Search Results (186)

Protein–polyelectrolyte nanostructures assembled via electrostatic interactions offer versatile applications in biomedicine, tissue engineering, and food science. However, several open questions remain regarding their intermolecular interactions and the influence of external conditions—such as temperature and pH—on their assembly, stability, and responsiveness. This study explores the formation and stability of networks between poly(acrylic acid) (PAA) and lysozyme (LYZ) at the nanoscale upon thermal treatment, using a combination of experimental and simulation measures. Experimental techniques of static and dynamic light scattering (SLS and DLS), Fourier transform infrared spectroscopy (FTIR), and circular dichroism (CD) are combined with all-atom molecular dynamics simulations. Model systems consisting of multiple PAA and LYZ molecules explore collective assembly and complexation in aqueous solution. Experimental results indicate that electrostatic complexation occurs between PAA and LYZ at pH values below LYZ’s isoelectric point. This leads to the formation of nanoparticles (NPs) with radii ranging from 100 to 200 nm, most pronounced at a PAA/LYZ mass ratio of 0.1. These complexes disassemble at pH 12, where both LYZ and PAA are negatively charged. However, when complexes are thermally treated (TT), they remain stable, which is consistent with earlier findings. Atomistic simulations demonstrate that thermal treatment induces partially reversible structural changes, revealing key microscopic features involved in the stabilization of the formed network. Although electrostatic interactions dominate under all pH and temperature conditions, thermally induced conformational changes reorganize the binding pattern, resulting in an increased number of contacts between LYZ and PAA upon thermal treatment. The altered hydration associated with conformational rearrangements emerges as a key contributor to the stability of the thermally treated complexes, particularly under conditions of strong electrostatic repulsion at pH 12. Moreover, enhanced polymer chain associations within the network are observed, which play a crucial role in complex stabilization. These insights contribute to the rational design of protein–polyelectrolyte materials, revealing the origins of association under thermally induced structural rearrangements. Full article

AAA+ ATPases are ring-shaped hexameric protein complexes that operate as elaborate macromolecular motors, driving a variety of ATP-dependent cellular processes. AAA+ ATPases undergo large-scale conformational changes that lead to the conversion of chemical energy from ATP into mechanical work to perform a wide range of functions, such as unfolding and translocation of the protein substrate inside a proteolysis chamber of an AAA+-associated protease. Despite extensive biochemical studies on these macromolecular assemblies, the mechanism of substrate unfolding and degradation has long remained elusive. Indeed, until recently, structural characterization of AAA+ protease complexes remained hampered by the size and complexity of the machinery, harboring multiple protein subunits acting together to process proteins to be degraded. Additionally, the major structural rearrangements involved in the mechanism of this complex represent a crucial challenge for structural biology. Here, we report the main advances in deciphering molecular details of the proteolytic reaction performed by AAA+ proteases, based on the remarkable progress in structural biology techniques. Particular emphasis is placed on the latest findings from high-resolution structural analysis of the ClpXP proteolytic complex, using crystallographic and cryo-EM investigations. In addition, this review presents some additional dynamic information obtained using solution-state NMR. This information provides molecular details that help to explain the protein degradation process by such molecular machines. Full article

Background/Objectives: Understanding the molecular interactions between small bioactive compounds and serum albumins is essential for drug development and pharmacokinetics. Noraucuparin, a biphenyl-type phytoalexin with promising pharmacological properties, has shown a strong binding affinity to bovine serum albumin (BSA), a model protein for drug transport. This study aims to elucidate the structural and energetic characteristics of the noraucuparin–BSA complex under physiological and slightly elevated temperatures. Methods: Microsecond-scale molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MMGBSA)-binding-free energy calculations were performed to investigate the interaction between noraucuparin and BSA at 298 K and 310 K. Conformational flexibility and per-residue energy decomposition analyses were conducted, along with interaction network mapping to assess ligand-induced rearrangements. Results: Noraucuparin preferentially binds to site II of BSA, near the ibuprofen-binding pocket, with stabilization driven by hydrogen bonding and hydrophobic interactions. Binding at 298 K notably increased the structural mobility of BSA, affecting its global conformational dynamics. Key residues, such as Trp213, Arg217, and Leu237, contributed significantly to complex stability, and the ligand induced localized rearrangements in the protein’s intramolecular interaction network. Conclusions: These findings offer insights into the dynamic behavior of the noraucuparin–BSA complex and enhance the understanding of serum albumin–ligand interactions, with potential implications for drug delivery systems. Full article

Turbo Codes (TCs) are a family of convolutional codes that provide powerful Forward Error Correction (FEC) and operate near the Shannon limit for channel capacity. In the context of modern communication systems, such as those conforming to the DVB-RCS2 standard, Turbo Encoders (TEs) play a crucial role in ensuring robust data transmission over noisy satellite links. A key computational bottleneck in the Turbo Encoder is the non-uniform interleaving stage, where input bits are rearranged according to a dynamically generated permutation pattern. This stage often requires the intermediate storage of data, resulting in increased latency and reduced throughput, especially in embedded or real-time systems. This paper introduces a vector processing algorithm designed to accelerate the interleaving stage of the Turbo Encoder. The proposed algorithm is tailored for vector DSP architectures (e.g., CEVA-XC4500), and leverages the hardware’s SIMD capabilities to perform the permutation operation in a structured, phase-wise manner. Our method adopts a modular Load–Execute–Store design, facilitating efficient memory alignment, deterministic latency, and hardware portability. We present a detailed breakdown of the algorithm’s implementation, compare it with a conventional scalar (serial) model, and analyze its compatibility with the DVB-RCS2 specification. Experimental results demonstrate significant performance improvements, achieving a speed-up factor of up to 3.4× in total cycles, 4.8× in write operations, and 7.3× in read operations, relative to the baseline scalar implementation. The findings highlight the effectiveness of vectorized permutation in FEC pipelines and its relevance for high-throughput, low-power communication systems. Full article

The mechanistic effects of Zanthoxylum bungeanum on the textural properties of Tibetan pig sausages remain inadequately elucidated. We conducted a dose–response analysis using Z. bungeanum aqueous extraction (ZBAE) containing 36.97 mg GAE/g polyphenols, applied at concentrations from 0.125% to 1.20% in the meat paste. Optimal textural enhancement was achieved at 0.25% ZBAE, as proved by significantly improving water holding capacity (1.77% increase), hardness (139.87% increase), and gel strength (46.04% increase) relative to the control group (p < 0.05). Specifically, this concentration: (i) promoted protein molecular rearrangement of by enhancing hydrophobic interactions (33.33% increase) and hydrogen bonding (287.99% increase); (ii) induced conformational transitions from α-helix (42.62% decrease) to β-sheet formations (21.11% increase); and (iii) generated a homogeneous three-dimensional protein network characterized by a fractal dimension of 2.769 ± 0.006 and a porosity of 38.350 ± 0.333%. The addition of natural polyphenols from Z. bungeanum may optimize the textural quality of processed meat products. Full article

This work investigates the effects of gamma irradiation (0.1–10 kGy) on four Italian wheat matrices, such as durum, conventional soft, integrated soft, and biological soft wheat, by coupling Raman, FTIR-ATR and EPR spectroscopies to provide complementary insights into the structural, conformational, and radical-based transformations occurring in starch, the primary polysaccharide in wheat. As a general trend, gamma irradiation up to 10 kGy does not induce drastic degradation or depolymerization of wheat components. However, deeper investigations reveal that wheat composition is crucial in modulating the effects of gamma irradiation on structural and conformational rearrangements of starch units. Raman and FTIR-ATR spectroscopy analyses showed an increase in random coil fractions, with the most significant changes observed in durum wheat, plausibly attributed to its higher protein content. EPR analyses confirmed a dose-dependent increase in free radicals, with different recombination kinetics between wheat types influenced by their intrinsic composition and molecular organization. The proposed spectroscopic approaches allow for rapid and non-destructive analyses of molecular structure, chemical composition, and free radical content in irradiated wheat matrices with minimal sample preparation. These approaches can be extended in the development of screening methods for a wide range of polysaccharides in a variety of crops. Full article

The innate immune response serves as the primary defense against viral infections, with the recognition of viral nucleic acids by pattern recognition receptors (PRRs) initiating antiviral responses. Mitochondrial antiviral-signaling protein (MAVS) acts as a pivotal adaptor protein in the RIG-I pathway. Alternative splicing further diversifies MAVS isoforms. In this study, we identified and characterized a novel rat MAVS variant (MAVS500) with a twenty-one-nucleotide deletion, resulting in a protein seven amino acids shorter than the wild-type (WT) rat MAVS. The MAVS500 was cloned from the rat bladder cancer cell line, NBT-II, using specific primers, and subsequently sequenced. MAVS500 was overexpressed in HEK293T and NBT-II cells and then analyzed using Western Blotting and fluorescence microscopy. MAVS500 overexpression increased downstream signaling proteins, NFκβ and pNFκβ, compared to WT rat MAVS in both human and rat cell lines. Structural analysis revealed a high similarity between MAVS500 and WT rat MAVS. The seven-amino-acid deletion in MAVS500 induces significant conformational rearrangements, reducing helical turns and altering structural dynamics, which may impact its interactions with downstream signaling molecules in the innate immune pathway. The identification of MAVS500 enhances our understanding of MAVS regulation and its role in the innate immune response, providing valuable insights into alternative splicing as a mechanism for diversifying protein function. Full article

Using the framework of an investigation of the stimuli-responsive behavior of peptide assembly on a solid surface, this study on the behavior of a chemisorbed peptide on a gold surface was performed. The studied peptide is a dimeric form of the antimicrobial peptide Trichogin GAIV, which was also modified by substituting the glycine with lysine residues, while the N-terminus octanoyl group was replaced by a lipoic one that was able to bind to the gold surface. In this way, a chemically linked peptide assembly that is pH-responsive was obtained because of the protonation/deprotonation of the sidechains of the Lys residues. Information about the effect of protonation/deprotonation equilibria switching the pH from acid (pH = 3) to basic (pH = 11) conditions was obtained macroscopically by performing Quartz crystal microbalance with dissipation monitoring (QCM-D), Surface Plasmon Resonance (SPR), Nanoplasmonic Sensing (NPS), and FTIR techniques. Using molecular dynamics (MD) simulations, it is possible to explain, at the molecular level, our main experimental results: (1) pH changes induce a squeezing behavior in the system, consisting in thickness and mass variations in the peptide layer, which are mainly due to the pH-driven hydrophilic/hydrophobic character of the lysine residues, and (2) the observed hysteresis is due to small conformational rearrangements from helix to beta sheets occurring mainly on the first half of the peptide, closer to the surface, while the second half remains almost unaffected. The latter result, together with the evidence that the layer thickness is not simply double the assembly of the monomeric analog, indicates that the dimeric peptide does not behave as a double monomer, but assumes very peculiar features. Full article

Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for the hydrolysis of the phosphodiester bond on the 5′ side of an apurinic/apyrimidinic site during base excision repair. Moreover, in DNA, this enzyme can recognize nucleotides containing such damaged bases as 5,6-dihydro-2′-deoxyuridine (DHU), 2′-deoxyuridine (dU), alpha-2′-deoxyadenosine (αA), and 1,N6-ethenoadenosine (εA). Previously, by pulsed electron–electron double resonance spectroscopy and pre-steady-state kinetic analysis, we have revealed multistep DNA rearrangements during the formation of the catalytic complex. In the present study, the modeling of the eversion trajectory of nucleotides with various damaged bases was performed by directed molecular dynamics simulations. It was found that each damaged base at the beginning of the eversion interacts with protein loop Val196-Arg201, which should be moved to enable further nucleotide eversion. This movement involves a shift in loop Val196-Arg201 away from loop Asn253-Thr257 and requires the disruption of contacts between these loops. The Glu260Ala substitution facilitates the separation of the two loops. Moreover, conformational changes in the Asn253-Thr257 loop should occur in the second half of the lesion eversion trajectory. All these perturbations within the protein globule tend to reduce steric interactions of each damaged base with the protein during the eversion of the nucleotide from DNA and movement to the active site. These perturbations are important determinants of substrate specificity of endonuclease APE1. Full article

The mechanism of transcription proceeds through the formation of R-loop structures containing a DNA–RNA heteroduplex and a single-stranded DNA segment that should be placed inside the elongation complex; therefore, these nucleic acid segments are limited in length. The attachment of each nucleotide to the 3′ end of an RNA strand requires a repeating cycle of incoming nucleoside triphosphate binding, catalysis, and enzyme translocation. Within these steps of transcription elongation, RNA polymerase sequentially goes through several states and is post-translocated, catalytic, and pre-translocated. Moreover, the backward movement of the polymerase, which is essential for transcription pausing and proofreading activity, gives rise to a backtracked state. In the present study, to analyze both the efficacy of transcription elongation complex (TEC) formation and the rate of RNA synthesis, we used a set of model R-loops that mimic the pre-translocated state, post-translocated state, backtracked state, and a misincorporation event. It was shown that TEC assembly proceeds as an equilibrium process, including the simultaneous formation of a catalytically competent TEC as well as a catalytically inactive conformation. Our data suggest that the inactive complex of RNA polymerase with an R-loop undergoes slow conformational changes, resulting in a catalytically competent TEC. It was revealed that the structural features of R-loops affect the ratio between active and inactive states of the TEC, the rate of conformational rearrangements required for the induced-fit transition from the inactive state to the catalytically competent TEC, and the rates of accumulation of both the total RNA products and long RNA products. Full article

This study analyzes the fractal aspects of the structures of S100 proteins to better understand their structural complexity. We take into account 33 solution structures and 18 crystal structures corresponding to human S100 proteins for the calculation of mass and surface fractal dimensions. The mass fractal dimension value is calculated as Dm = 1.54, confirming the extended conformation of the dimers of these proteins. The mean value of the surface fractal dimension is Ds = 2.35 ± 0.09 when computed using solution structures and Ds = 2.23 ± 0.05 when computed using crystal structures, revealing the surface irregularities of S100 proteins. Changes in surface fractal dimensions have been recorded for S100 proteins due to the changes in the pH of the environment, due to mutations in their sequences that alter how the protein folds, and/or due to their interactions with ions and/or ligands that reflect the structural rearrangements that occur upon binding. These changes can significantly influence the biological activity of the protein, making the fractal dimension of the surface a valuable parameter in studying protein functions, interactions, and potential therapeutic targeting. Full article

Ethyl maltol was investigated using matrix isolation infrared spectroscopy and DFT calculations. In an argon matrix (14.5 K), the compound was found to exist in a single conformer (form I), characterized by an intramolecular hydrogen bond with an estimated energy of ~17 kJ mol⁻¹. The IR spectrum of this conformer was assigned, and the molecule’s potential energy landscape was explored to understand the relative stability and isomerization dynamics of the conformers. Upon annealing the matrix to 41.5 K, ethyl maltol was found to predominantly aggregate into a centrosymmetric dimer (2× conformer I) bearing two intermolecular hydrogen bonds with an estimated energy of ca. 28 kJ mol⁻¹ (per bond). The UV-induced (λ > 235 nm) photochemistry of the matrix-isolated ethyl maltol was also investigated. After 1 min of irradiation, band markers of two rearrangement photoproducts formed through the photoinduced detachment-attachment (PIDA) mechanism, in which the ethyl maltol radical acts as an intermediate, were observed: 1-ethyl-3-hydroxy-6-oxibicyclo [3.1.0] hex-3-en-2-one and 2-ethyl-2H-pyran-3,4-dione. The first undergoes subsequent reactions, rearranging to 4-hydroxy-4-propanoylcyclobut-2-en-1-one and photofragmenting to cyclopropenone and 2-hydroxybut-1-en-1-one. Other final products were also observed, specifically acetylene and CO (the expected fragmentation products of cyclopropenone), and CO₂. Overall, the study demonstrated ethyl maltol’s high reactivity under UV irradiation, with significant photochemical conversion occurring within minutes. The rapid photochemical conversion, with complete consumption of the compound in 20 min, should be taken into account in designing practical applications of ethyl maltol. Full article

Despite the success of AlphaFold2 approaches in predicting single protein structures, these methods showed intrinsic limitations in predicting multiple functional conformations of allosteric proteins and have been challenged to accurately capture the effects of single point mutations that induced significant structural changes. We examined several implementations of AlphaFold2 methods to predict conformational ensembles for state-switching mutants of the ABL kinase. The results revealed that a combination of randomized alanine sequence masking with shallow multiple sequence alignment subsampling can significantly expand the conformational diversity of the predicted structural ensembles and capture shifts in populations of the active and inactive ABL states. Consistent with the NMR experiments, the predicted conformational ensembles for M309L/L320I and M309L/H415P ABL mutants that perturb the regulatory spine networks featured the increased population of the fully closed inactive state. The proposed adaptation of AlphaFold can reproduce the experimentally observed mutation-induced redistributions in the relative populations of the active and inactive ABL states and capture the effects of regulatory mutations on allosteric structural rearrangements of the kinase domain. The ensemble-based network analysis complemented AlphaFold predictions by revealing allosteric hotspots that correspond to state-switching mutational sites which may explain the global effect of regulatory mutations on structural changes between the ABL states. This study suggested that attention-based learning of long-range dependencies between sequence positions in homologous folds and deciphering patterns of allosteric interactions may further augment the predictive abilities of AlphaFold methods for modeling of alternative protein sates, conformational ensembles and mutation-induced structural transformations. Full article

Hi-C sequencing is a DNA-based next-generation sequencing method that preserves the 3D genome conformation and has shown promise in detecting genomic rearrangements in translational research studies. To evaluate Hi-C as a potential clinical diagnostic platform, analytical concordance with routine laboratory testing was assessed using primary pediatric leukemia and sarcoma specimens. Archived viable and non-viable frozen leukemic cells and formalin-fixed paraffin-embedded (FFPE) tumor specimens were analyzed. Pediatric acute myeloid leukemia (AML) and alveolar rhabdomyosarcoma (A-RMS) specimens with known genomic rearrangements were subjected to Hi-C to assess analytical concordance. Subsequently, a discovery cohort consisting of AML and acute lymphoblastic leukemia (ALL) cases without known genomic rearrangements based on prior clinical diagnostic testing was evaluated to determine whether Hi-C could detect rearrangements. Using a standard sequencing depth of 50 million raw read-pairs per sample, or approximately 5X raw genomic coverage, we observed 100% concordance between Hi-C and previous clinical cytogenetic and molecular testing. In the discovery cohort, a clinically relevant gene fusion was detected in 45% of leukemia cases (5/11). This study provides an institutional proof of principle evaluation of Hi-C sequencing to medical diagnostic testing as it identified several clinically relevant rearrangements, including those that were missed by current clinical testing workflows. Full article

The pH- and thermo-responsive behavior of polymeric hydrogels $\left({\mathrm{M}}_{\mathrm{C}}-\mathrm{c}\mathrm{o}-{\mathrm{M}}_{\mathrm{A}}\right)$ have been studied in detail using dynamic light scattering $\left(\mathrm{D}\mathrm{L}\mathrm{S}\right)$, scanning electron microscopy$\left(\mathrm{S}\mathrm{E}\mathrm{M}\right)$, nuclear magnetic resonance (¹H NMR) and rheology to evaluate the conformational changes, swelling–shrinkage, stability, the ability to flow and the diffusion process of nanoparticles at several temperatures. Furthermore, polymeric systems functionalized with acrylic acid $\left({\mathrm{M}}_{\mathrm{C}}\right)$ and acrylamide $\left({\mathrm{M}}_{\mathrm{A}}\right)$ were subjected to a titration process with a calcium chloride $\left({\mathrm{C}\mathrm{a}\mathrm{C}\mathrm{l}}_2\right)$ solution to analyze its effect on the average particle diameter$\left({\mathrm{D}}_{\mathrm{z}}\right)$, polymer structure and the intra- and intermolecular interactions in order to provide a responsive polymer network that can be used as a possible nanocarrier for drug delivery with several benefits. The results confirmed that the structural changes in the sensitive hydrogels are highly dependent on the corresponding critical solution temperature $\left(\mathrm{C}\mathrm{S}\mathrm{T}\right)$ of the carboxylic (–COOH) and amide (–CONH₂) functional groups and the influence of calcium ions $\left({\mathrm{C}\mathrm{a}}^{2+}\right)$ on the formation or breaking of hydrogen bonds, as well as the decrease in electrostatic repulsions generated between the polymer chains contributing to a particle agglomeration phenomenon. The temperature leads to a re-arrangement of the polymer chains, affecting the viscoelastic properties of the hydrogels. In addition, the diffusion coefficients $\left(D\right)$ of nanoparticles were evaluated, showing a closeness among with the morphology, shape, size and temperature, resulting in slower diffusions for larger particles size and, conversely, the diffusion in the medium increasing as the polymer size is reduced. Therefore, the hydrogels exhibited a remarkable response to pH and temperature variations in the environment. During this research, the functionality and behavior of the polymeric nanoparticles were observed under different analysis conditions, which revealed notable structural changes and further demonstrated the nanoparticles promising high potential for drug delivery applications. Hence, these results have sparked significant interest in various scientific, industrial and technological fields. Full article