the syntheses can still be difficult. In the current study, a new format of GAG mimetic structure, supramolecularly assembled polymers, have been easily prepared by mixing fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF) and sulfated glyco-modified fluorenylmethoxy derivatives (FGS and FG3S). The self-assembly behavior of these polymers into different structural formats of nanoparticles, nanofibers and macroscopic hydrogels upon adjusted concentrations and composite ratios have been detailed studied. The nanofibers modified with highly sulfated glycol groups (FG3S/Fmoc-FF) showed strong promotion effect for cell proliferation, which efficiency was even similar to that of natural heparin, higher than nanoparticles or non-/low-sulfated glyco-modified nanofibers. Moreover, the supramolecular polymers were further made into hydrogels that capable of 3D cell culture. This study provided a novel and efficient approach for GAG mimicking, showing great potential for tissue engineering related applications.

Ultraviolet-Visible Multifunctional Vortex Metaplates by Breaking Conventional Rotational Symmetry

Metasurfaces have shown remarkable potential to manipulate many of light's intrinsic properties, such as phase, amplitude, and polarization. Recent advancements in nanofabrication technologies and persistent efforts from the research community result in the realization of highly efficient, broadband, and multifunctional metasurfaces. Simultaneous control of these characteristics in a single-layered metasurface will be an apparent technological extension. Here, we demonstrate a broadband multifunctional metasurface platform with the unprecedented ability to independently control the phase profile for two orthogonal polarization states of incident light over dual-wavelength spectra (ultraviolet to visible). In this work, multiple single-layered metasurfaces composed of bandgap-engineered silicon nitride nanoantennas are designed, fabricated, and optically characterized to demonstrate broadband multifunctional light manipulation ability, including structured beam generation and meta-interferometer implementation. We envision the presented metasurface platform opening new avenues for broadband multifunctional applications including ultraviolet-visible spectroscopy, spatially modulated illumination microscopy, optical data storage, and information encoding.

Neural-Network-Enabled Design of a Chiral Plasmonic Nanodimer for Target-Specific Chirality Sensing

Quantitative analysis of chiral molecules in various solvents is essential. However, there are still many challenges to enhancing the sensitivity in precisely determining both concentration and chirality. Here, we built an algorithmic methodology to predict and optimally design the chiroptical response of chiral plasmonic sensors for a specific target chiral analyte with the aid of deep learning. Based upon the analytic and intuitive understanding of the Born-Kuhn type plasmonic nanodimer, we designed and trained the neural networks that can successfully predict the chiroptical properties and further inversely design the plasmonic structure to achieve the intended circular dichroism. The developed algorithm could identify the optimum structure exhibiting the maximum sensitivity for the given specific analytes. Surprisingly, we discovered that sensitivity strongly depends on the various conditions of analytes and can be finely tuned with the structural parameters of plasmonic nanodimers. We envision that this study can provide a general platform to develop ultrasensitive chiral plasmonic sensors whose structure and sensitivity have been evolved algorithmically for adoption in specific applications.

Expression, purification, and characterisation of the p53 binding domain of Retinoblastoma binding protein 6 (RBBP6)

RBBP6 is a 250 kDa eukaryotic protein known to be a negative regulator of p53 and essential for embryonic development. Furthermore, RBBP6 is a critical element in carcinogenesis and has been identified as a potential biomarker for certain cancers. RBBP6's ability to interact with p53 and cause its degradation makes it a potential drug target in cancer therapy. Therefore, a better understating of the p53 binding domain of RBBP6 is needed. This study presents a three-part purification protocol for the polyhistidine-tagged p53 binding domain of RBBP6, expressed in Escherichia coli bacterial cells. The purified recombinant domain was shown to have structure and is functional as it could bind endogenous p53. We characterized it using clear native PAGE and far-UV CD and found that it exists in a single form, most likely monomer. We predict that its secondary structure is predominantly random coil with 19% alpha-helices, 9% beta-strand and 14% turns. When we exposed the recombinant domain to increasing temperature or known denaturants, our investigation suggested that the domain undergoes relatively small structural changes, especially with increased temperature. Moreover, we notice a high percentage recovery after returning the domain close to starting conditions. The outcome of this study is a pure, stable, and functional recombinant RBBP6-p53BD that is primarily intrinsically disordered.

Structural characteristics of a low molecular weight velvet antler protein and the anti-tumor activity on S180 tumor-bearing mice

Velvet antler is a traditional Chinese medicine with various pharmacological values, which is an important raw material for traditional Chinese medicinal wine. Nevertheless, the chemical compositions and bioactivities of velvet antler residue used for making medicinal wine are rarely reported, leading to a waste of resources. In this study, a velvet antler protein (VA-pro) was extracted from velvet antler residue by simulating the gastrointestinal digestion, and its composition, structural characteristics and in vivo anti-tumor activities were determined and investigated. VA-pro possessed high purity with a relatively low molecular weight as 22.589 kDa under HPLC, one- and two-dimensional electrophoresis, and it contained high contents of Pro, Gly, Glu and Ala. Besides, the secondary structure of VA-pro was dominated by β-turn and β-sheet, and VA-pro possessed similar protein sequence, isoelectric point and amino acid compositions to hypothetical protein G4228_020061. The in vivo results substantiated that VA-pro could improve the body weights and immune organ indices, increase the expressions of sera cytokines and regulate the distributions of T and B lymphocytes subsets in peripheral blood of S180 tumor-bearing mice. Furthermore, VA-pro could effectively inhibit solid S180 tumors growth by inducing S phase cell cycle arrest mediated through mitochondria. To summarize, our study provided theoretical support that VA-pro had the potential to be used as an immunopotentiator in immunocompromised or cancer-bearing hosts.