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Bacteria have evolved elaborate mechanisms to thrive in stressful environments. F-like plasmids in gram-negative bacteria encode for a multi-protein Type IV Secretion System (T4SSF) that is functional for bacterial proliferation and adaptation through the process of conjugation. The periplasmic protein TrbB is believed to have a stabilizing chaperone role in the T4SSF assembly, with TrbB exhibiting disulfide isomerase (DI) activity. In the current report, we demonstrate that the deletion of the disordered N-terminus of TrbBWT, resulting in a truncation construct TrbB37-161, does not affect its catalytic in vitro activity compared to the wild-type protein (p = 0.76). Residues W37-K161, which include the active thioredoxin motif, are sufficient for DI activity. The N-terminus of TrbBWT is disordered as indicated by a structural model of GST-TrbBWT based on ColabFold-AlphaFold2 and Small Angle X-Ray Scattering data and 1H-15N Heteronuclear Single Quantum Correlation (HSQC) spectroscopy of the untagged protein. This disordered region likely contributes to the protein's dynamicity; removal of this region results in a more stable protein based on 1H-15N HSQC and Circular Dichroism Spectroscopies. Lastly, size exclusion chromatography analysis of TrbBWT in the presence of TraW, a T4SSF assembly protein predicted to interact with TrbBWT, does not support the inference of a stable complex forming in vitro. This work advances our understanding of TrbB's structure and function, explores the role of structural disorder in protein dynamics in the context of a T4SSF accessory protein, and highlights the importance of redox-assisted protein folding in the T4SSF.
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Increased plasma levels of serum amyloid A (SAA), an acute-phase protein that is secreted in response to inflammation, may lead to the accumulation of amyloid in various organs thereby obstructing their functions. Severe cases can lead to a systemic disorder called AA amyloidosis. Previous studies suggest that the N-terminal helix is the most amyloidogenic region of SAA. Moreover, computational studies implicated a significant role for Arg-1 and the residue-specific interactions formed during the fibrillization process. With a focus on the N-terminal region of helix-1, SAA1-13, mutational analysis was employed to interrogate the roles of the amino acid residues, Arg-1, Ser-5, Glu-9, and Asp-12. The truncated SAA1-13 fragment was systematically modified by substituting the key residues with alanine or uncharged but structurally similar amino acids. We monitored the changes in the amyloidogenic propensities, associated conformational markers, and morphology of the amyloids resulting from the mutation of SAA1-13. Mutating out Arg-1 resulted in much reduced aggregation propensity and a lack of detectable ß-structures alluding to the importance of salt-bridge interactions involving Arg-1. Our data revealed that by systematically mutating the key amino acid residues, we can modulate the amyloidogenic propensity and alter the time-dependent conformational variation of the peptide. When the behaviors of each mutant peptide were analyzed, they provided evidence consistent with the aggregation pathway predicted by MD simulation studies. Here, we detail the important temporal molecular interactions formed by Arg-1 with Ser-5, Glu-9, and Asp-12 and discuss its mechanistic implications on the self-assembly of the helix-1 region of SAA.
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To understand the role of an additional coordination site in the linker in chirality sensing, we designed and synthesized an S-2-methylbutanamido-substituted m-phthalic diamide-linked zinc bisporphyrinate, [Zn2(S-MAABis)] and investigated its ability to sense the chirality of amino acid esters. The 1H NMR spectra and the crystal structure showed that the amido oxygen adjacent to the chiral carbon was coordinated with zinc. NMR and UV-vis titration showed that the binding of [Zn2(S-MAABis)] to amino acid esters occurred via two equilibria, forming 1:1 and 1:2 host-guest complexes. The CD spectra suggested that [Zn2(S-MAABis)] can effectively recognize the absolute configuration of amino acid esters. The sign of the CD spectra remained unchanged during the titration, indicating that the corresponding 1:1 and 1:2 host-guest complexes had the same chirality. This is different from previously studied amino-substituted m-phthalic diamide-linked zinc bisporphyrinate [Zn2(AmBis)], which showed chirality inversion during titration. Theoretical calculations indicated that the additional coordination sites (amido or amino) in the 1:1 host-guest complexes played different roles, leading to differences in chirality. Our studies suggest that the introduction of a coordination site can influence the chirality transfer process, but the results of chirality transfers are dependent on the specific binding modes.
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Cytochrome c (CytC), a one-electron carrier, transfers electrons from complex bc1 to cytochrome c oxidase (CcO) in the electron-transport chain. Electrostatic interaction with the partners, complex bc1 and CcO, is ensured by a lysine cluster near the heme forming the Universal Binding Site (UBS). We constructed three mutant variants of mitochondrial CytC with one (2Mut), four (5Mut), and five (8Mut) Lys->Glu substitutions in the UBS and some compensating Glu->Lys substitutions at the periphery of the UBS for charge compensation. All mutants showed a 4-6 times increased peroxidase activity and accelerated binding of cyanide to the ferric heme of CytC. In contrast, decomposition of the cyanide complex with ferrous CytC, as monitored by magnetic circular dichroism spectroscopy, was slower in mutants compared to WT. Molecular dynamic simulations revealed the increase in the fluctuations of Cα atoms of individual residues of mutant CytC compared to WT, especially in the Ω-loop (70-85), which can cause destabilization of the Fe S(Met80) coordination link, facilitation of the binding of exogenous ligands cyanide and peroxide, and an increase in peroxidase activity. It was found that only one substitution K72E is enough to induce all these changes, indicating the significance of K72 and the Ω-loop (70-85) for the structure and physiology of mitochondrial CytC. In this work, we also propose using a ferro-ferricyanide buffer as a substrate to monitor the peroxidase activity of CytC. This new approach allows us to determine the rate of peroxidase activity at moderate (200 µM) concentrations of H2O2 and avoid complications of radical formation during the reaction.
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Citocromos c , Simulação de Dinâmica Molecular , Sítios de Ligação , Ligantes , Citocromos c/metabolismo , Citocromos c/química , Citocromos c/genética , Peroxidase/metabolismo , Peroxidase/química , Peroxidase/genética , Substituição de Aminoácidos , Ligação Proteica , Cianetos/metabolismo , Cianetos/química , Animais , Heme/metabolismo , Heme/química , MutaçãoRESUMO
Mefloquine, a widely used antimalarial agent, has spurred ongoing research into the development of derivatives with enhanced efficacy and reduced side effects. In this investigation, we synthesized two compounds containing N-allyl or N-tert-butylacetamid groups. A chiral liquid chromatography with polysaccharide chiral stationary phase was utilized to separate the enantiomers of both derivatives. We employed spectroscopic chiroptical and non-polarizable methods such as electronic and vibrational circular dichroism, infrared absorption and ultraviolet spectroscopies. Combined with density functional theory calculations, the stable conformers were found in solution and their spectra were subsequently simulated. We elucidated the three-dimensional structure of the enantiomerically pure compounds and assigned the absolute configuration of all prepared derivatives using both experimental and simulated spectra.
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The study aims to explore the effects of Eugenol (EUG) as an antioxidant on α-Chymotrypsin (α-Chy) and its interaction mechanism, with potential implications for new therapy development. The interaction between EUG and α-Chy was demonstrated through ultraviolet (UV) spectroscopy, which resulted in a shift in absorption with docking energies of -22.76 kJ/mol. An increase in fluorescence intensity indicated that the Trp residues moved to a less polar environment, which is consistent with the changes in accessible surface area (ASA) values. The presence of EUG led to a decrease in α-helix, ß-turn, and random coil structures as shown by circular dichroism (CD) and Fourier-transform infrared (FTIR) analysis. Additionally, there was a slight increase in ß-sheet structures, indicating a decrease in enzyme stability. However, tests for thermal stability showed a decrease in folding upon the introduction of EUG, which contradicted the results obtained from molecular dynamics (MD) simulations. The docking studies revealed that EUG forms hydrogen bonds and van der Waals forces with the enzyme, indicating the interaction mechanism. Kinetic studies confirmed that EUG acts as a mixed inhibitor. However, further research involving live organisms is necessary to fully understand its potential.
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Iron oxide nanoparticles (IONPs) have been extensively explored in biomedicine, bio-sensing, hyperthermia, and drug/gene delivery, attributed to their versatile and tunable properties. However, owing to its numerous applications, the functionalization of IONPs with appropriate materials is in demand. To achieve optimal functionalization of IONPs, polydopamine (PDA) was utilized due to its ability to provide a superior functionalized surface, near-infrared light absorption, and adhesive nature to customize desired functionalized IONPs. This notion of involving PDA led to the successful synthesis of magnetite-PDA nanoparticles, where PDA is surface-coated on magnetite (Fe3O4@PDA). The Fe3O4@PDA nanoparticles were characterized using techniques like TEM, FESEM, PXRD, XPS, VSM, and FTIR, suggesting PDA's successful attachment with magnetite crystal structure retention. Human serum albumin (HSA), the predominant protein in blood plasma, interacts with the delivered nanoparticles. Therefore, we have employed various spectroscopic techniques, along with cytotoxicity, to inspect the effect of Fe3O4@PDA NPs on the stability and structure of HSA. The structural alterations were examined using circular dichroism (CD) and synchronous fluorescence spectroscopy (SFS). It has been observed that there are no structural perturbations in the secondary structure of the HSA protein after interaction with Fe3O4@PDA. Studies using steady-state fluorescence revealed that the inherent fluorescence intensities of HSA were suppressed after interaction with Fe3O4@PDA. In addition, temperature-dependent fluorescence measurements suggested that the type of quenching consists of both static and dynamic quenching simultaneously. A cytotoxicity study in Drosophila melanogaster larvae revealed no cytotoxic effects but did show a minor genotoxic effect only at higher concentrations.
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We have studied binding properties of three detergents, i.e., sodium dodecyl sulfate (SDS), Sarkosyl and sodium lauroyl glutamate (SLG), to model proteins based on their effects on electrophoretic mobilities of the proteins using agarose native gel electrophoresis and circular dichroism (CD). This simple technology can evaluate the dissociative properties of bound detergents from the proteins and their effects on protein structure. SDS influenced the electrophoretic mobilities of all model proteins more strongly than the other two detergents, implying a stronger inclination for protein binding and subsequent alterations in protein structure or reductions in activity, which are supported by CD analysis. On the contrary, Sarkosyl and SLG showed weaker binding and interfered less with the structure and biological activities, indicating that these detergents may be useful for protein purification and analysis. It appeared that SLG was weaker in protein binding than Sarkosyl, although the effects of these two detergents appeared to depend on the proteins.
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Thirty years since the first report on the PilY1 protein in bacteria, only the C-terminal domain has been crystallized; there is no study in which the N-terminal domain, let alone the complete protein, has been crystallized. In our laboratory, we are interested in characterizing the Type IV Pili (T4P) of Acidithiobacillus thiooxidans. We performed an in silico characterization of PilY1 and other pilins of the T4P of this acidophilic bacterium. In silico characterization is crucial for understanding how proteins adapt and function under extreme conditions. By analyzing the primary and secondary structures of proteins through computational methods, researchers can gain valuable insights into protein stability, key structural features, and unique amino acid compositions that contribute to resilience in harsh environments. Here, it is presented a description of the particularities of At. thiooxidans PilY1 through predictor software and homology data. Our results suggest that PilY1 from At. thiooxidans may have the same role as has been described for other PilY1 associated with T4P in neutrophilic bacteria; also, its C-terminal interacts (interface interaction) with the minor pilins PilX, PilW and PilV. The N-terminal region comprises domains such as the vWA and the MIDAS, involved in signaling, ligand-binding, and protein-protein interaction. In fact, the vWA domain has intrinsically disordered regions that enable it to maintain its structure over a wide pH range, not only at extreme acidity to which At. thiooxidans is adapted. The results obtained helped us design the correct methodology for its heterologous expression. This allowed us partially experimentally characterize it by obtaining the N-terminal domain recombinantly and evaluating its acid stability through fluorescence spectroscopy. The data suggest that it remains stable across pH changes. This work thus provides guidance for the characterization of extracellular proteins from extremophilic organisms.
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Low-dimensional metal halide perovskites have unique optical and electrical properties that render them attractive for the design of diluted magnetic semiconductors. However, the nature of dopant-exciton exchange interactions that result in spin-polarization of host-lattice charge carriers as a basis for spintronics remains unexplored. Here, we investigate Mn2+-doped CsPbCl3 nanocrystals using magnetic circular dichroism spectroscopy and show that Mn2+ dopants induce excitonic Zeeman splitting which is strongly dependent on the nature of the band-edge structure. We demonstrate that the largest splitting corresponds to exchange interactions involving the excited state at the M-point along the spin-orbit split-off conduction band edge. This splitting gives rise to an absorption-like C-term excitonic MCD signal, with the estimated effective g-factor (geff) of ca. 70. The results of this work help resolve the assignment of absorption transitions observed for metal halide perovskite nanocrystals and allow for a design of new diluted magnetic semiconductor materials for spintronics applications.
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As a host for exchange bias (EB), van der Waals (vdW) magnetic materials have exhibited intriguing and distinct functionalities from conventional magnetic materials. The EB in most vdW systems is far below room temperature, which poses a challenge for practical applications. Here, by using Kerr microscopy, we demonstrate a record-high blocking temperature that approaches room temperature and a huge positive EB field that nears 2 kOe at 100 K in naturally oxidized two-dimensional (2D) vdW ferromagnetic Fe3GaTe2 nanoflakes. Moreover, we realized a reversible manipulation of both the presence/absence and positive/negative signs of EB via a training magnetic field without multiple field cooling processes. Thus, our study clearly reveals the robust, sizable, and sign-tunable EB in vdW magnetic materials up to near room temperature, thereby establishing Fe3GaTe2 as an emerging room-temperature-operating vdW material and paving the way for designing practical 2D spintronic devices.
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Magnetic anisotropy and magnetic exchange interactions are crucial parameters that characterize the hybrid metal-organic interface, a key component of an organic spintronic device. It is shown that the incorporation of 4f RE atoms to hybrid metal-organic interfaces of CuPc/REAu2 type (RE = Gd, Ho) constitutes a feasible approach toward on-demand magnetic properties and functionalities. The GdAu2 and HoAu2 substrates differ in their magnetic anisotropy behavior. Remarkably, the HoAu2 surface promotes the inherent out-of-plane anisotropy of CuPc, owing to the match between the anisotropy axis of substrate and molecule. Furthermore, the presence of RE atoms leads to a spontaneous antiferromagnetic exchange coupling at the interface, induced by the 3d-4f superexchange interaction between the unpaired 3d electron of CuPc and the 4f electrons of the RE atoms. It is shown that 4f RE atoms with unquenched quantum orbital momentum ( L $L$ ), as it is the case of Ho, induce an anisotropic interfacial exchange coupling.
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Skyrmions in two-dimensional (2D) magnetic materials are considered as ideal candidates for information carriers in next-generation spintronic devices. However, conventional methods for elucidating the physical properties of skyrmions have limited the development of skyrmions in diverse 2D magnetic material systems due to their requirements for electrical conductivity. To overcome this limitation, we propose to utilize an optical method (magneto-optical Kerr technique) to detect the skyrmions in 2D magnetic materials. Herein, the graphene/Fe3GeTe2/graphene vertical van der Waals (vdW) heterostructure devices are fabricated to generate stabilized skyrmions by applying out-of-plane current. In combination with magnetic circular dichroism measurements, we observe topological-reflective magnetic circular dichroism (T-RMCD) effects in Fe3GeTe2 flakes and attribute the peak-shaped component in T-RMCD to the annihilation of skyrmion magnetic domains. Notably, the T-RMCD signal can maintain up to a temperature as high as the Curie temperature of Fe3GeTe2 flakes (â¼200 K). Our work provides a universal, contactless, and nondestructive approach for studying the physical properties of skyrmions in 2D vdW magnetic materials while adding another degree of freedom to the modulation of skyrmions.
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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.
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Here, we report a novel kind of protein nanoparticles of 11 nm in size, which have a central protein core surrounded by two layers of lipid. One layer of the lipid was covalently attached to the protein, while the other layer has been physically assembled around the protein core. Particle synthesis is highly modular, while both the size and charge of the protein nanoparticles are controlled in a predictable manner. Circular dichroism studies of the conjugate showed that the protein secondary structure is retained, while biophysical characterizations indicated the particle purity, size, and charge. The conjugate had a high thermal stability to steam sterilization conditions at 121°C (17 psi). After labeling the protein core with few different fluorescent dyes, they were strongly fluorescent with the corresponding colors independent of their size, unlike quantum dots. They are readily digested by proteases, and these water-soluble, non-toxic, highly stable, biocompatible, and biodegradable conjugates are suitable for cell imaging and drug delivery applications.
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Corantes Fluorescentes , Lipoproteínas , Nanopartículas , Nanopartículas/química , Corantes Fluorescentes/química , Lipoproteínas/química , Dicroísmo Circular , Tamanho da PartículaRESUMO
In the realm of parasitology, autophagy has emerged as a critical focal point, particularly in combating Leishmaniasis. Central to this endeavour is the recognition of the protein ATG8 as pivotal for the survival and infectivity of the parasitic organism Leishmania major, thereby making it a potential target for therapeutic intervention. Consequently, there is a pressing need to delve into the structural characteristics of ATG8 to facilitate the design of effective drugs. In this study, our efforts centered on the purification of ATG8 from Leishmania major, which enabled novel insights into its structural features through meticulous spectroscopic analysis. We aimed to comprehensively assess the stability and behaviour of ATG8 in the presence of various denaturants, including urea, guanidinium chloride, and SDS-based chemicals. Methodically, our approach included secondary structural analysis utilizing CD spectroscopy, which not only validated but also augmented computationally predicted structures of ATG8 reported in previous investigations. Remarkably, our findings unveiled that the purified ATG8 protein retained its folded conformation, exhibiting the anticipated secondary structure. Moreover, our exploration extended to the influence of lipids on ATG8 stability, yielding intriguing revelations. We uncovered a nuanced perspective suggesting that targeting both the lipid composition of Leishmania major and ATG8 could offer a promising strategy for future therapeutic approaches in combating leishmaniasis. Collectively, our study underscores the importance of understanding the structural intricacies of ATG8 in driving advancements towards the development of targeted therapies against Leishmaniasis, thereby providing a foundation for future investigations in this field.
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Protein conformation is affected by interaction of several small molecules resulting either stabilization or disruption depending on the nature of the molecules. In our earlier communication, Hg2+ was known to disrupt the native structure of α-Cgn A leading to aggregation (Ansari, N.K., Rais, A. & Naeem, A. Methotrexate for Drug Repurposing as an Anti-Aggregatory Agent to Mercuric Treated α-Chymotrypsinogen-A. Protein J (2024). https://doi.org/10.1007/s10930-024-10187-z ). Accumulation of ß-rich aggregates in the living system is found to be linked with copious number of disorders. Here, we have investigated the effect of varying concentration of doxorubicin (DOX) i.e. 0-100 µM on the preformed aggregates of α-Cgn A upon incubation with 120 µM Hg2+. The decrease in the intrinsic fluorescence and enzyme activity with respect to increase in the Hg2+ concentration substantiate the formation of aggregates. The DOX showed the dose dependent decrease in the ThT fluorescence, turbidity and RLS measurements endorsing the dissolution of aggregates which were consistent with red shift in ANS, confirming the breakdown of aggregates. The α-Cgn A has 30% α-helical content which decreases to 3% in presence of Hg2+. DOX increased the α-helicity to 28% confirming its anti-aggregatory potential. The SEM validates the formation of aggregates with Hg2+ and their dissolution upon incubation with the DOX. Hemolysis assay checked the cytotoxicity of α-Cgn A aggregates. Docking revealed that the DOX interacted Lys203, Cys201, Cys136, Ser159, Leu10, Trp207, Val137 and Thr134 of α-Cgn A through hydrophobic interactions and Gly133, Thr135 and Lys202 forms hydrogen bonds.
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Circular dichroism (CD) based enantiomeric excess (ee) determination assays are optical alternatives to chromatographic ee determination in high-throughput screening (HTS) applications. However, the implementation of these assays requires calibration experiments using enantioenriched materials. We present a data-driven approach that circumvents the need for chiral resolution and calibration experiments for an octahedral Fe(II) complex (1) used for the ee determination of α-chiral primary amines. By computationally parameterizing the imine ligands formed in the assay conditions, a model of the circular dichroism (CD) response of the Fe(II) assembly was developed. Using this model, calibration curves were generated for four analytes and compared to experimentally generated curves. In a single-blind ee determination study, the ee values of unknown samples were determined within 9% mean absolute error, which rivals the error using experimentally generated calibration curves.
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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.
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Dicroísmo Circular , Ácidos Nucleicos , Peptídeos , Peptídeos/química , Peptídeos/análise , Ácidos Nucleicos/análise , Ácidos Nucleicos/químicaRESUMO
Human telomeres (HTs) can form DNA G-quadruplex (G4), an attractive target for anticancer and antiviral drugs. HT-G4s exhibit inherent structural polymorphism, posing challenges for understanding their specific recognition by ligands. Here, we aim to explore the impact of different topologies within a small segment of the HT (Tel22) on its interaction with BRACO19, a rationally designed G4 ligand with high quadruplex affinity, already employed in in-vivo treatments. Our multi-technique approach is based on the combined use of a set of contactless spectroscopic tools. Circular dichroism and UV resonance Raman spectroscopy probe ligand-induced conformational changes in the G4 sequence, while UV-visible absorption, coupled with steady-state fluorescence spectroscopy, provides further insights into the electronic features of the complex, exploiting the photoresponsive properties of BRACO19. Overall, we find that modifying the topology of the unbound Tel22 through cations (K+ or Na+), serves as a critical determinant for ligand interactions and binding modes, thus influencing the HT-G4's assembly capabilities. Furthermore, we show how fluorescence serves as a valuable probe for recognizing cation-driven multimeric structures, which may be present in living organisms, giving rise to pathological forms.