Search Results (699)

Background/Objectives: Antimicrobial resistance (AMR) contributes to millions of deaths globally each year, creating an urgent need for new therapeutic agents. Antimicrobial peptides (AMPs) have emerged as promising candidates due to their potential to combat AMR pathogens. This study aimed to evaluate the antimicrobial activity of an AMP from a soil-derived bacterial isolate against Gram-negative bacteria. Method: Soil bacteria were isolated and screened for antimicrobial activity. The bioactive peptide was purified and determined its structure and antimicrobial efficacy. Genomic analysis was conducted to predict the biosynthetic gene clusters (BGCs) responsible for AMP production. Results: Genomic analysis identified the isolate as Paenibacillus sp. Na14, which exhibited low genomic similarity (61.0%) to other known Paenibacillus species, suggesting it may represent a novel species. The AMP from the Na14 strain exhibited heat stability up to 90 °C for 3 h and retained its activity across a broad pH range from 3 to 11. Structural analysis revealed that the Na14 peptide consisted of 14 amino acid residues, adopting an α-helical structure. This peptide exhibited bactericidal activity at concentrations of 2–4 µg/mL within 6–12 h, and its killing rate was concentration-dependent. The peptide was found to disrupt the bacterial membranes. The Na14 peptide shared 64.29% sequence similarity with brevibacillin 2V, an AMP from Brevibacillus sp., which also belongs to the Paenibacillaceae family. Genomic annotation identified BGCs associated with secondary metabolism, with a particular focus on non-ribosomal peptide synthetase (NRPS) gene clusters. Structural modeling of the predicted NRPS enzymes showed high similarity to known NRPS modules in Brevibacillus species. These genomic findings provide evidence supporting the similarity between the Na14 peptide and brevibacillin 2V. Conclusions: This study highlights the discovery of a novel AMP with potent activity against Gram-negative pathogens and provides new insight into conserved AMP biosynthetic enzymes within the Paenibacillaceae family. Full article

The white-spotted jellyfish, Phyllorhiza punctata, is an invasive species with significant ecological and economic relevance spreading across various regions. While its ecological impact is well-documented, its molecular and biochemical characteristics remain poorly understood. In this study, we integrate proteomic data generated by LC-MS/MS with publicly available transcriptomic information to characterize P. punctata, analyzing differential protein expression across three distinct tissues: oral arms, mantle, and gonads. A total of 2764 proteins and 25,045 peptides were identified, including several venom components such as jellyfish toxins (JFTs) and phospholipase A2 (PLA2), which were further investigated and compared to toxins from other species. Enrichment analyses revealed clear tissue-specific functions. Additionally, deep learning and machine learning tools identified 274 promising AMP candidates, including the α-helical, β-sheet, and αβ-motif peptides. This dataset provides new insights into the protein composition of P. punctata and highlights strong AMP candidates for further characterization, underscoring the biotechnological potential of underexplored cnidarian species. Full article

Glutamate dehydrogenase (GDH) is ubiquitous in organisms and crucial for amino acid metabolism, energy production, and redox balance. The gdhA and gudB genes encoding GDH were identified in Bacillus altitudinis AS19 and shown to be regulated by iron. However, their functions remain unclear. In this study, gdhA and gudB were analyzed using bioinformatics tools, such as MEGA, Expasy, and SWISS-MODEL, expressed with a prokaryotic expression system, and the induction conditions were optimized to increase the yield of soluble proteins. Phylogenetic analysis revealed that GDH is evolutionarily conserved within the genus Bacillus. GdhA and GudB were identified as hydrophobic proteins, not secreted or membrane proteins. Their structures were primarily composed of irregular coils and α-helices. SWISS-MODEL predicts GdhA to be an NADP-specific GDH, whereas GudB is an NAD-specific GDH. SDS-PAGE analysis showed that GdhA was expressed as a soluble protein after induction with 0.2 mmol/L IPTG at 24 °C for 16 h. GudB was expressed as a soluble protein after induction with 0.1 mmol/L IPTG at 16 °C for 12 h. The proteins were confirmed by Western blot and mass spectrometry. The enzyme activity of recombinant GdhA was 62.7 U/mg with NADPH as the coenzyme. This study provides a foundation for uncovering the functions of two GDHs of B. altitudinis AS19. Full article

Large-conductance, voltage- and calcium-activated potassium (BK) channels are crucial regulators of cellular excitability, influenced by various signaling molecules, including heme. The BK channel contains a heme-sensitive motif located at the sequence ⁶¹²CKACH⁶¹⁶, which is a conserved heme regulatory motif (HRM) found in the cytochrome c protein family. This motif is situated within a linker region of approximately 120 residues that connect the RCK1 and RCK2 domains, and it also includes terminal α-helices similar to those found in cytochrome c family proteins. However, much of this region has yet to be structurally defined. We conducted a sequence alignment of the BK linker region with mitochondrial cytochrome c and cytochrome c domains from various hemoproteins to better understand this functionally significant region. In addition to the HRM motif, we discovered that important structural and functional elements of cytochrome c proteins are conserved in the BK RCK1-RCK2 linker. Firstly, the part of the BK region that is resolved in available atomic structures shows similarities in secondary structural elements with cytochrome c domain proteins. Secondly, the Met80 residue in cytochrome c domains, which acts as the second axial ligand to the heme iron, aligns with the BK channel. Beyond its role in electron shuttling, cytochrome c domains exhibit various catalytic properties, including peroxidase activity—specifically, the oxidation of suitable substrates using peroxides. Our findings reveal that the linker region endows human BK channels with peroxidase activity, showing an apparent H₂O₂ affinity approximately 40-fold greater than that of mitochondrial cytochrome c under baseline conditions. This peroxidase activity was reduced when substitutions were made at ⁶¹²CKACH⁶¹⁶ and other relevant sites. These results indicate that the BK channel possesses a novel module similar to the cytochrome c domains of hemoproteins, which may give rise to unique physiological functions for these widespread ion channels. Full article

Cold environments challenge the structural and functional integrity of membrane proteins, requiring specialized adaptations to maintain activity under low thermal energy. Here, we investigate the molecular basis of cold tolerance in the peptide transporter PepT1 from the Antarctic icefish (Chionodraco hamatus, ChPepT1) using molecular dynamics simulations, binding free energy calculations (MM/GBSA), and dynamic network analysis. We compare ChPepT1 to its human ortholog (hPepT1), a non-cold-adapted variant, to reveal key features enabling psychrophilic function. Our simulations show that ChPepT1 displays enhanced global flexibility, particularly in domains adjacent to the substrate-binding site and the C-terminal domain (CTD). While hPepT1 loses substrate binding affinity as temperature increases, ChPepT1 maintains stable peptide interactions across a broad thermal range. This thermodynamic buffering results from temperature-sensitive rearrangement of hydrogen bond networks and more dynamic lipid interactions. Importantly, we identify a temperature-responsive segment (TRS, residues 660–670) within the proximal CTD that undergoes an α-helix to coil transition, modulating long-range coupling with transmembrane helices. Dynamic cross-correlation analyses further suggest that ChPepT1, unlike hPepT1, reorganizes its interdomain communication in response to temperature shifts. Our findings suggest that cold tolerance in ChPepT1 arises from a combination of structural flexibility, resilient substrate binding, and temperature-sensitive interdomain dynamics. These results provide new mechanistic insight into thermal adaptation in membrane transporters and offer a framework for engineering proteins with enhanced functionality in extreme environments. Full article

Pangasius (Pangasianodon hypophthalmus) minced muscle with 1 and 2% salt was treated with different high-pressure processing and thermal methods, including conventional heat-induced gels (HIGs), high-pressure processing (HPP) prior to cooking (PC), HPP prior to setting (PS), and setting prior to HPP (SP), to evaluate for their effects on the selected physicochemical properties. The results showed that the PC treatment produced gels with a significantly higher gel strength (496.72–501.26 N·mm), hardness (9.62–10.14 N), and water-holding capacity (87.79–89.74%) compared to the HIG treatment, which showed a gel strength of 391.24 N·mm, a hardness of 7.36 N, and a water-holding capacity of 77.98%. PC gels also exhibited the typical microstructure of pressure-induced gels, with a denser and homogeneous microstructure compared to the rough and loosely connected structure of HIGs. In contrast, SP treatment exhibited the poorest gel quality in all parameters, with gel strength ranging from 319.79 to 338.34 N·mm, hardness from 5.87 to 6.31 N, and WHC from 71.91 to 73.72%. Meanwhile, the PS treatment showed a comparable gel quality to HIGs. SDS-PAGE analysis revealed protein degradation and aggregation in HPP-treated samples, with a decrease in the intensity of myosin heavy chains and actin bands. Fourier-transform infrared spectroscopy (FTIR) analysis showed minor shifts in protein secondary structures, with the PC treatment showing a significant increase in α-helices (28.09 ± 0.51%) and a decrease in random coil content (6.69 ± 0.92%) compared to α-helices (23.61 ± 0.83) and random coil structures (9.47 ± 1.48) in HIGs (p < 0.05). Only the PC treatment resulted in a significant reduction in total plate count (TPC) (1.51–1.58 log CFU/g) compared to 2.33 ± 0.33 log CFU/g in the HIG treatment. These findings suggest that HPP should be applied prior to thermal treatments (cooking or setting) to achieve an improved gel quality in reduced-salt pangasius products. Full article

Aggregation of tau protein is a hallmark feature of tauopathies such as Alzheimer’s disease. The microtubule-binding domain of tau plays a crucial role in the tau aggregation process. In this study, we investigated the dual effects of membrane interactions of tau_298–317, a fragment peptide from the microtubule-binding domain, on peptide-induced membrane disruption and membrane-mediated peptide self-assembly. Our results show that neither wild-type tau_298–317 nor its P301L or Ser305-phosphorylated mutants aggregate in the presence of zwitterionic POPC vesicles or cause lipid vesicle leakage, indicating weak peptide–membrane interactions. In contrast, tau_298–317 strongly interacts with negatively charged POPG liposomes, leading to a rapid transition of the peptide conformation from random coils to α-helical intermediate conformation upon membrane adsorption, which may further promote peptide self-association to form oligomers and β-sheet-rich fibrillar structures. Tau_298–317-induced rapid POPG membrane leakage indicates a synergistic process of the peptide self-assembly at the membrane interface and the aggregation-induced membrane disruption. Notably, phosphorylation at Ser305 disrupts favorable electrostatic interactions between the peptide and POPG membrane surface, thus preventing peptide aggregation and membrane leakage. In contrast, the P301L mutation significantly enhances membrane-mediated peptide aggregation and peptide-induced membrane disruption, likely due to alleviation of local conformational constraints and enhancement of local hydrophobicity, which facilitates fast conformational conversion to β-sheet structures. These findings provide mechanistic insights into the molecular mechanisms underlying membrane-mediated aggregation of crucial regions of tau and peptide-induced membrane damage, indicating potential strategies to prevent tau aggregation and membrane rupture by targeting critical electrostatic interactions between membranes and key local regions of tau. Full article

The increasing circulation of multi-drug-resistant pathogens, coupled with the sluggish development of new antibiotics, is weakening our capacity to combat human infections, resulting in elevated death tolls. To address this worldwide crisis, antimicrobial peptides (AMPs) are viewed as promising substitutes or adjuvants for combating bacterial infections caused by multidrug-resistant organisms. Here, the antimicrobial activity and structural characterization of a novel 13-amino acid cationic peptide named RKW (RKWILKWLRTWKK-NH2), designed based on known AMPs sequences and the identification of a key tryptophan-rich structural motif, were described. RKW displayed a broad-spectrum and potent antimicrobial and antibiofilm activity against Gram-positive and Gram-negative pathogens, including ESKAPE bacteria and fungi with minimal inhibitory concentrations (MBC) ranging from 5 µM to 20 μM. Structural results by fluorescence and Circular Dichroism (CD) spectroscopy revealed that the peptide was folded into a regular α-helical conformation in a membrane-like environment, remaining stable in a wide range of pH and temperature for at least 48 h of incubation. Furthermore, RKW showed low toxicity in vitro against mammalian fibroblast cells, indicating its potential as a promising candidate for the development of new antimicrobial or antiseptic strategies. Full article

Chemical communication is based on the release of chemical cues, including odorants, tastants and semiochemicals, which can be perceived by animals and trigger physiological and behavioral responses. These compounds exhibit a wide size and properties range, spanning from small volatile molecules to soluble proteins, and are perceived by various chemosensory receptors (CRs). The structure of these receptors is very well conserved across all organisms and within the family to which they belong, the G-protein-coupled receptor (GPCR) family. It is characterized by highly conserved seven-transmembrane (7TM) α-helices. However, the characteristics of these proteins and the methods used to study their structures are limiting factors for resolving their structures. Due to the importance of CRs—especially olfactory and taste receptors, responsible for two of our five basic senses—alternative methods are utilized to overcome these structural challenges. Indeed, in silico structural biology is an expanding field that is very useful for CR structural studies. Since the 1960s, many algorithms have been developed and improved in an attempt to resolve protein structure. We review the current knowledge regarding different vertebrate CRs in this study, with an emphasis on the in silico structural methods employed to improve our understanding of CR structures. Full article

Peptide-induced disruption of lipid membranes is central to both amyloid diseases and the activity of antimicrobial peptides. Here, we combine all-atom molecular dynamics simulations with biophysical experiments to investigate how four amphipathic peptides interact with lipid bilayers. All peptides adsorb on the membrane surface. Peptide M01 [Ac-(FKFE)₂-NH₂] self-assembles into $\beta$-sheet nanofibrils that span both leaflets of the membrane, creating water-permeable channels. The other three peptides adopt $\alpha$-helical structures at the water–lipid interface. Peptide M02 [Ac-FFKKFFEE-NH₂], a sequence isomer of M01, does not form $\beta$-sheet aggregates and is too short to span the bilayer, resulting in no observable water permeation across the membrane. Peptides M03 and M04 are $\alpha$-helical isomers long enough to span the bilayer, with a polar face that allows the penetration of water deep inside the membrane. For the M03 peptide [Ac-(FFKKFFEE)₂-NH₂], insertion into the bilayer starts with the nonpolar N-terminal amino acids penetrating the hydrophobic core of the bilayer, while electrostatic interactions hold negative residues at the C-terminus on the membrane surface. The M04 peptide, [Ac-FFKKFFEEFKKFFEEF-NH₂], is made by relocating a single nonpolar residue from the central region of M03 to the C-terminus. This nonpolar residue becomes unfavorably exposed to the solvent upon insertion of the N-terminal region of the peptide into the membrane. Consequently, higher concentrations of M04 peptides are required to induce water permeation compared to M03. Overall, our comparative analysis reveals how subtle rearrangements of polar and nonpolar residues modulate peptide-induced water permeation. This provides mechanistic insights relevant to amyloid pathology and antimicrobial peptide design. Full article

Nowadays, healthcare systems face two global challenges: the rise of multidrug-resistant pathogens and the growing incidence of cancer. Due to their broad spectrum of activities, antimicrobial peptides emerged as potential alternatives against both threats. Our group previously described the antifungal activity of the α-helical peptide Cm-p5, a derivative of the natural peptide Cm-p1, isolated from the coastal mollusk Cenchritis muricatus; however, its anti-cancer properties remained unexplored. Analyses through calorimetry and molecular dynamics simulations suggest the relevance of phosphatidylserine for the attachment of Cm-p5 to cancer cell membranes. Cm-p5 exhibited cytotoxic activity in a dose-dependent manner against A375 melanoma cells, without toxicity against non-malignant cells or hemolytic activity. DAPI/PI and DiSC3(5) staining confirmed permeabilization, disruption, and depolarization of A375 cytoplasmic membranes by Cm-p5. Furthermore, Annexin V-FITC/PI assay revealed the induction of cellular death in melanoma cells, which can result from the cumulative membrane damage and oxidative stress due to the overproduction of reactive oxygen species (ROS). Moreover, after the treatment, the proliferation of A375 cells was dampened for several days, suggesting that Cm-p5 might inhibit the recurrence of melanomas. These findings highlight the multifunctional nature of Cm-p5 and its potential for treating malignant melanoma. Full article

This review investigates the novel idea that proteins catalyze chemical reactions through conformational changes driven by energy derived from their collisions with water molecules. Recent studies have suggested that proteins in solution undergo constant deformation due to collisions with water molecules, generating potential energy that can be harnessed for catalytic functions. We detail the existing evidence supporting this idea, including how structures in proteins such as α-helices and β-sheets facilitate energy conversion, how conformational changes can affect the ways in which substrates attach, and how reactions occur. Combining information from computer-based methods—such as molecular dynamics simulations and machine learning models (e.g., AlphaFold)—we suggest a more complete model for understanding how proteins function beyond simply looking at their fixed shapes. This emerging view has implications for drug design, enzyme engineering, and our fundamental understanding of biological catalysis. Full article

We investigate the transport coefficients $\alpha$ and $\beta$ in plasma systems with varying Reynolds numbers while maintaining a unit magnetic Prandtl number (${Pr}_{\mathrm{M}}$). The $\alpha$ and $\beta$ tensors parameterize the turbulent electromotive force (EMF) in terms of the large-scale magnetic field $\overline{\mathbf{B}}$ and current density as follows: $⟨\mathbf{u}\times \mathbf{b}⟩=\alpha \overline{\mathbf{B}}-\beta \nabla \times \overline{\mathbf{B}}$. In astrophysical plasmas, high fluid Reynolds numbers ($Re$) and magnetic Reynolds numbers ($R{e}_{\mathrm{M}}$) drive turbulence, where $Re$ governs flow dynamics and $R{e}_{\mathrm{M}}$ controls magnetic field evolution. The coefficients ${\alpha }_{\mathrm{semi}}$ and ${\beta }_{\mathrm{semi}}$ are obtained from large-scale magnetic field data as estimates of the $\alpha$ and $\beta$ tensors, while ${\beta }_{\mathrm{theo}}$ is derived from turbulent kinetic energy data. The reconstructed large-scale field $\overline{B}$ agrees with simulations, confirming consistency among $\alpha$, $\beta$, and $\overline{B}$ in weakly nonlinear regimes. This highlights the need to incorporate magnetic effects under strong nonlinearity. To clarify $\alpha$ and $\beta$, we introduce a field structure model, identifying $\alpha$ as the electrodynamic induction effect and $\beta$ as the fluid-like diffusion effect. The agreement between our method and direct simulations suggests that plasma turbulence and magnetic interactions can be analyzed using fundamental physical quantities. Moreover, ${\alpha }_{\mathrm{semi}}$ and ${\beta }_{\mathrm{semi}}$, which successfully reproduce the numerically obtained magnetic field, provide a benchmark for future theoretical studies. Full article

Regulating the innate immune response against infections, particularly drug-resistant bacteria, is a key focus in anti-infection therapy. Cathelicidins, found in vertebrates, are crucial for pathogen resistance. Few studies have explored gecko cathelicidins’ anti-infection properties. Recently, five new cathelicidins (Gj-CATH1-5) were identified in Gekko japonicus. The peptide Gj-CATH5, from G. japonicus, shows promise against Pseudomonas aeruginosa through various mechanisms. This study examined Gj-CATH5’s protective effects using in vitro and in vivo models, finding that it significantly reduced bacterial load in a mouse infection model when administered before or shortly after infection. Flow cytometry and the plate counting method showed that Gj-CATH5 boosts neutrophil and macrophage activity, enhancing chemotaxis, phagocytosis, and bactericidal functions. Gj-CATH5 increases ROS production, MPO activity, and NET formation, aiding pathogen clearance. Its amphipathic α-helical structure supports broad-spectrum bactericidal activity (MBC: 4–8 μg/mL) against Gram-negative and antibiotic-resistant bacteria. Gj-CATH5 is minimally cytotoxic (<8% hemolysis at 200 μg/mL) and preserves cell viability at therapeutic levels. These results highlight Gj-CATH5’s dual role in pathogen elimination and immune modulation, offering a promising approach to combat multidrug-resistant infections while reducing inflammation. This study enhances the understanding of reptilian cathelicidins and lays the groundwork for peptide-based immune therapies against difficult bacterial infections. Full article

Iron deficiency is a global health issue, making the development of novel iron supplements to enhance iron absorption critically important. In this study, low molecular weight donkey-hide gelatin peptides (LMW DHGP) were enzymatically hydrolyzed from donkey-hide gelatin. Experimental results demonstrated that the iron chelating capacity of LMW DHGP reached 249.98 μg/mg. Key amino acids (Asn, Gly, Cys, Lys) may participate in chelation. Scanning electron microscopy (SEM) and X-ray diffraction (XRD) analysis showed rough, porous amorphous structures of LMW DHGP-iron complexes. The results of circular dichroism spectroscopy (CD) indicated that the self-assembly of LMW DHGP-iron complexes appears to be primarily mediated by peptide α-helical structural conformations. Fourier transform infrared (FTIR) spectroscopy further indicated that the interaction between LWM DHGP and Fe²⁺ likely occurs through carboxyl and amino functional groups. In vitro digestion stability studies demonstrated that LMW DHGP-iron complexes exhibited superior iron ion solubility compared to FeSO₄ in simulated gastrointestinal conditions. PGPAG-iron complexes exhibited the highest antioxidant activity, with scavenging rates of 71.64% (DPPH radical) and 88.79% (ABTS radical). These findings collectively suggest that LMW DHGP-iron complexes possess significant potential as a novel iron supplement in food applications, which provides valuable theoretical insights for the development of innovative iron supplementation strategies. Full article