Biophysical Chemistry

Imipramine is known as an older generation tricyclic antidepressant drug. It has been identified in prior studies that imipramine blocks Apolipoprotein E4 (ApoE4)-induced amyloid-{beta}(A{beta}) aggregation and is associated with an improved AD diagnosis [Johnson et al. Alzheimers Research Therapy, 2022, 14, 88]. Using NMR methods such as 1H-1H NOESY and Saturation Transfer Difference Spectroscopy, we demonstrate the binding of A{beta} monomers to imipramine when the full-length A{beta} (1-42) sequence is considered. The more abundant but less toxic form, A{beta} (1-40) does not show interaction with imipramine.

This paper presents and critically reviews the results of original and some literature based experimental studies conducted by the authors last years on the structural organization of DNA in dormant (starvation stress), anabiotic dormant (4 HR treatment) E. coli cells, as well as the K12 {Delta}dps strain, which lacks the Dps protein (Dps null E. coli). The experimental data includes small-angle synchrotron radiation diffraction (SAXS) and transmission electron microscopy (TEM) data. Synchrotron radiation diffraction experiments on K12{Delta}dps cells allowed us to conclude that peaks at 44.3, 22.1, and 14.8 angstrom resolutions are associated exclusively with ordered DNA organization. Peaks at 44.3, 22.1, and 14.8 angstrom resolutions are also observed for samples of dormant (starvation stress) cells and anabiotically dormant cells. Therefore, this ordered DNA organization also applies to samples of dormant and anabiotically dormant cells. A model is proposed that considers the ordered DNA organization in the cell as a cholesteric liquid crystal. The powder diffraction pattern calculated based on this model is compared with experimental small angle X ray scattering (SAXS) data obtained on Dps-null cell samples. The model completely reproduces the key features of the experimental diffraction pattern from Dps-null cell samples. Accordingly, the cholesteric liquid crystal model corresponds to DNA packaging in dormant and anabiotically dormant cells. Cholesteric liquid crystal ordering should be further considered in all models of cellular DNA packaging. To address the question of which structural organization of DNA predominates in the cell: the cholesteric liquid crystal or nanocrystalline or whether they coexist and fully manifest themselves under different external conditions, it is necessary to utilize the latest methodological advances in structural analysis.

Neutron scattering is a powerful technique to investigate atomic structures and molecular dynamics of proteins at the nano-scale. When it comes to dynamics, incoherent and coherent scattering respectively provide information on the single and collective dynamics of nuclei. In proteins, hydrogen has the highest incoherent cross-section, and it is common practice to overlook the contribution of coherent terms stemming from all nuclei. However, the fast collective dynamics of heavier nuclei could also be studied if coherent scattering and incoherent scattering were experimentally separated. The recent advent of polarized neutron spectroscopy with sufficient flux and energy resolution has made it possible, and opens new perspectives to investigate the relative importance of coherent scattering and the information it provides on biological samples. The present study reports on the use of polarized quasi-elastic neutron scattering (QENS) and the application of a minimalistic model adapted to both individual and collective dynamics. Using a perdeuterated green fluorescent protein as a model globular protein, the study provides an interpretation of the dynamical parameters obtained with QENS, and a comparative study of the Elastic Coherent and Incoherent Scattering Factor. Based on both experiments and calculations, we discuss the relative importance of distinct and self components of coherent scattering, which is often wrongly assumed to be representative of collective dynamics only. The results highlight the current impediments rendering complicated a straightforward analysis of fast collective dynamics in hydrated protein samples.

Eukaryotic translation initiation is tightly regulated by interactions among translation initiation factors (eIFs) that ensure accurate start codon selection. The translation regulator, eIF5 mimic protein 1 (5MP1) contributes to this process by competing with eIF5 for binding to eIF2, thereby increasing the stringency of translation initiation. Despite its important regulatory role and emerging involvement in tumorigenesis, structural information on human 5MP1 remains limited. Here, we report the near-complete backbone and partial side-chain NMR resonance assignments of the C-terminal domain of human 5MP1 (residues 250-419), carrying a W404E substitution that disrupts dimerization. The WT protein forms a dimer at NMR concentrations, which increases the effective size of the protein and also causes disappearance of peaks corresponding to aminoacids at the dimer interface due to conformational exchange. Backbone resonance assignments were completed for 96.4% of the non-proline residues. Secondary structure was analyzed using Chemical Shift Index (CSI) and compared with the AlphaFold structural model. Regions of disagreement between the experimental and computational secondary structure assignments were further examined using 15N-NOESY-HSQC spectra, allowing experimental validation of local structural features. While the AlphaFold model accurately reproduces the overall fold of the 5MP1 C-terminal domain, several localized discrepancies were identified, particularly near the N- and C-terminal regions of the domain, where experimental NMR data support alternative secondary structure assignments. These resonance assignments and experimentally validated structural features provide a foundation for future investigations of the molecular interactions, dynamics, and functions of 5MP1 in translation initiation.

We present the solution structures of HIV-1 proteins NC(p7)1-55 corresponding to the full-length NC(p7) and mature p6. The studies were carried in water and, to mimic the membrane, in micellar DPC (Dodecylphosphocholine) conditions. Our results unravel for the first time the structure adopted by the N-terminal amino acids of the free NC(p7)1-55, with the formation of a small helix spanning residues F6 to R10. Our NMR and Fluorescence Anisotropy data disclose an interaction between NC(p7)1-55 and p6 both in water and DPC, with respective Kd of 2.5mM and 370 mM at 23{degrees}C. The interaction is thus strengthened in lipidic conditions. Protein p6 stabilizes the N-terminus of NC(p7)1-55 while increasing at the same time the dynamic of the first zinc finger. Although the entire p6 sequence is involved in the interaction, we show that its C-terminal region is particularly sensitive to the presence of NC(p7)1-55, with a propensity of forming a a helix ranging from amino acids S111 to F116. This study brings experimental evidence of a direct protein-protein interaction between p6 and the N-terminal region of NC(p7)1-55. We further show that such interaction is readily accommodated within the NC(p15) framework and hypothesize that it may facilitate the selective assembly of assembly of the viral genomic RNA (gRNA) in the cell.

Nanodiscs and bicelles are widely used as membrane mimetics for structural studies of membrane-associated systems. Studies have reported that their magnetic alignment behavior and phase stability are highly sensitive to composition and temperature. In this study, we systematically investigate the effects of cholesterol on bicelle formation and magnetic alignment in DMPC + 0.2 glycyrrhizic acid (GA) systems using a combined 31P and 14N solid-state NMR experimental and simulation-based approach. Temperature dependent 31P NMR spectra reveal a clear transition from vesicle dominant to aligned bicelles/nanodsics phase, while 1N quadrupolar splitting and lineshape analysis provides quantitative insights into heterogeneous lipid bilayer populations, distinguishing large aligned nanodiscs (B(L)), small nanodiscs (B(S)), and isotropic/random components (B(R)). A strong correlation is observed between the 31P derived bicelle fraction and the 14N B(L) population, confirming that macroscopic alignment in the presence of an external magnetic field directly reflects the growth of large, well-ordered nanodiscs. Cholesterol is found to play a critical dual role by modulating membrane order and curvature. At low cholesterol concentration (0 to 5 mole percent), nanodiscs alignment occurs gradually with increasing temperature, while at higher cholesterol concentration (15 to 25 mole percent), the alignment is delayed and accompanied by broader spectral features, indicating structural heterogeneity. Notably, 10 mole percent cholesterol consistently provides the optimal balance, enabling efficient temperature dependent conversion to aligned bicelles while maintaining high B(L) populations (about 70-80 percentage) and minimal isotropic fractions. In contrast, higher cholesterol maintains significant B(S) and B(R) populations, even at elevated temperature. The 14N quadrupolar coupling (Cq is approximately 8.5 to 9.2 kHz for aligned nanodiscs) remains nearly invariant across compositions, showing that cholesterol does not change local headgroup dynamics but instead redistributes lipid populations. These findings establish a combined 31P and 14N solid -state NMR approach provides a valuable platform for quantitatively correlating membrane structure, dynamics, and alignment, offering practical guidelines for optimizing bicelle systems for high resolution solid-state NMR studies of membrane associated biomolecules.

Phosphatase and tensin homolog (PTEN)-induced putative kinase 1 (PINK1), a key regulator of mitophagy, has been linked to the pathogenesis of Parkinson's disease (PD). PINK1 recruits Parkin, an E3 ubiquitin ligase, triggering mitophagy in response to mitochondrial damage. During mitophagy, the quantity, stability, and activity of PINK1 must be strictly regulated; however, the mechanisms governing these parameters under cellular stress are still unclear. Herein, we determined the structural basis for PINK1 maturation mediated by heat shock protein 90/cell division cycle 37/FK506-binding protein 51 (HSP90/CDC37/FKBP51) chaperone complex. We identified PINK1-associated proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and determined the structures of the complexes using Cryo-Electron Microscopy (Cryo-EM). Results showed that FKBP51 potentially interacts with a conserved leucine-proline-phenylalanine (LPF) motif on the activation loop of PINK1 and negatively regulates PINK1 functions in mitophagy. A PINK1 mutation located at the FKBP51 recognition site is linked to mitophagy deficiency, which can be partially rescued by specific inhibition of FKBP51. These findings reveal a general mechanism for PINK1 recognition by the HSP90/CDC37/FKBP51 chaperone complex and suggest a potential approach for upregulating PINK1 activity, which is impaired in PD.

Circadian disruption, notably sleep disturbances, serves as an early indicator of Alzheimers disease (AD), preceding cognitive symptoms like memory loss. The suprachiasmatic nucleus (SCN) governs biological rhythms and receives direct retinal input via melanopsin-expressing retinal ganglion cells (mRGCs) to synchronize with environmental light cycles. The anatomical and functional basis for circadian disruption in AD remains unclear. Here, we explored the multi-level relationships between gene expression, the SCN connectome, and regulations of sleep and circadian rhythms in the APP/PS1 mouse model. The sleep architecture of APP/PS1 mice displayed significantly reduced rapid eye movement sleep (REM), associated with a reduced daily core body temperature amplitude and locomotor hyperactivity. Lastly, APP/PS1 mice showed an impaired response to acute light pulse stimulation and present hyperactivity of mRGCs at a young age and hypoactivity of these cells at older ages. These physiological functions are known to be, at least in part, regulated by the SCN, the main target of mRGCs. We noted several modifications in SCN connectomics using serial blockface electron microscopy (SBEM), including a reduction of the dendro-dendritic chemical synapse (DDCS) network that receives a large part of the retinal input and is thought to be crucial for synchronicity between SCN neurons. In addition, we observed multiple signs of dystrophy, including modifications of the shape of dendrites and cell soma, accumulation of aggregated lysosomes, and swelling of axons. At the same time, we investigated the changes in gene expression using spatial transcriptomics. The SCN presents changes in the expression of genes associated with synapse formation, cell adhesion, and neurite growth. These results suggest that, despite the absence of amyloid plaques in the ventral hypothalamus, the SCN of APP/PS1 mice still undergo profound gene expression changes, impacting connectomics and physiological functions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/744599v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@ceedb0org.highwire.dtl.DTLVardef@156cfaaorg.highwire.dtl.DTLVardef@5bc262org.highwire.dtl.DTLVardef@36df4d_HPS_FORMAT_FIGEXP M_FIG C_FIG

The rising incidence of invasive fungal diseases emphasizes the need for novel therapeutic strategies, including membrane-targeting antifungal agents, which require representative lipid models for detailed molecular-level studies. In this work, we propose a consensus quinary fungal plasma membrane model based on lipidomic literature data, specifically PC:PE:PI:PA:PS phospholipid model with ratio of 44:29:13:8:6. Using a bottom-up approach, we characterized the biophysical properties of this system - with particular emphasis on mechanical parameters such as bending rigidity and area compressibility - by combining molecular dynamics simulations with experimental flicker-noise and ATR-FTIR spectroscopies. Furthermore, we investigated the effect of two key non-phospholipid components: ergosterol and triacylglycerols. Biophysical analysis revealed that DPPI and its specific interactions with DSPS induced the most substantial deviations in baseline membrane parameters, particularly area per lipid, membrane thickness, and area compressibility, while DSPS influenced bending rigidity change and DLiPA primarily affected lipid packing defects. In addition, ergosterol and TGs were found to influence all of the investigated parameters to different degree. Notably, the overall biophysical profile of the proposed FPMM closely mimicked that of natural vesicles derived from yeast lipid extracts, establishing this model may provide a reliable platform for studying fungal membrane biophysics and lipid-targeting interactions.

Sleep disturbance in Alzheimer's disease (AD), particularly the reduction of slow wave sleep (SWS), has been proposed as a novel therapeutic target, with disease-modifying potential. Trazodone, an antidepressant with robust SWS-promoting properties, is currently the most prescribed sleep-promoting medication in the United States. Here, we demonstrate that chronic trazodone administration consolidates sleep in the APP NL-F knock-in mouse model of AD, increasing NREM sleep duration and slow wave power during the rest phase while promoting wake during the active phase. These sleep consolidating effects were accompanied by lower regional glial activation and amyloid burden, particularly in male mice. Most notably, hippocampal amyloid plaque burden was 45% lower in mice treated from 14 to 16 months of age than in vehicle-treated controls. Chronic trazodone treatment was also associated with better short-term and long-term recognition memory. Together, these findings support the potential of repurposing trazodone as a well-tolerated, disease-modifying therapeutic for AD, capable of enhancing sleep quality, improving cognition, and lowering AD-relevant neuropathology.

Background: Natural compounds from avocado fruit (avocadene, avocadyne, and acetate derivatives) exhibit notable biological activity, although their molecular mechanisms remain unclear. The avocado-derived lipids exert potent nematocidal activity against several parasitic nematodes. In Caenorhabditis elegans (C. elegans), those compounds caused concentration-dependent toxicity, impairing first stage larval growth, egg hatching, and adult survival. Treated worms exhibited impaired mitochondrial respiration, reduced oxygen consumption, and elevated reactive oxygen species. These effects suggest that avocado lipids disrupt mitochondrial function and lipid metabolism, in part by inhibiting acetyl-CoA carboxylase, the rate-limiting enzyme of fatty acid biosynthesis. Methods: We investigated the effects of these compounds on the lipid profile of C. elegans and their association with endogenous lipid pools using NMR spectroscopy, click-chemistry-based fluorescence labeling, thin-layer chromatography (TLC), and microscopy. Results: Lipidomic analysis of stage 4 larvae (L4) and embryos treated with avocadene acetate revealed increased lipid NMR signals. Fluorescence-assisted TLC and NMR further suggested that avocadyne preferentially associates with triglyceride-linked fatty acids, particularly monounsaturated and flexible polyunsaturated chains, without detectable interactions with conformationally-constrained polyunsaturated species. Fluorescent avocadyne derivatives were efficiently internalized with distinct localization patterns in L4 larvae and embryonic cells. Conclusions: Overall, the lipid homeostasis remodeling of L4 larvae in response to lipotoxic shock was associated with phospholipid increase and remarkable lipid droplets onset, whereas embryos showed accumulation of lipids in enlarged droplets and developmental arrest.

The process of drug unbinding is of immense importance in the field of biophysics and therapeutics. The behavior of these systems is greatly influenced by their thermodynamic and kinetic properties. Therefore, it is crucial to accurately estimate the ligand binding free energies and rate of ligand dissociation, yet these processes are often governed by rare event transitions that lie beyond the reach of standard brute-force molecular dynamics simulations. While enhanced sampling simulations offer a solution, their efficacy is strictly contingent upon the selection of appropriate collective variables (CVs) which is non-trivial for complex systems like protein-ligand complexes. In this study, we present a method to derive optimized CV from transition state region (TS) via an interpretable machine learning (ML) model, Elastic Net. By employing some physically intuitive order parameters, the derived optimized CV from the TS-region greatly accelerate ligand binding-unbinding transitions and achieves rapid free energy surface (FES) convergence across diverse systems including buried and solvent exposed active sites such as Trpsin-benzamidine complex, host-guest systems and sodium epoxidase etc. Intriguingly significant contribution of the ligand hydration is found in the optimized CV which depicts crucial role of solvent in driving ligand binding-unbinding transitions. The estimated binding free energies for different protein-ligand complexes match quite well with experiments, while maintaining a low computational cost. The derived optimized CV is also used to calculate the ligand residence times across different systems and calculated residence times are within the experimental range for all systems, again with very little computational costs. Moreover, we show that the optimized CV constructed from TS region via an interpretable ML model is transferable across diverse systems, offering a robust and scalable framework for drug discovery and investigation of complex biomolecular recognition.

1A-adrenoceptor (1A-AR) is a class A G-protein coupled receptor (GPCR) that stimulates smooth muscle contraction in response to adrenaline and noradrenaline. GPCRs exist in a dynamic equilibrium between multiple conformational states. Ligand binding induces structural rearrangements via conserved microswitches, which are thought to shift the equilibrium and trigger signalling. For structural and biochemical studies, GPCRs must be solubilised from the membrane, typically using detergent micelles. However, detergents can disrupt native dynamics of membrane proteins, potentially confounding experimental results. To address this, phospholipid bilayer mimetics such as nanodiscs and saposin nanoparticles (SNPs) have been developed to provide a more native-like environment. Thermostabilised 1A-AR serves as a GPCR prototype and can be expressed and isotopically labelled for NMR purposes. To investigate how membrane mimetics influence the conformational diversity of 1A-AR, we compared 1H 13C3-HMQC NMR experiments of 13CH3-Met labelled 1A-AR incorporated into either DDM, LMNG, or SNPs, in presence of ligands with varying efficacies. Several methionine residues are positioned near key microswitches, including M2035.57, located closed to the G protein binding site. Its resonance has been proposed as a readout of receptor conformational state, shifting with ligand efficacy. Spectra of 13CH3-Met labelled 1A-AR in LMNG closely resembled those in DDM with some temperature-dependent dynamic variation. In contrast, incorporation into SNPs led to a complete loss of M2035.57 signal, consistent with an intermediate exchange rate. These findings demonstrate that the membrane environment can profoundly influence conformational dynamics in GPCR NMR studies. Our results highlight the need to carefully consider membrane environment when interpreting NMR data and underscore the value of benchmarking against biologically relevant controls.

Valproic acid/sodium valproate (VPA) is a widely prescribed anticonvulsant and has also been used against certain tumor cells. It is a potent modulator of gene expression. Its ability to induce apoptosis has been well documented in HeLa cells. However, another form of cell death - mitotic catastrophe - has not yet been explored in VPA-treated HeLa cells. Here, we investigated the effects of VPA treatment on mitotic catastrophe characteristics, including morphological features and their frequencies, fluorescence intensity signals of caspase-2 and p53, and the expression and abundance of DNMT1 and DNMT3B. An increased frequency of mitotic catastrophe was observed not only morphologically, but also through enhanced induction of caspase-2, involvement of p53, at least under more drastic VPA treatment, but without a decrease in DNMT1 or DNMT3B levels. Additionally, enhancement of mitotic catastrophe coincided with a reduction in mitotic chromosome abnormalities. Increased DNMT3B expression following VPA action, may be favored by previously reported chromatin decondensation induced by this drug. Enhanced CpG methylation of specific DNA sites could thus be promoted. In conclusion, VPA was shown to trigger metabolic pathways linked to different forms of cell death in HeLa cells, supporting its oncosuppressive potential.

Interleukin-13 (IL-13) is an immunomodulatory cell signaling cytokine that has been implicated in neurodegenerative disease and chronic inflammation. IL-13 binds to its low and high affinity receptors, IL-13 receptor 1 (IL-13R1) and IL-13 receptor 2 (IL-13R2), respectively, with residence times that vary accordingly. As the binding kinetics of the cytokine-receptor complexes influence cellular responses, we employed the molecular dynamics (MD) simulation-based{tau} -random acceleration molecular dynamics method ({tau}RAMD) to compute relative residence times for wild-type (WT) IL-13 and 19 IL-13 mutants to the two receptors. Comparison with experimental kinetic data shows that the{tau} RAMD computations capture the trends in residence times. Analysis of simulated dissociation trajectories of the cytokine-receptor complexes reveals two distinct dissociation pathways of IL-13 from each of the receptors. This study thus pinpoints key determinants of the interaction of IL-13 with its receptors which could be targeted for therapeutic design. Statement of SignificanceCytokines are regulatory proteins that bind to cell surface receptors and thereby send signals to the cellular interior. Interleukin-13 (IL-13) is a cytokine that has a low and a high affinity receptor. It has important physiological roles, and its deregulation is involved in diseases such as atopic dermatitis and asthma. We employed a molecular dynamics simulation-based method to compute the effects of changes in the sequence of IL-13 on the lifetimes of complexes of IL-13 and its receptors. Comparison with experiments supports the validity of the computational approach and analysis of the simulations reveals two distinct ways in which IL-13 dissociates from each receptor. These results thus provide a map for targeting IL-13 - receptor interactions for the design of therapeutics.

Directional anisotropy in electron density provides key information about chemical bonding that is not readily accessible from conventional electron-density maps. Here, a model-independent framework is presented for decomposing experimental structure factors into angular components using spherical harmonics. Reciprocal-space projection onto spherical harmonics followed by standard Fourier synthesis yields angularly filtered density maps. The{ell} = 0 component captures the isotropic part of the density, while the{ell} = 1 components resemble px, py and pz-like dipolar functions that highlight directional electronic structure. Applications to high-resolution datasets, including urea, the Gly-Ala dipeptide and a 0.97 [A]{beta}-lactamase structure, reveal chemically interpretable dipolar features associated with carbonyl and amide bonds, N-H interactions and aromatic{pi} systems. Quantitative analysis using bond-centred sampling demonstrates stable dipolar signatures that remain detectable under moderate resolution truncation. These results establish spherical-harmonic angular decomposition as a practical framework for extracting directional electronic information from crystallographic electron-density maps. SynopsisAngular decomposition of experimental structure factors reveals dipolar anisotropy and directional electron-density features that are directly meaningful for chemical interpretation.

Mucopolysaccharidosis IIIC (Sanfilippo syndrome type C) is a rare lysosomal storage disorder caused by loss-of-function mutations in HGSNAT, which encodes an enzyme involved in heparan sulfate (HS) degradation, leading to impaired HS catabolism, lysosomal accumulation, and progressive neurodegeneration. Because enzyme replacement therapies have limited penetration across the blood-brain barrier, substrate-reduction therapy represents an alternative therapeutic strategy. Here, N-deacetylase/N-sulfotransferase 1 (NDST1), a key enzyme responsible for HS biosynthesis, was investigated as a potential substrate-reduction target. A structure-based computational pipeline was used to identify and evaluate inhibitors targeting the NDST1 sulfotransferase domain. Approximately 4.1 million drug-like compounds and FDA-approved drugs were screened by molecular docking, followed by pharmacokinetic filtering, molecular dynamics simulations, and MM/PBSA binding free energy calculations. In parallel, peptide binders targeting the same site were generated using diffusion-based protein design and evaluated using molecular dynamics and MM/GBSA analysis. Four chemically distinct small-molecule scaffolds and three peptide candidates were identified as stable binders to the NDST1 active site. The lead small-molecule candidate exhibited a predicted binding free energy of -13.36 {+/-} 5.87 kcal mol-1. These provide a focused set of candidates for further investigation and support the feasibility of targeting NDST1 as a substrate-reduction strategy for MPS IIIC.

Residual dipolar couplings (RDCs) obtained via magnetic field-induced alignment offer a powerful, media-free approach for the structural analysis of biomolecules. However, their detection in short, fast-tumbling nucleic acids remains elusive at conventional magnetic fields due to insufficient alignment and sensitivity. Here, we demonstrate the direct observation of these RDCs at 1.3 GHz in a 14-mer hairpin fragment derived from an HIV-1 Vif-targeting aptamer. The 1JNH scalar couplings of imino protons were measured at fields ranging from 600 MHz to 1.3 GHz. While the coupling constants remained invariant between 600 and 900 MHz, a clear deviation was exclusively captured at 1.3 GHz for all base-paired stem residues, demonstrating the first media-free detection of field-induced RDCs in a short RNA of this size. This breakthrough arises from a synergistic B07/2 scaling, combining enhanced alignment ({propto} B02) and sensitivity ({propto} B03/2). These RDCs showed excellent agreement with the NOE-derived structure. Additionally, the flexible loop residue G8 exhibited no detectable RDC, but displayed a field-dependent TROSY/anti-TROSY intensity inversion at 1.3 GHz, reflecting an unusual 1H chemical shift anisotropy (CSA) tensor that corroborates the local base-packing environment. Our findings highlight 1.3 GHz NMR as an indispensable tool for the structural analysis of short RNAs.

Parkinson's disease (PD) is a progressive neurodegenerative condition characterized by the loss of dopaminergic (DA) neurons and alpha-synuclein aggregation, with ferroptosis playing a critical pathological role. This study investigated the neuroprotective potential of Kocuria rhizophila strain CDMP12, a marine bacterium isolated from the Gulf of Mannar, India, using Caenorhabditis elegans models of PD. Dietary supplementation with K. rhizophila (CDMP12) significantly preserved DA neuron structure, rescued neuro-sensory and motor deficits, and attenuated both alpha-synuclein expression in the C. elegans models. Transcriptomic and qRT-PCR analyses revealed that CDMP12 systematically suppressed ferroptosis by significantly downregulating iron and lipid regulatory genes such as smf-3, ftn-1, and acs-4, while upregulating the protective antioxidant gene gpx-1. Furthermore, BODIPY staining demonstrated that CDMP12 treatment markedly reduced lipid peroxidation, lowering the oxidized-to-non-oxidized lipid ratio in PD worms. Collectively, these findings identify K. rhizophila (CDMP12) as a promising marine-derived neuroprotective candidate that mitigates PD-associated pathology, accompanied by reduced alpha-synuclein burden, preservation of DA neuronal function, and attenuation of ferroptosis-associated molecular and lipid peroxidation signatures.

The High Mobility Group Box 1 (HMGB1) protein performs multiple essential functions in the body, ranging from DNA regulation to the activation and mediation of immune responses. However, HMGB1 has been also implicated in several pathological conditions, such as rheumatoid arthritis, sepsis, autoimmune diseases, tumors, and Alzheimer's disease. As a result, HMGB1 is of increasing interest as a therapeutic target. Binding to heparin has been reported to inhibit HMGB1's pathological activity during sepsis in clinical settings. In this work, we compare the interactions of HMGB1 with heparin and its' synthetic analog linear polyglycerol sulfate (lPGS) from the viewpoint of stability and changes to association behavior. This analysis focuses on thermal stability, secondary-structure changes, and particle-size evolution using nano-differential scanning fluorimetry (nanoDSF), circular dichroism spectroscopy (CD), and dynamic light scattering (DLS).