Search Results (414)

Rhodopsin, the prototypical Class A G protein-coupled receptor (GPCR) and visual pigment of rod photoreceptors, has long served as a structural and mechanistic model for GPCR biology. Mutations in rhodopsin are the leading cause of autosomal dominant retinitis pigmentosa (adRP), making this receptor a critical therapeutic target. In this review, we summarize the chemical, structural, and biophysical features of small-molecule modulators of this receptor, spanning both classical retinoid analogs and emerging non-retinoid scaffolds. These ligands reveal recurrent binding modes within the orthosteric chromophore pocket as well as peripheral allosteric and bitopic sites, where they mediate folding, rescue trafficking, photocycle modulation, and mutant stabilization. We organize ligand performance into a three-tier framework linking binding affinity, cellular rescue potency, and stability gains. Chemotypes in tier 2, which show sub-micromolar to low-micromolar activity with broad mutant coverage, emerge as promising candidates for optimization into next-generation scaffolds. Across scaffolds, a recurring minimal pharmacophore is evident by a contiguous hydrophobic π-surface anchored in the β-ionone region, coupled with a strategically oriented polar handle that modulates the Lys296/Glu113 microenvironment, offering tractable design vectors for non-retinoid chemotypes. Beyond the chromophore binding pocket, we highlight opportunities to exploit extracellular loop epitopes, cytoplasmic microswitch clefts, dimer/membrane interfaces, and ion co-binding sites to engineer safer, state-biased control with fewer photochemical liabilities. By integrating rhodopsin photobiophysics with environment-aware, multi-state medicinal chemistry, and by addressing current translational challenges in drug delivery, this review outlines a rational framework for advancing rhodopsin-targeted therapeutics toward clinically credible interventions for RP and related retinal degenerations. Full article

Soil CO₂ emissions, driven primarily by microbial respiration, represent a major component of terrestrial carbon flux and play a crucial role in global climate change. Although several soil physicochemical factors regulating microbial activity are well known, the role of soil solution viscosity remains largely unexplored. This study evaluated how polyethylene glycol (PEG6000)-induced increases in soil solution viscosity affect microbial activity-derived CO₂ emissions in a Rhodic Ferralsol (eutric). Three concentrations of PEG6000 (50, 75, and 100 g L⁻¹), corresponding to viscosities of 1.93, 2.76, and 3.88 cP, respectively, were compared to a water-based control (1.11 cP). Soil CO₂ emissions, soil O₂ capture, temperature, and water content were measured over a 60-day period using standard methods. Results showed significant reductions in cumulative CO₂ emissions of 20%, 25%, and 12% for PEG6000 treatments, respectively, compared to the control. Decreased O₂ capture at viscosities of 1.93 and 2.76 cP (50 and 75 g L⁻¹, respectively) indicated reduced microbial activity. These findings reveal a previously underappreciated biophysical mechanism regulating soil carbon emissions. Understanding and managing soil solution viscosity could offer a novel strategy to mitigate CO₂ emissions in tropical soils, thus contributing to climate change mitigation and sustainable soil management, particularly in highly weathered tropical ecosystems. Full article

Nitrogen in all of its forms sustains Earth. In every known terrestrial and aquatic habitat, nitrogen controls microbial activity, plant productivity, trophic dynamics, and animal and human growth. This review has tried to show how nitrogen cycling is influenced by both terrestrial and marine ecosystems in addition to by changes spurred on by the climate. The availability, transformation, and final fate of nitrogen throughout the various ecosystems are influenced by these interconnected biochemical and biophysical processes, which are fueled by microbial communities. Predicting and reducing human impacts on the changing ecosystem requires an understanding of these complex interconnections. Anthropogenic and climatic changes alter the structure and function of soil microbial communities, as well as the main metabolic processes of the nitrogen cycle, such as nitrification, denitrification, nitrogen fixation, and ammonification. The mechanisms by which anthropogenic stress alters nitrogen cycling processes, the effects on ecosystem function, and possible mitigation techniques for a balanced nitrogen cycle are all discussed in this review. Full article

Enteroviruses initiate genomic replication via a highly conserved mechanism that is controlled by an RNA platform, also known as the 5’ cloverleaf (5’CL). Here, we present a biophysical analysis of the 5’CL conformation of three enterovirus serotypes under various ionic conditions, utilizing CD spectroscopy, size-exclusion chromatography, and small-angle X-ray scattering. In general, a tendency toward a smaller monomeric hydrodynamic radius in the presence of salts was observed, but the exact structural signature of each 5’CL varied depending upon the serotype. Rhinovirus B14 (RVB14) exhibited at least two monomeric conformations and a low propensity for dimerization, while poliovirus 1 (PV1) showed a high propensity for dimerization, which was enhanced by the presence of salts. Enterovirus D70 was observed to be somewhat intermediate, with primarily a monomeric structure, but possessing some potential for dimerization. The equilibrium between the two monomeric and the dimeric conformations is also discussed. These results indicate that the 5’CL conformation may be more complex than the current literature suggests, thus underscoring the need for a combined crystal and solution approach for the accurate representation of the 5’CL conformation, and the conformation of other RNA structural elements, under native conditions. Full article

The growing demand for natural and sustainable skincare products has driven interest in plant-based active ingredients, especially from in vitro cultures. This placebo-controlled study investigated the impact of a facial cream containing 2% Kickxia elatine (L.) Dumort cell suspension culture extract on various skin biophysical parameters. The cream was applied to the cheek once daily for six weeks on 40 healthy female volunteers between the ages of 40 to 49. The evaluated skin parameters including skin hydration, transepidermal water loss (TEWL), erythema intensity (EI), melanin intensity (MI), skin surface pH, and skin structure, wrinkle depth, vascular lesions, and vascular discolouration. The results indicated that significant improvements were observed in skin hydration (from 40.36 to 63.00 AU, p < 0.001) and there was a decrease in TEWL score (14.82 to 11.76 g/h/m², p < 0.001), while the skin surface pH was maintained (14.82 to 11.76 g/h/m², p < 0.001). Moreover, the K. elatine cell extract significantly improved skin structure values (9.23 to 8.50, p = 0.028), reduced vascular lesions (2.72 to 1.54 mm², p = 0.011), and lowered skin discolouration (20.98% to 14.84%, p < 0.001), indicating its moisturising, protective, brightening, and soothing properties. These findings support the potential use of K. elatine cell extract in dermocosmetic formulations targeting dry, sensitive, or ageing skin. Full article

Nucleocytoplasmic trafficking is a highly regulated process that allows the cell to control the partitioning of proteins and nucleic acids between the cytosolic and nuclear compartments. The Ebola virus minor matrix protein VP24 (eVP24) hijacks this process by binding to a region on the NPI-1 subfamily of karyopherin alpha (KPNA) nuclear importers. This region overlaps with the activated transcription factor STAT1 binding site on KPNAs, preventing STAT1 nuclear localization and activation of antiviral gene transcription. However, the molecular interactions of eVP24-KPNA5 binding that lead to the nuclear localization of eVP24 remain poorly characterized. Here, we show that trafficking of eVP24 into the nucleus by KPNA5 requires simultaneous binding of cargo. We also describe the conformational dynamics of KPNA5 and interactions with eVP24 and cargo nuclear localization sequences (NLS) using biophysical approaches. Our results reveal that eVP24 binding to KPNA5 does not impact cargo NLS binding to KPNA5, indicating that simultaneous binding of both cellular cargo and eVP24 to KPNA5 is likely required for nuclear trafficking. Together, these results provide a biophysical basis for how Ebola virus VP24 protein gains access to the nucleus during Ebola virus infection. Full article

Protein association and aggregation are fundamental processes that play critical roles in a variety of biological phenomena from cell signaling to the development of incurable diseases, including amyloidoses. Understanding the basic biophysical principles governing protein aggregation processes is of crucial importance for developing treatment strategies for diseases associated with protein aggregation, including sarcopenia, as well as for the treatment of pathological processes associated with the disruption of functional protein complexes. This work, using a set of methods such as atomic force microscopy (AFM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction, as well as bioinformatics analysis, investigated the structures of complexes formed by titin and myosin-binding protein C (MyBP-C). TEM revealed the formation of morphologically ordered aggregates in the form of beads during co-incubation of titin and MyBP-C under close-to-physiological conditions (175 mM KCl, pH 7.0). AFM showed the formation of a relatively homogeneous film with local areas of relief change. Fluorimetry with thioflavin T, as well as FTIR spectroscopy, revealed signs of an amyloid-like structure, including a signal in the cross-β region. X-ray diffraction showed the presence of a cross-β structure characteristic of amyloid aggregates. Such structural features were not observed in the control samples of the investigated proteins separately. In sarcomeres, these proteins are associated with each other, and this interaction plays a partial role in the formation of a strong sarcomeric cytoskeleton. We found that under physiological ionic-strength conditions titin and MyBP-C form complexes in which an amyloid-like structure is present. The possible functional significance of amyloid-like aggregation of these proteins in muscle cells in vivo is discussed. Full article

Despite significant advances in understanding neuronal development, a fully quantitative framework that integrates intracellular mechanisms with environmental cues during axonal growth remains incomplete. Here, we present a unified biophysical model that captures key mechanochemical processes governing axonal extension on micropatterned substrates. In these environments, axons preferentially align with the pattern direction, form bundles, and advance at constant speed. The model integrates four core components: (i) actin–adhesion traction coupling, (ii) lateral inhibition between neighboring axons, (iii) tubulin transport from soma to growth cone, and (iv) orientation dynamics guided by substrate anisotropy. Dynamical systems analysis reveals that a saddle–node bifurcation in the actin adhesion subsystem drives a transition to a high-traction motile state, while traction feedback shifts a pitchfork bifurcation in the signaling loop, promoting symmetry breaking and robust alignment. An exact linear solution in the tubulin transport subsystem functions as a built-in speed regulator, ensuring stable elongation rates. Simulations using experimentally inferred parameters accurately reproduce elongation speed, alignment variance, and bundle spacing. The model provides explicit design rules for enhancing axonal alignment through modulation of substrate stiffness and adhesion dynamics. By identifying key control parameters, this work enables rational design of biomaterials for neural repair and engineered tissue systems. Full article

Background/Objectives: Recently, shear wave elastography (SWE) and dispersion (SWD) targeting the pancreas have been attempted as noninvasive procedures to evaluate personalized conditions. This study aimed to analyze the feasibility of utilizing them for evaluating the individual need of introducing insulin therapy, combined with the C-peptide index (CPI), in patients with type 2 diabetes mellitus (T2DM). Methods: This study involved 51 patients with T2DM aged ≥20 years old and 20 control subjects without impaired glucose tolerance (CTRL). T2DM were divided into non-insulin-treated (non-INS) and insulin-treated (INS) groups. Their background data, shear wave speed (SWS), and dispersion slope (DS) of the pancreas were obtained on the same day. Results: Pancreatic SWS was higher in T2DM than in CTRL (p < 0.0001), with an AUC of 0.840, sensitivity of 89.1%, and specificity of 70.6%, using a Youden index cutoff of 1.31 m/s. INS and non-INS were discriminated with the cutoff value of 1.70 m/s (p = 0.031, AUC 0.736, sensitivity 55.6% and specificity 89.2%). Pancreatic DS of INS and non-INS was 13.52 and 12.16 (m/s)/kHz, respectively (p = 0.046). Using 12.38 (m/s)/kHz as the cutoff, AUC was 0.718, with sensitivity of 88.9%, specificity of 56.8% and negative predictive value of 95.5%. CPI had AUC of 0.724, sensitivity of 66.7% and specificity of 83.3% with the cutoff of 0.63. With combination of SWS and CPI, all patients with SWS < 1.70 m/s and CPI > 0.476 belonged to non-INS. Conclusions: Simultaneous non-invasive SWE and CPI evaluation showed the feasibility for estimating personalized insulin initiation needs in T2DM, integrating biophysical and hormonal perspectives. Further investigation with a larger, multi-center study population is warranted to enhance the level of evidence. Full article

The deformability of cells reflects their capacity for shape changes under external forces; however, the systematic investigation of deformation-influencing factors remains conspicuously underdeveloped. In this work, by using an incompressible neo-Hookean viscoelastic solid model, coupled with the Kelvin–Voigt model, the effects of flow rate, fluid viscosity, cell diameter, and shear modulus on cell deformability were systematically calculated and simulated. Additionally, the relationship between cell deformability and relaxation time within a dissipative process was also simulated. The results indicate that cell deformation is positively correlated with flow rate, with an approximate linear relationship between the deformation index and flow velocity. Fluid viscosity also significantly affects cell deformation, as an approximate linear relationship with the deformation index is observed. Cell diameter has a more prominent impact on cell deformability than do flow rate or fluid viscosity, with the deformation index increasing more rapidly than the cell diameter. As the Young’s modulus increases, cell deformation decreases non-linearly. Cell deformation in the channel also gradually decreases with the increase in relaxation time. These findings enhance the understanding of cell biophysical characteristics and provide a basis for the precise control of cell deformation in deformability cytometry. This research holds significant implications for cell analysis-based animal health monitoring in the field of agriculture, as well as for other related areas. 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

Introduction: Intermittent claudication, an early symptom of peripheral artery disease, can be treated by cilostazol to alleviate symptoms and improve walking distance. Our previous investigation focused on cilostazol-induced alterations in the thermodynamic properties of plasma, utilizing differential scanning calorimetry (DSC) as a potential monitoring tool. The current proof-of-concept study aimed to enhance the interpretation of DSC data through deconvolution techniques, specifically examining protein transitions within the plasma proteome during cilostazol therapy. Results: Notable differences in thermal unfolding profiles were found between cilostazol-treated patients and healthy controls. The fibrinogen-associated transition exhibited a downward shift in denaturation temperature and decreased enthalpy by the third month. The albumin-related transition shifted to higher temperatures, accompanied by lower enthalpy. Transitions associated with globulins showed changes in thermal stability, while the transferrin-related peak demonstrated increased structural rigidity in treated patients compared to controls. Discussion: These observations suggest that cilostazol induces systemic changes in the thermodynamic behavior of plasma proteins. DSC, when combined with deconvolution methods, presents a promising approach for detecting subtle, therapy-related alterations in plasma protein stability. Materials and methods: Ten patients (median age: 58.6 years) received 100 milligrams of cilostazol twice daily. Blood samples were collected at the baseline and after 2 weeks, 1 month, 2 months, and 3 months of therapy. Walking distances were also assessed. The DSC curves were retrieved from the thermal analysis investigated by deconvolution mathematical methods. Conclusions: Although the exact functional consequences remain unclear, the observed biophysical changes may reflect broader molecular adaptations involving protein–protein interactions, post-translational modifications, or acute phase response elements. Full article

Cholesterol plays an essential role in biological membranes and is crucial for maintaining their stability and functionality. In addition to biological membranes, cholesterol is also used in various synthetic lipid-based structures such as liposomes, proteoliposomes, and nanodiscs. Cholesterol regulates membrane properties by influencing the density of lipids, phase separation into liquid-ordered (Lo) and liquid-disordered (Ld) areas, and stability of protein–membrane interactions. For planar bilayers, cholesterol thickens the membrane, decreases permeability, and brings lipids into well-ordered domains, thereby increasing membrane rigidity by condensing lipid packing, while maintaining lateral lipid mobility in disordered regions to preserve overall membrane fluidity. It modulates membrane curvature in curved bilayers and vesicles, and stabilizes low-curvature regions, which are important for structural integrity. In liposomes, cholesterol facilitates drug encapsulation and release by controlling bilayer flexibility and stability. In nanodiscs, cholesterol enhances structural integrity and protein compatibility, which enables the investigation of protein–lipid interactions under physiological conditions. In proteoliposomes, cholesterol regulates the conformational stability of embedded proteins that have implications for protein–lipid interaction. Developments in molecular dynamics (MD) techniques, from coarse-grained to all-atom simulations, have shown how cholesterol modulates lipid tail ordering, membrane curvature, and flip-flop behavior in response to concentration. Such simulations provide insights into the mechanisms underlying membrane-associated diseases, aiding in the design of efficient drug delivery systems. In this review, we combine results from MD simulations to provide a synoptic explanation of cholesterol’s complex function in regulating membrane behavior. This synthesis combines fundamental biophysical information with practical membrane engineering, underscoring cholesterol’s important role in membrane structure, dynamics, and performance, and paving the way for rational design of stable and functional lipid-based systems to be used in medicine. In this review, we gather evidence from MD simulations to provide an overview of cholesterol’s complex function regulating membrane behavior. This synthesis connects the fundamental biophysical science with practical membrane engineering, which highlights cholesterol’s important role in membrane structure, dynamics, and function and helps us rationally design stable and functional lipid-based systems for therapeutic purposes. Full article

A platform of two-component cross-linked hydrogel (cGEL) based on gelatinous peptides and anhydride-containing cross-linkers (oPNMA, oPDMA) is extended for use in peripheral nerve regeneration. Hybrid composites with bio-/chemical cues for enhanced biophysical and biochemical properties were fabricated by covalently grafting small molecular, heterobifunctional amines including the nerve growth factor mimetic LM11A-31 to the oligomeric cross-linkers prior to hydrogel formation. The cytocompatibility and growth-supportive conditions within the matrix are confirmed for pristine and modified hydrogels using L929 mouse fibroblasts and human adipose-derived stem cells (hASCs). For hASCs, cell behavior depends on the type of cross-linker and integrated amine. In a subsequent step, neonatal rat Schwann cells (SCs) are seeded on pristine and functionalized cGEL to investigate the materials’ capabilities to support SC growth and morphology. Within all formulations, cell viability, adherence, and cell extension are maintained though the cell elongation and orientation vary compared to the two-dimensional control. It is possible to merge adjustable two-component hydrogels with amines as biochemical signals, leading to improved nervous cell proliferation and activity. This indicates the potential of tunable bioactive cGEL as biomaterials in nerve implants, suggesting their use as a foundational component for nerve conduits. Full article

Upon engagement of one of the nineteen secreted Wnt signaling proteins with one of the ten Frizzled transmembrane Wnt receptors (FZD_1–10), a wide variety of cellular Wnt signaling responses can be elicited, the selectivity of which depends on the following: (1) the specific Wnt-FZD pairing, (2) the participation of Wnt co-receptors and (3) the cellular context. Co-receptors play a pivotal role in guiding the specificity of Wnt signaling, most notably between β-catenin-dependent and -independent pathways, where co-receptors such as LRP5/6 and ROR1/2/PTK7 play major roles, respectively. It remains less understood how specific Wnt/FZD combinations contribute to the selectivity of downstream Wnt signaling, and we lack accurate comparative data on their binding properties under physiological conditions. Here, using fluorescently tagged Wnt3a, Wnt5a and Wnt16 proteins and cell lines expressing HiBiT-tagged Frizzled, we build on our ongoing efforts to provide a complete overview of the biophysical properties of all Wnt/FZD interactions using full-length proteins. Our real-time NanoBRET analysis using living cells expressing low receptor levels provides more accurate quantification of binding and will help us understand how these binary engagements control Wnt signaling outputs. We also provide evidence that LRP6 regulates the binding affinity of Wnt/FZD interactions in the trimeric Wnt-FZD-LRP6 complex. Full article