Search Results (2,253)

Collagen possesses distinctive chemical properties and biological functions due to its unique triple helix structure. However, recombinant collagen expressed in Escherichia coli without post-translational modifications such as hydroxylation lacks full function since hydroxylation is considered to be critical to the stability of the collagen triple-helix at body temperature. Here, a proline-deficient E. coli strain was constructed and employed to prepare hydroxylated recombinant collagens by incorporating proline (Pro) and hydroxyproline (Hyp) from the culture medium. By controlling the ratio of Pro to Hyp in the culture medium, collagen with different degrees of hydroxylation (0–88%) can be obtained. When the ratio of Pro and Hyp was adjusted to 12:8 mM, the proline hydroxylation rate of recombinant human collagen (rhCol, 55 kDa) ranged from 40–50%, which was also the degree of natural collagen. After proline hydroxylation, both the thermal stability and cell binding of rhCol were significantly enhanced. Notably, when the hydroxylation rate approached that of native human collagen (40–50%), the improvements were most pronounced. Moreover, the cell binding of rhCol with a hydroxylation rate of 43% increased by 29%, and the melting temperature (Tm) rose by 5 °C compared to the non-hydroxylated rhCol. The system achieved a yield of 1.186 g/L of rhCol by batch-fed in a 7 L fermenter. This innovative technology is expected to drive the development and application of collagen-related biomaterials with significant application value in the fields of tissue engineering, regenerative medicine, and biopharmaceuticals. Full article

The investigation of the central and external zones of ten industrial and artisanal Maroilles cheeses showed differences in their physicochemical parameters, namely fat, pH, moisture content, ash, and color. This difference significantly impacted the rheological properties of the investigated cheeses, which depended on the protein network englobing lipid and water and its interaction with the other components. Overall, Maroilles cheeses had an elastic-like behavior, with the central zones exhibiting the greatest viscoelastic modules (G′ and G″). The mid-infrared (MIR) spectra highlighted the presence of lipids, proteins, and sugars. A significant difference in α-helix and β-sheet levels in the central zones was noted between artisanal and industrial Maroilles cheeses. It is suggested that the difference between artisanal and industrial Maroilles cheeses observed at the macroscopic level, due to the cheese-making procedure and ripening stage, affects the structure at the molecular level, which can be determined by MIR spectroscopy. This trend was confirmed by the FDA when applied to the MIR spectra, since 96.67% correct classification was noted between artisanal and industrial cheeses. The present study indicates that MIR spectroscopy can be used successfully to study Maroilles cheese samples belonging to different production chains. Full article

The duocarmycin family is a group of potent cytotoxic agents originally isolated from the bacterium Streptomyces. This discovery has spurred significant interest due to duocarmycins’ unique chemical structures and powerful mechanism of action. This review comprehensively details the history of the duocarmycin family, the current understanding of their therapeutic potential, and the major clinical trials that have been conducted. Chemically, the duocarmycin family is characterized by a DNA-binding unit that confers specificity, a subunit-linking amide that positions the molecule within the DNA helix, and an alkylating unit that interacts with the DNA. This configuration allows them to bind selectively to the minor groove of DNA and alkylate adenine bases, a notable deviation from the more common guanine targeting performed by other alkylating agents. Duocarmycin’s mechanism of action involves the formation of covalent adducts with DNA, leading to the disruption of the DNA architecture and subsequent inhibition of replication and transcription. Recent advancements in drug delivery systems, such as antibody–drug conjugates (ADCs), have further elevated the therapeutic prospects of duocarmycin analogs by providing a promising mechanism for enhancing intracellular concentrations and selective tumor delivery. Preclinical studies have highlighted the efficacy of duocarmycin derivatives in various in vitro models, providing a strong foundation for translational research. However, further biological research is required to fully understand the toxicology of duocarmycin family members before it can be clinically relevant. The major focus of this review is to cache the major biologically relevant findings of different duocarmycin analogs as well as their biological shortcomings to propose next steps in the field of cancer therapy with these potent therapeutics. Full article

The effect of resveratrol (RESV) on α-lactalbumin (α-LA) thermal stability was evaluated using differential scanning calorimetry (DSC), circular dichroism (CD) and dynamic light scattering (DLS) measurements. Complementary information offered by molecular docking served to identify the binding site of the ligand on the native structure of protein and the type of interacting forces. DSC thermograms revealed a double-endotherm pattern with partial overlapping of the two components. The most relevant effect of RESV is manifested in the narrowing of the protein thermal fingerprint: the first process (peak temperature T₁) is shifted to higher temperatures while the second one (peak temperature T₂) to lower values. The CD data indicated partial conformational changes in the protein non-α-helix domain at T₁, resulting in a β-sheet richer intermediate (BSRI) with an unaffected, native-like α-helix backbone. The RESV influence on this process may be defined as slightly demoting, at least within DSC conditions (linear heating rate of 1 K min⁻¹). On further heating, unfolding of the α-helix domain takes place at T₂, with RESV acting as a promoter of the process. Long time incubation at 333 K produced the same type of BSRI: no significant effect of RESV on the secondary structure content was detected by CD spectroscopy. Nevertheless, the size distribution of the protein population obtained from DLS measurements revealed the free (non-bound) RESV action manifested in the developing of larger size aggregates. Full article

As with all new fields of discovery, work on the biological role of G-quadruplexes (GQs) has produced a number of results that at first glance are quite baffling, sometimes because they do not fit well together, but mostly because they are different from commonly held expectations. Like other classes of flipons, those that form G-quadruplexes have a repeat sequence motif that enables the fold. The canonical DNA motif (G₃N_1–7)₃G₃, where N is any nucleotide and G is guanine, is a feature that is under active selection in avian and mammalian genomes. The involvement of G-flipons in genome maintenance traces back to the invertebrate Caenorhabditis elegans and to ancient DNA repair pathways. The role of GQs in transcription is supported by the observation that yeast Rap1 protein binds both B-DNA, in a sequence-specific manner, and GQs, in a structure-specific manner, through the same helix. Other sequence-specific transcription factors (TFs) also engage both conformations to actuate cellular transactions. Noncoding RNAs can also modulate GQ formation in a sequence-specific manner and engage the same cellular machinery as localized by TFs, linking the ancient RNA world with the modern protein world. The coevolution of noncoding RNAs and sequence-specific proteins is supported by studies of early embryonic development, where the transient formation of G-quadruplexes coordinates the epigenetic specification of cell fate. Full article

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics of calcium, membranes, hyperstructures, and networks, are based on physical and physico-chemical concepts such as ion condensation, phase transition, crowding, liquid crystal immiscibility, collective vibrational modes, reptation, and water availability. I draw on ideas from subjects such as the ‘prebiotic ecology’ and phenotypic diversity to help with the hunt. Given the fundamental nature of the snark, I would expect that its capture would make sense of other parts of biology. The route, therefore, followed by the hunt has involved trying to answer questions like “why do cells replicate their DNA?”, “why is DNA replication semi-conservative?”, “why is DNA a double helix?”, “why do cells divide?”, “is cell division a spandrel?”, and “how are catabolism and anabolism balanced?”. Here, I propose some relatively unexplored, experimental approaches to testing snark-related hypotheses and, finally, I propose some possibly original ideas about DNA packing, about phase separations, and about computing with populations of virtual bacteria. Full article

Carotenoids are important natural pigments that are responsible for the fruit and flower colors of many plants. The composition and content of carotenoid can greatly influence the color phenotype of plants. However, the regulatory mechanism underling the divergent behaviors of carotenoid accumulation, especially in flower, remains unclear. In this study, a new cultivar Osmanthus fragrans ‘Yanzhi Hong’ was used to study the regulation of carotenoid pigmentation in flower. Liquid chromatograph–mass spectrometer (LC-MS) analysis showed that β-carotene, phytoene, lycopene, γ-carotene, and lutein were the top five pigments enriched in the petals of ‘Yanzhi Hong’. Through transcriptome analysis, we found that the expression of the structural genes in carotenoid pathway was imbalanced: most of the structural genes responsible for lycopene biosynthesis were highly expressed throughout the flower developmental stages, while those for lycopene metabolism kept at a relatively lower level. The downregulation of LYCE, especially at the late developmental stages, suppressed the conversion from lycopene to α-carotene but promoted the accumulation of β-carotene, which had great effect on the carotenoid composition of ‘Yanzhi Hong’. Ethylene response factor (ERF), WRKY, basic helix-loop-helix (bHLH), v-myb avian myeloblastosis viral oncogene homolog (MYB), N-Acetylcysteine (NAC), auxin response factor (ARF), and other transcription factors (TFs) have participated in the flower color regulation of ‘Yanzhi Hong’, which formed co-expression networks with the structural genes and functioned in multiple links of the carotenoid pathway. The results suggested that the cyclization of lycopene is a key link in determining flower color. The modification of the related TFs will break the expression balance between the upstream and downstream genes and greatly influence the carotenoid profile in flowers, which can be further used for creating colorful plant germplasms. Full article

A feasibility study on the compensation of 3D mispositioning errors of the probe occurring in the characterization of a long antenna, via a non-redundant (NR) near to far-field (NTFF) transformation with helicoidal scan, is conducted in this article. Such types of errors can result from imperfections in the rail driving the linear motion of the probe and from an imprecise synchronization of the linear and rotational movements of the probe and the antenna when drawing the scan helix. To correct them, an approach, which proceeds through two steps, is proposed. The former step uses a technique called cylindo rical wave (CW) correction for compensating the phase of the near-field (NF) samples, which, owing to the rail imperfections, result in not being acquired over the measurement cylinder surface. The latter exploits an iterative scheme to restore the samples at the sampling points required by the adopted NR representation along the scan helix from those obtained by applying the CW correction technique and impaired by 2D mispositioning errors. The so compensated NF samples are then effectively recovered via a 2D optimal sampling interpolation (OSI) scheme to accurately obtain the input data required to carry out the standard cylindrical NTFF transformation. The OSI representation is determined here by assuming a long antenna under test as enclosed in a prolate ellipsoid or cylinder ending into two hemispheres (cigar) in order to make, depending on the particular geometry of the considered antenna, the representation effectively non-redundant. The reported numerical simulation results show the capability of the proposed approach to compensate even severe 3D mispositioning errors, thus enabling its usage in a real measurement scenario. Full article

HMGR (3-hydroxy-3-methylglutaryl-CoA reductase) plays a crucial role as the first rate-limiting enzyme in the mevalonate (MVA) pathway, which is the upstream pathway of natural rubber biosynthesis. In this study, we carried out whole-genome identification of Taraxacum kok-saghyz (TKS), a novel rubber-producing alternative plant, and obtained six members of the TkHMGR genes. Bioinformatic analyses were performed including gene structure, protein properties, chromosomal localization, evolutionary relationships, and cis-acting element analyses. The results showed that HMGR genes were highly conserved during evolution with a complete HMG-CoA reductase conserved domain and were closely related to Asteraceae plants during the evolutionary process. The α-helix is the most prominent feature of the secondary structure of the TkHMGR proteins. Collinearity analyses demonstrated that a whole-genome duplication (WGD) event and tandem duplication event play a key role in the expansion of this family and TkHMGR1 and TkHMGR6 have more homologous gene between other species. Cis-acting element analysis revealed that the TkHMGR gene family had a higher number of MYB-related, light-responsive, hormone-responsive elements. In addition, we investigated the expression patterns of family members induced by ethylene (ETH) and methyl jasmonate (MeJA), and their expression levels at different stages of T. kok-saghyz root development. Finally, subcellular localization results showed that six TkHMGR members were all located in the endoplasmic reticulum. In conclusion, the results of our study lay a certain theoretical basis for the subsequent improvement of rubber yield, molecular breeding of rubber-producing plants, and genetic improvement of T. kok-saghyz. Full article

This study identified a salt-tolerant GH11 xylanase, Xyn^st, which was isolated from a soil bacterium Bacillus sp. SC1 and can resist as high as 4 M NaCl. After rational design and high-throughput screening of site-directed mutant libraries, a double mutant W6F/Q7H with a 244% increase in catalytic activity and a 10 °C increment in optimal temperature was obtained. Both Xyn^st and W6F/Q7H xylanases were stimulated by high concentrations of salts. In particular, the activity of W6F/Q7H was more than eight times that of Xyn^st in the presence of 2 M NaCl at 65 °C. Kinetic parameters indicated they have the highest affinity for beechwood xylan (K_m = 0.30 mg mL⁻¹ for Xyn^st and 0.18 mg mL⁻¹ for W6F/Q7H), and W6F/Q7H has very high catalytic efficiency (K_cat/K_m = 15483.33 mL mg⁻¹ s⁻¹). Molecular dynamic simulation suggested that W6F/Q7H has a more compact overall structure, improved rigidity of the active pocket edge, and a flexible upper-end alpha helix. Hydrolysis of different xylans by W6F/Q7H released more xylooligosaccharides and yielded higher proportions of xylobiose and xylotriose than Xyn^st did. The conversion efficiencies of Xyn^st and W6F/Q7H on all tested xylans exceeded 20%, suggesting potential applications in the agricultural and food industries. Full article

During the axial modification in helical gear form grinding, the contact line between the grinding wheel and the gear constantly changes, and the additional radial motion can cause a “tooth surface twist” phenomenon. An optimization method for tooth surface twist error was proposed to address this. Based on the gear meshing principles, a mathematical model for axial modification in form grinding was established to solve for the instantaneous contact lines at various positions on the actual modified tooth surface. By analyzing the influence of the grinding wheel installation angle on the axial modification contact line, an optimization model was constructed to reduce the twist of the transverse profile, reduce the twist of the flank profile, reduce the helix deviation, and improve the form grinding efficiency. The practical implications of this research are significant, as the Particle Swarm Optimization (PSO) algorithm was employed to optimize the form grinding parameters, leading to a method that effectively reduced tooth surface twist error and improved the form grinding accuracy of the modified tooth surface. Full article

Polyphenol oxidase (PPO) plays a key role in the enzymatic browning process, and this study employed Gaussian-accelerated molecular dynamics (GaMD) simulations to investigate the catalytic efficiency mechanisms of lotus root PPO with different substrates, including catechin, epicatechin, and chlorogenic acid, as well as the inhibitor oxalic acid. Key findings reveal significant conformational changes in PPO that correlate with its enzymatic activity. Upon substrate binding, the alpha-helix in the Q53-D63 region near the copper ion extends, likely stabilizing the active site and enhancing catalysis. In contrast, this helix is disrupted in the presence of the inhibitor, resulting in a decrease in enzymatic efficiency. Additionally, the F350-V378 region, which covers the substrate-binding site, forms an alpha-helix upon substrate binding, further stabilizing the substrate and promoting catalytic function. However, this alpha-helix does not form when the inhibitor is bound, destabilizing the binding site and contributing to inhibition. These findings offer new insights into the substrate-specific and inhibitor-induced structural dynamics of lotus root PPO, providing valuable information for enhancing food processing and preservation techniques. Full article

This research identified a marine fungal isolate, Aspergillus sp. strain GAD7, which produces an acidic and sulfated extracellular polysaccharide (EPS) with notable anticoagulant and antioxidant properties. Six fungal strains from the Egyptian Mediterranean Sea were screened for EPS production, with Aspergillus sp. strain GAD7 (EPS-AG7) being the most potent, yielding ~5.19 ± 0.017 g/L. EPS-AG7 was characterized using UV-Vis and FTIR analyses, revealing high carbohydrate (87.5%) and sulfate (24%) contents. HPLC and GC-MS analyses determined that EPS-AG7 is a heterogeneous acidic polysaccharide with an average molecular weight $(\overline{Mw})$ of ~7.34 × 10³ Da, composed of mannose, glucose, arabinose, galacturonic acid, galactose, and lyxose in a molar ratio of 6.6:3.9:1.8:1.3:1.1:1.0, linked through α- and β-glycosidic linkages as confirmed by NMR analysis. EPS-AG7 adopted a triple helix-like conformation, as evidenced by UV-Vis (Congo Red experiment) and circular dichroism (CD) studies. This helical arrangement demonstrated stability under various experimental conditions, including concentration, ionic strength, temperature, and lipid interactions. EPS-AG7 exhibited significant anticoagulant activity, doubling blood coagulation time at a concentration of 3.0 mg/mL, and showed significant antioxidant activity, with scavenging activities reaching up to 85.90% and 58.64% in DPPH and ABTS⁺ assays at 5.0 mg/mL, and EC50 values of 1.40 mg/mL and 3.80 mg/mL, respectively. These findings highlight the potential of EPS-AG7 for therapeutic applications due to its potent biological activities. Full article

Solenaia oleivora, a rare freshwater shellfish with high protein quality, is unique to China. However, the poor hydrosolubility and functional properties of Solenaia oleivora proteins hinder their utilization in food products. Herein, the alkaline dissolution-isoelectric precipitation method was used for the extraction of Solenaia oleivora proteins. Furthermore, the impact of high-pressure homogenization (HPH) treatment varying from 0 to 100 MPa on the structure and functional properties of Solenaia oleivora proteins was investigated. The obtained results indicated that HPH treatment decreased the α-helix content and enhanced the β-sheet and random coil content. Furthermore, the HPH caused the unfolding of protein structure, exposing aromatic amino acids, increasing the free thiol group content, and enhancing surface hydrophobicity. As the homogenization pressure increased from 0 to 100 MPa, the particle size of Solenaia oleivora proteins decreased from 899 to 197 nm with the polymer dispersity index (PDI) value decreased from 0.418 to 0.151, the ζ-potential increased from −22.82 to −43.26 mV, and the solubility increased from 9.54% to 89.96%. Owing to the significant changes in protein structure and solubility, the emulsifying, foaming, and digestive properties of Solenaia oleivora proteins have been significantly improved after treatment with HPH. Full article

The human cytomegalovirus (HCMV) glycoprotein B (gB) is the viral fusogen required for entry into cells and for direct cell-to-cell spread of the virus. We have previously demonstrated that the exchange of the carboxy-terminal domain (CTD) of gB for the CTD of the structurally related fusion protein G of the vesicular stomatitis virus (VSV-G) resulted in an intrinsically fusion-active gB variant (gB/VSV-G). In this present study, we employed a dual split protein (DSP)-based cell fusion assay to further characterize the determinants of fusion activity in the CTD of gB. We generated a comprehensive library of gB CTD truncation mutants and identified two mutants, gB-787 and gB-807, which were fusion-competent and induced the formation of multinucleated cell syncytia in the absence of other HCMV proteins. Structural modeling coupled with site-directed mutagenesis revealed that gB fusion activity is primarily mediated by the CTD helix 2, and secondarily by the recruitment of cellular SH2/WW-domain-containing proteins. The fusion activity of gB-807 was inhibited by gB-specific monoclonal antibodies (MAbs) targeting the antigenic domains AD-1 to AD-5 within the ectodomain and not restricted to MAbs directed against AD-4 and AD-5 as observed for gB/VSV-G. This finding suggested a differential regulation of the fusion-active conformational state of both gB variants. Collectively, our findings underscore a pivotal role of the CTD in regulating the fusogenicity of HCMV gB, with important implications for understanding the conformations of gB that facilitate membrane fusion, including antigenic structures that could be targeted by antibodies to block this essential step in HCMV infection. Full article