Search Results (390)

Background/Objectives: Understanding the stabilization mechanisms of amino acid conformations in different solvent environments is crucial for elucidating biomolecular interactions and crystallization processes. This study presents a comprehensive computational investigation of glycine, the simplest amino acid, in both its canonical and zwitterionic forms when interacting with dimethyl sulfoxide (DMSO) molecules. Methods: Using density functional theory (DFT) calculations at the B3LYP/6-311++G(d,p) level with empirical dispersion corrections, we examined the conformational landscape of glycine–DMSO clusters with one and two DMSO molecules, as well as implicit solvent calculations, and compared them with analogous water clusters. Results: Our results demonstrate that while a single water molecule is insufficient to stabilize the zwitterionic form of glycine, one DMSO molecule successfully stabilizes this form through specific interactions between the S=O and the methyl groups of DMSO and the NH₃⁺ and the oxoanion group of zwitterionic glycine, respectively. Topological analysis of the electron density using QTAIM and NCI methods reveals the nature of these interactions. When comparing the relative stability between canonical and zwitterionic forms, we found that two DMSO molecules significantly reduce the energy gap to approximately 12 kJ mol⁻¹, suggesting that increasing DMSO coordination could potentially invert this stability. Implicit solvent calculations indicate that in pure DMSO medium, the zwitterionic form becomes more stable below 150 K, while remaining less stable at room temperature, contrasting with aqueous environments where the zwitterionic form predominates. Conclusions: These findings provide valuable insights into DMSO’s unique role in biomolecular stabilization and have implications for protein crystallization protocols where DMSO is commonly used as a co-solvent. Full article

Intrinsically disordered regions (IDRs), defined as protein segments lacking stable tertiary structures, are ubiquitously present in the human proteome and enriched with disease-associated mutations. IDRs harbor molecular recognition features (MoRFs) and post-translational modification sites (e.g., phosphorylation), enabling dynamic intermolecular interactions through conformational plasticity. Furthermore, IDRs drive liquid–liquid phase separation (LLPS) of biomacromolecules via multivalent interactions such as electrostatic attraction and pi–pi interactions, generating biomolecular condensates that are essential throughout the cellular lifecycle. These condensates separate intracellular space, forming a physical barrier to avoid interference between other molecules, thereby improving reaction specificity and efficiency. As a dynamically equilibrated process, LLPS formation and maintenance are regulated by multiple factors, endowing the condensates with rapid responsiveness to environmental cues and functional versatility in modulating diverse signaling cascades. Consequently, disruption of LLPS homeostasis can derail its associated biological processes, ultimately contributing to disease pathogenesis. Moreover, precisely because liquid–liquid phase separation (LLPS) is co-regulated by multiple factors, it may provide novel insights into the pathogenic mechanisms of disorders such as autism spectrum disorder (ASD), which result from the cumulative effects of multiple etiological factors. Full article

We report on the synthesis and characterization of a novel fluorenyl-methoxycarbonyl (Fmoc)-containing thioxo-triazole-bearing dipeptide 5, evaluated for potential therapeutic applications. The compound was tested for its antioxidant and antimicrobial properties, demonstrating significant effects in scavenging reactive oxygen species (ROS) and inhibiting microbial growth, particularly when combined with plant extracts from an endemic Peonia species from the Caucasus. Circular dichroism (CD) binding studies with bovine serum albumin (BSA) and calf thymus DNA revealed important interactions, suggesting the dipeptide’s potential in biomedically relevant conditions that involve DNA modulation. Molecular docking and CD spectra deconvolution provided additional insights into the binding mechanisms and structural characteristics of the formed complexes with the biomolecular targets. The Fmoc group enhances the dipeptide’s lipophilicity, which may facilitate its interaction with cellular membranes, supporting efficient drug delivery. A computational evaluation at the ωB97XD/aug-cc-pVDZ level of theory was carried out, confirming the experimental results and revealing a powerful potential of the peptide as an antioxidant, through FMOs, MEP analysis, and antioxidant mechanism assessments. Together, these findings suggest that this dipeptide could be valuable as an antimicrobial and antioxidant agent, with potential applications in pathologies involving oxidative stress, DNA modulation, and microbial infections. Full article

This article presents a comprehensive overview of recent advancements in photonic crystal fiber (PCF)-based sensors, with a particular focus on the surface plasmon resonance (SPR) phenomenon for biosensing. With their ability to modify core and cladding structures, PCFs offer exceptional control over light guidance, dispersion management, and light confinement, making them highly suitable for applications in refractive index (RI) sensing, biomedical imaging, and nonlinear optical phenomena such as fiber tapering and supercontinuum generation. SPR is a highly sensitive optical phenomenon, which is widely integrated with PCFs to enhance detection performance through strong plasmonic interactions at metal–dielectric interfaces. The combination of PCF and SPR technologies has led to the development of innovative sensor geometries, including D-shaped fibers, slotted-air-hole structures, and internal external metal coatings, each optimized for specific sensing goals. These PCF-SPR-based sensors have shown promising results in detecting biomolecular targets such as excess cholesterol, glucose, cancer cells, DNA, and proteins. Furthermore, this review provides an in-depth analysis of key design parameters, plasmonic materials, and sensor models used in PCF-SPR configurations, highlighting their comparative performance metrics and application prospects in medical diagnostics, environmental monitoring, and chemical analysis. Thus, an exhaustive analysis of various sensing parameters, plasmonic materials, and sensor models used in PCF-SPR sensors is presented and explored in this article. Full article

Arginine plays a critical role in biomolecular interactions due to its guanidinium side chain, which enables multivalent electrostatic and hydrogen bonding contacts. In this study, atomistic molecular dynamics simulations were conducted across a broad concentration range (26–605 mM) to investigate the thermodynamic and structural features of arginine self-assembly in aqueous solution. Key observables—including hydrogen bond count, radius of gyration, contact number, and isobaric heat capacity—were analyzed to characterize emergent behavior. A three-regime aggregation pattern (dilute, cooperative, and saturated) was identified and quantitatively modeled using the Hill equation, revealing a non-linear transition in clustering behavior. Spatial analyses were supplemented with trajectory-based clustering and radial distribution functions. The heat capacity peak observed near 360 mM was interpreted as a thermodynamic signature of hydration rearrangement. Trajectory analyses utilized both GROMACS tools and the MDAnalysis library. While force field limitations and single-replica sampling are acknowledged, the results offer mechanistic insight into how arginine concentration modulates molecular organization—informing the understanding of biomolecular condensates, protein–nucleic acid complexes, and the design of functional supramolecular systems. The findings are in strong agreement with experimental observations from small-angle X-ray scattering and differential scanning calorimetry. Overall, this work establishes a cohesive framework for understanding amino acid condensation and reveals arginine’s concentration-dependent behavior as a model for weak, reversible molecular association. Full article

The imidazo[4,5-b]pyridine scaffold, a versatile heterocyclic system, is renowned for its biological and chemical significance, yet its coordination chemistry with biologically relevant metal dications remains underexplored. This study investigates the proton and metal dication affinities of twelve tetracyclic organic molecules based on the imidazo[4,5-b]pyridine core, focusing on their interactions with Ca(II), Mg(II), Zn(II), and Cu(II). Employing a dual approach of electrospray ionization mass spectrometry (ESI-MS) and density functional theory (DFT) calculations, we characterized the formation, stability, and structural features of metal–ligand complexes. ESI-MS revealed distinct binding behaviors, with Cu(II) and Zn(II) forming stable mono- and dinuclear complexes, often accompanied by reduction processes (e.g., Cu(II) to Cu(I)), while Ca(II) and Mg(II) exhibited lower affinities. DFT analysis elucidated the electronic structures and thermodynamic stabilities, highlighting the imidazole nitrogen as the primary binding site and the influence of regioisomeric variations on affinity. Substituent effects were found to modulate binding strength, with electron-donating groups enhancing basicity and metal coordination. These findings provide a comprehensive understanding of the coordination chemistry of imidazo[4,5-b]pyridine derivatives, offering insights into their potential applications in metalloenzyme modulation, metal-ion sensing, and therapeutic chelation. Full article

The integration of two-dimensional graphene with gold nanostructures has significantly advanced surface plasmon resonance (SPR)-based optical biosensors, due to graphene’s exceptional optical, electronic, and surface properties. This review examines recent developments in graphene-based hybrid nanomaterials designed to enhance SPR sensor performance. The synergistic combination of graphene and other functional materials enables superior plasmonic sensitivity, improves biomolecular interaction, and enhances signal transduction. Key focus areas include the fundamental principle of graphene-enhanced SPR, the functional advantages of graphene hybrid platforms, and their recent applications in detecting biomolecules, disease biomarkers, and pathogens. Finally, current limitations and potential future perspectives are discussed, highlighting the transformative potential of these hybrid nanomaterials in next-generation optical biosensing Full article

Accurate detection of biomolecular interactions is essential in many areas, from the detection of the presence of biomarkers in the clinic to the development of therapeutic drugs and biologics in biopharma to the understanding of various biological processes in basic research. Traditional endpoint approaches can suffer from false-negative results for biomolecular interactions with fast kinetics. By contrast, real-time detection techniques like surface plasmon resonance (SPR) monitor interactions as they form and disassemble, reducing the risk of false-negative results. By leveraging cell-free expressed proteins captured on either glass or SPR biosensors and using two different commercial antibodies with variable off-rates that both target HaloTag antigens as a model, we compare and contrast results from a fluorescence endpoint assay versus real-time sensor-integrated proteome on chip (SPOC^®) SPR-based detection. In this study, we illustrate the limitations of the representative immunofluorescent endpoint assay when investigating transient interactions characterized by fast dissociation rates. We highlight the importance of choosing reagents well suited to the selected assay, as well as the importance of considering binding kinetics and protein ligand conformational states when interpreting results from binding assays, especially for applications as critical as the off-target screening of therapeutics. Full article

Surface plasmon resonance (SPR) is a powerful tool for analyzing biomolecular interactions and is widely used in basic biomedical research and drug discovery. Heparan sulfate (HS) is a linear complex polysaccharide and a key component of the extracellular matrix and cell surfaces. HS plays a pivotal role in maintaining cellular functions and tissue homeostasis by interacting with numerous proteins, making it essential for normal physiological processes and disease states. Deciphering the interactome of HS unlocks the mechanisms underlying its biological functions and the potential for novel HS-related therapeutics. This review presents an overview of the recent advances in the application of SPR technology to HS interactome research. We discuss methodological developments, emerging trends, and key findings that illustrate how SPR is expanding our knowledge of HS-mediated molecular interactions. Additionally, we highlight the potential of SPR-based approaches in identifying novel therapeutic targets and developing HS-mimetic drugs, thereby opening new avenues for intervention in HS-related diseases. Full article

PDE11A is a little-studied phosphodiesterase sub-family that breaks down cAMP/cGMP, with the PDE11A4 isoform enriched in the memory-related hippocampal formation. Age-related increases in PDE11A expression occur in human and rodent hippocampus and cause age-related cognitive decline of social memories. Interestingly, age-related increases in PDE11A4 protein ectopically accumulate in spherical clusters that group together in the brain to form linear filamentous patterns termed “PDE11A4 ghost axons”. The biophysical/physiochemical mechanisms underlying this age-related clustering are not known. Here, we determine if age-related clustering of PDE11A4 reflects liquid–liquid phase separation (LLPS; biomolecular condensation), and if PDE11A inhibitors can reverse this LLPS. We show human and mouse PDE11A4 exhibit several LLPS-promoting sequence features, including intrinsically disordered regions, non-covalent pi–pi interactions, and prion-like domains that were particularly enriched in the N-terminal regulatory region. Further, multiple bioinformatic tools predict PDE11A4 undergoes LLPS. Consistent with these predictions, aging-like PDE11A4 clusters in HT22 hippocampal neuronal cells were membraneless spherical droplets that progressively fuse over time in a concentration-dependent manner. Deletion of the N-terminal intrinsically disordered region prevented PDE11A4 LLPS despite equal protein expression between WT and mutant constructs. 1,6-hexanediol, along with tadalafil and BC11-38 that inhibit PDE11A4, reversed PDE11A4 LLPS in HT22 hippocampal neuronal cells. Interestingly, PDE11A4 inhibitors reverse PDE11A4 LLPS independently of increasing cAMP/cGMP levels via catalytic inhibition. Importantly, orally dosed tadalafil reduced PDE11A4 ghost axons in old mouse ventral hippocampus by 50%. Thus, PDE11A4 exhibits the four defining criteria of LLPS, and PDE11A inhibitors reverse this age-related phenotype both in vitro and in vivo. Full article

The continued effective control of retroviral infections will no doubt require the development of new clinical interventions targeting underexploited areas of retroviral biology such as genome selection and virion assembly. In our previous work, we demonstrated that both the Gag-psi (Ψ) interaction and genomic RNA (gRNA) dimerization each uniquely contribute to the formation, morphology, and stability of Rous sarcoma virus (RSV) Gag-viral RNA (vRNA) biomolecular condensates (BMCs). The present work builds upon those observations, utilizing atomic force microscopy (AFM) and fluorescence correlation spectroscopy (FCS) to elucidate the nanoscale morphology, resistance to mechanical deformation, and constituent diffusivity of RSV Gag-vRNA BMCs. These approaches revealed a novel role for gRNA dimerization in nanoscale condensate architecture and mechanical stability that aids in our understanding of why gRNA dimerization is critical for efficient packaging of the retroviral genome. Further biophysical characterization of RSV Gag-gRNA BMCs therefore possesses great potential to reveal novel avenues for therapeutic intervention. Full article

Backgroud: Glutamate dehydrogenase (GDH) is involved in the metabolism of glutamate and ammonia. It is regulated by multiple ligand variants, and hyper-active GDH mutants have been reported for hyperinsulinism hyperammonemia syndrome (HHS). Methods: Here, we constructed the wild-type human GDH and three human GDH454 mutants and investigated their degradation activity and performance under different GDH inhibitors. Results: Protein activity test and SDS-PAGE analysis of the purified proteins showed that the GDH454 mutant from HHS has weaker GDH enzymatic activity but greater resistance to trypsin hydrolysis than the wild type. Interestingly, using the biomolecular interactions technique, it showed that the GDH454 mutant has 10⁹ times weaker affinity for trypsin and 10-fold weaker for epigallocatechin gallate (EGCG) than the wild-type GDH. Subsequently, native-PAGE gel analysis demonstrated that EGCG could break down the GDH hexamer into monomers and form a complex with trypsin to enhance the degradation of both types of GDH. Conclusions: EGCG showed good affinity to both the wild-type and the mutant GDH proteins, promoting protein degradation; this provides a new strategy for the treatment of HHS and other hyper-active GDH-related diseases. Full article

Breast cancer (BC) frequently metastasizes to bone, leading to poor patient prognosis. The infiltration of cancer cells in bone impairs its homeostasis, triggering a pathological interaction between tumors and resident cells. Preclinical models able to mimic the bone microenvironment are needed to advance translational findings on BC mechanisms and treatments. We designed strontium-doped calcium phosphate cement to be employed for culturing cancer and bone cells and developed an in vitro bone metastasis model. The platform was established step by step, starting with the monoculture of cancer cells, mature osteoblasts (OBs) differentiated from mesenchymal stem cells, and mature osteoclasts (OCs) differentiated from Peripheral Blood Mononuclear Cells. The model was implemented with the co-culture of cancer cells with OBs or OCs, or the co-culture of OBs and OCs, allowing us to discriminate the interaction between the actors of the bone metastatic niche. The biomimetic material was further challenged with bone metastasis patient-derived material, showing good versatility and biocompatibility, suggesting its potential use as bone substitute. Overall, we developed a bone-mimicking model able to reproduce reciprocal interactions between cancer and bone cells in a biomimetic environment suitable for studying the biomolecular determinants of bone metastasis and, in the future, as a drug efficacy platform. Full article

SPR biosensors operate on the principle of evanescent wave propagation at metal–dielectric interfaces in total internal reflection conditions, with consequent photonic energy attenuation. This plasmonic excitation occurs in specific conditions of incident light wavelength, angle, and the dielectric refractive index. This principle has been the basis for SPR-based biosensor setups wherein mass/concentration-induced changes in the refractive indices of dielectric media reflect as plasmonic resonance condition changes quantitatively reported as arbitrary response units. SPR biosensors operating on this conceptual framework have been designed to study biomolecular interactions with real-time readout and in label-free setups, providing key kinetic characterization that has been valuable in various applications. SPR biosensors often feature antibodies as target affinity probes. Notably, the operational challenges encountered with antibodies have led to the development of aptamers—oligonucleotide biomolecules rationally designed to adopt tertiary structures, enabling high affinity and specific binding to a wide range of targets. Aptamers have been extensively adopted in SPR biosensor setups with promising clinical and industrial prospects. In this paper, we explore the growing literature on SPR setups featuring aptamers, specifically providing expert commentary on the current state and future implications of these SPR aptasensors for drug discovery as well as disease diagnosis and monitoring. Full article

The coordination chemistry, structural characterization, and biomolecular interactions of europium(III) and iron(III) complexes with the pyridoxal-semicarbazone (PLSC) ligand were thoroughly examined using experimental and computational approaches. Single-crystal X-ray diffraction revealed that the europium complex exhibits a nine-coordinate geometry with one protonated and one deprotonated PLSC ligand and nitrato and aqua ligands. In contrast, the iron complex adopts a six-coordinate structure featuring a monoprotonated PLSC, two chlorido, and an aqua ligand. Hirshfeld surface analysis confirmed the significance of intermolecular contacts in stabilizing the crystal lattice. Theoretical geometry optimizations using DFT methods demonstrated excellent agreement with experimental bond lengths and angles, thereby validating the reliability of the chosen computational levels for subsequent quantum chemical analyses. Quantum Theory of Atoms in Molecules (QTAIM) analysis was employed to investigate the nature of metal–ligand interactions, with variations based on the identity of the donor atom and the ligand’s protonation state. The biological potential of the complexes was evaluated through spectrofluorimetric titration and molecular docking. Eu-PLSC displayed stronger binding to human serum albumin (HSA), while Fe-PLSC showed higher affinity for calf thymus DNA (CT-DNA), driven by intercalation. Thermodynamic data confirmed spontaneous and enthalpy-driven interactions. These findings support using PLSC-based metal complexes as promising candidates for future biomedical applications, particularly in drug delivery and DNA targeting. Full article