Search Results (15)

A versatile and robust procedure is developed that allows the identification of individual target molecules using antibodies bound to a DeepTip^TM functionalized atomic-force microscopy probe. The model system used for the validation of this process consists of a biotinylated anti-lactate dehydrogenase antibody immobilized on a streptavidin-decorated AFM probe. Lactate dehydrogenase (LDH) is employed as target molecule and covalently immobilized on functionalized MicroDeck^TM substrates. The interaction between sensor and target molecules is explored by recording force–displacement (F–z) curves with an atomic-force microscope. F–z curves that correspond to the genuine sensor–target molecule interaction are identified based on the following three criteria: (i) number of peaks, (ii) value of the adhesion force, and (iii) presence or absence of the elastomeric trait. The application of these criteria leads to establishing seven groups, ranging from no interaction to multiple sensor–target molecule interactions, for which force–displacement curves are classified. The possibility of recording consistently single-molecule interaction events between an antibody and its specific antigen, in combination with the high proportion of successful interaction events obtained, increases remarkably the possibilities offered by affinity atomic-force microscopy for the characterization of biological and biomimetic systems from the molecular to the tissue scales. Full article

Proteins in the crowded environment of human cells have often been studied regarding nonspecific interactions, misfolding, and aggregation, which may cause cellular malfunction and disease. Specifically, proteins with high abundance are more susceptible to these issues due to the law of mass action. Therefore, the surfaces of highly abundant cytoplasmic (HAC) proteins directly exposed to the environment can exhibit specific physicochemical, structural, and geometrical characteristics that reduce nonspecific interactions and adapt to the environment. However, the quantitative relationships between the overall surface descriptors still need clarification. Here, we used machine learning to identify HAC proteins using hydrophobicity, charge, roughness, secondary structures, and B-factor from the protein surfaces and quantified the contribution of each descriptor. First, several supervised learning algorithms were compared to solve binary classification problems for the surfaces of HAC and extracellular proteins. Then, logistic regression was used for the feature importance analysis of descriptors considering model performance (80.2% accuracy and 87.6% AUC) and interpretability. The HAC proteins showed positive correlations with negatively and positively charged areas but negative correlations with hydrophobicity, the B-factor, the proportion of beta structures, roughness, and the proportion of disordered regions. Finally, the details of each descriptor could be explained concerning adaptative surface strategies of HAC proteins to regulate nonspecific interactions, protein folding, flexibility, stability, and adsorption. This study presented a novel approach using various surface descriptors to identify HAC proteins and provided quantitative design rules for the surfaces well-suited to human cellular crowded environments. Full article

Cutinase from Fusarium solani pisi is an enzyme that bridges functional properties between lipases and esterases, with applications in detergents, food processing, and the synthesis of fine chemicals. The purification procedure of recombinant cutinase from E. coil extracts is a well-established but time-consuming process, which involves a sequence of two anionic exchange chromatography steps followed by dialysis. Affinity chromatography is the most efficient method for protein purification, the major limitation of its use being often the availability of a ligand selective for a given target protein. Synthetic affinity ligands that specifically recognize certain sites on the surface of proteins are highly desirable for affinity processes due to their cost-effectiveness, durability, and reusability across multiple cycles. Additionally, these ligands establish moderate affinity interactions with the target protein, making it possible to purify proteins under gentle conditions while maintaining high levels of activity recovery. This study aimed to develop a new method for purifying cutinase, utilizing triazine-scaffolded biomimetic affinity ligands. These ligands were previously screened from a biased-combinatorial library to ensure their binding ability to cutinase without compromising its biological function. A lead ligand, designated as 11/3′, [4-({4-chloro-6-[(2-methylbutyl)amino]-1,3,5-triazin-2-yl}amino)benzoic acid], was chosen and directly synthesized onto agarose. Experiments conducted at different scales demonstrated that this ligand (with an affinity constant K_a ≈ 10⁴ M⁻¹) exhibited selectivity towards cutinase, enabling the purification of the enzyme from an E. coli crude production medium in a single step. Under optimized conditions, the protein and activity yields reached 25% and 90%, respectively, with a resulting cutinase purity of 85%. Full article

The occurrence of bone disorders is steadily increasing worldwide. Bone tissue engineering (BTE) has emerged as a promising alternative to conventional treatments of bone defects, developing bone scaffolds capable of promoting bone regeneration. In this research, biomimetic scaffolds based on ion-substituted calcium phosphates, derived from cuttlefish bone, were prepared using a hydrothermal method. To synthesize Mn²⁺-substituted scaffolds, three different manganese concentrations (corresponding to 1, 2.5, and 5 mol% Mn substitutions for Ca into hydroxyapatite) were used. Also, syntheses with the simultaneous addition of an equimolar amount (1 mol%) of two (Mg²⁺ and Sr²⁺) or three ions (Mn²⁺, Mg²⁺, and Sr²⁺) were performed. A chemical, structural, and morphological characterization was carried out using X-ray diffraction, Fourier transform infrared spectroscopy, and scanning electron microscopy. The effects of the ion substitutions on the lattice parameters, crystallite sizes, and fractions of the detected phases were discussed. Multi-substituted (Mn²⁺, Mg²⁺, and Sr²⁺) scaffolds were coated with polycaprolactone (PCL) using simple vacuum impregnation. The differentiation of human mesenchymal stem cells (hMSCs), cultured on the PCL-coated scaffold, was evaluated using histology, immunohistochemistry, and reverse transcription–quantitative polymerase chain reaction analyses. The expression of collagen I, alkaline phosphatase, and dentin matrix protein 1 was detected. The influence of PCL coating on hMSCs behavior is discussed. Full article

Biomineralization peptides are versatile tools for generating nanostructures since they can make specific interactions with various inorganic metals, which can lead to the formation of intricate nanostructures. Previously, we examined the influence that multivalency has on inorganic structures formed by p53 tetramer-based biomineralization peptides and noted a connection between the geometry of the peptide and its ability to regulate nanostructure formation. To investigate the role of multivalency in nanostructure formation by biomineralization peptides more thoroughly, silver biomineralization peptides were engineered by linking them to additional self-assembling molecules based on coiled-coil peptides and multistranded DNA oligomers. Under mild reducing conditions at room temperature, these engineered biomineralization peptides self-assembled and formed silver nanostructures. The trimeric forms of the biomineralization peptides were the most efficient in forming a hexagonal disk nanostructure, with both the coiled-coil peptide and DNA-based multimeric forms. Together, the results suggest that the spatial arrangement of biomineralization peptides plays a more important role in regulating nanostructure formation than their valency. Full article

The interaction between the plant lipid transfer protein Pru p 3 and phytosphingosine was assessed using an atomic force microscope. Phytosphingosine was covalently immobilized on DeepTip^TM probes and Pru p 3 on MicroDeck^TM functionalized substrates. Single-molecular interaction events between both molecules were retrieved and classified and the distribution for each one of the identified types was calculated. A success rate of over 70% was found by comparing the number of specific Pru p 3-phytosphingosine interaction events with the total number of recorded curves. The analysis of the distribution established among the various types of curves was further pursued to distinguish between those curves that can mainly be used for assessing the recognition between phytosphingosine (sensor molecule) and Pru p 3 (target molecule) in the context of affinity atomic force microscopy, and those that entail details of the interaction and might be employed in the context of force spectroscopy. The successful application of these functionalized probes and substrates to the characterization of the low-intensity hydrophobic interaction characteristic of this system is a clear indication of the potential of exploiting this approach with an extremely wide range of different biological molecules of interest. The possibility of characterizing molecular assembly events with single-molecule resolution offers an advantageous procedure to plough into the field of molecular biomimetics. Full article

Biomimetics, which are similar to natural compounds that play an important role in the metabolism, manifestation of functional activity and reproduction of various fungi, have a pronounced attraction in the current search for new effective antifungals. Actual trends in the development of this area of research indicate that unnatural amino acids can be used as such biomimetics, including those containing halogen atoms; compounds similar to nitrogenous bases embedded in the nucleic acids synthesized by fungi; peptides imitating fungal analogs; molecules similar to natural substrates of numerous fungal enzymes and quorum-sensing signaling molecules of fungi and yeast, etc. Most parts of this review are devoted to the analysis of semi-synthetic and synthetic antifungal peptides and their targets of action. This review is aimed at combining and systematizing the current scientific information accumulating in this area of research, developing various antifungals with an assessment of the effectiveness of the created biomimetics and the possibility of combining them with other antimicrobial substances to reduce cell resistance and improve antifungal effects. Full article

Since the proposal of the brainstem axis theory, increasing research attention has been paid to the interactions between bacterial amyloids produced by intestinal flora and the amyloid β−protein (Aβ) related to Alzheimer’s disease (AD), and it has been considered as the possible cause of AD. Therefore, phenol−soluble modulin (PSM) α3, the most virulent protein secreted by Staphylococcus aureus, has attracted much attention. In this work, the effect of PSMα3 with a unique cross−α fibril architecture on the aggregation of pathogenic Aβ₄₀ of AD was studied by extensive biophysical characterizations. The results proposed that the PSMα3 monomer inhibited the aggregation of Aβ₄₀ in a concentration−dependent manner and changed the aggregation pathway to form granular aggregates. However, PSMα3 oligomers promoted the generation of the β−sheet structure, thus shortening the lag phase of Aβ₄₀ aggregation. Moreover, the higher the cross−α content of PSMα3, the stronger the effect of the promotion, indicating that the cross−α structure of PSMα3 plays a crucial role in the aggregation of Aβ₄₀. Further molecular dynamics (MD) simulations have shown that the Met1−Gly20 region in the PSMα3 monomer can be combined with the Asp1−Ala2 and His13−Val36 regions in the Aβ₄₀ monomer by hydrophobic and electrostatic interactions, which prevents the conformational conversion of Aβ₄₀ from the α−helix to β−sheet structure. By contrast, PSMα3 oligomers mainly combined with the central hydrophobic core (CHC) and the C−terminal region of the Aβ₄₀ monomer by weak H−bonding and hydrophobic interactions, which could not inhibit the transition to the β−sheet structure in the aggregation pathway. Thus, the research has unraveled molecular interactions between Aβ₄₀ and PSMα3 of different structures and provided a deeper understanding of the complex interactions between bacterial amyloids and AD−related pathogenic Aβ. Full article

Reactive oxygen species are implicated in several human diseases, including neurodegenerative disorders, cardiovascular dysfunction, inflammation, hereditary diseases, and ageing. Mn^III–salen complexes are superoxide dismutase (SOD) and catalase (CAT) mimetics, which have shown beneficial effects in various models for oxidative stress. These properties make them well-suited as potential therapeutic agents for oxidative stress diseases. Here, we report the synthesis of the novel glycoconjugates of salen complex, EUK-108, with glucose and galactose. We found that the complexes showed a SOD-like activity higher than EUK-108, as well as peroxidase and catalase activities. We also investigated the conjugate activities in the presence of Ricinus communis agglutinin (RCA₁₂₀) lectin. The hybrid protein–galactose–EUK-108 system showed an increased SOD-like activity similar to the native SOD1. Full article

Tuberculosis, caused by Mycobacterium tuberculosis, is a lethal infectious disease of significant public health concern. The rise of multidrug-resistant and drug-tolerant strains has necessitated novel approaches to combat the disease. Toxin–antitoxin (TA) systems, key players in bacterial adaptive responses, are prevalent in prokaryotic genomes and have been linked to tuberculosis. The genome of M. tuberculosis strains harbors an unusually high number of TA systems, prompting questions about their biological roles. The VapBC family, a representative type II TA system, is characterized by the VapC toxin, featuring a PilT N-terminal domain with nuclease activity. Its counterpart, VapB, functions as an antitoxin, inhibiting VapC’s activity. Additionally, we explore peptide mimics designed to replicate protein helical structures in this review. Investigating these synthetic peptides offers fresh insights into molecular interactions, potentially leading to therapeutic applications. These synthetic peptides show promise as versatile tools for modulating cellular processes and protein–protein interactions. We examine the rational design strategies employed to mimic helical motifs, their biophysical properties, and potential applications in drug development and bioengineering. This review aims to provide an in-depth understanding of TA systems by introducing known complex structures, with a focus on both structural aspects and functional and molecular details associated with each system. Full article

The reaction condition for purifying carbonic anhydrase from Sulfurihydrogenibium yellowstonense (SspCA) by direct heating without prior cell lysis was optimized; heating at 70 °C for 5 min resulted in the highest total activity of 23,460 WAU (Wilbur–Anderson unit) from a 50 mL culture. Heat-purified SspCA was examined for its capability to increase the rate of the mineralization of CO₂; compared with an uncatalyzed control, the onset time of CaCO₃ formation was shortened by up to 71%. Cyanase can be used to degrade toxic cyanate; however, one of the limitations of this biomimetic process is that the reaction needs HCO₃⁻ as a substrate. Heat-purified SspCA was combined with heat-purified cyanase from Thermomyces lanuginosus to alleviate the HCO₃⁻ dependence; in industrial wastewater, the HCO₃⁻ required was reduced by 50% when 0.75 WAU of SspCA was added. Heat-purified SspCA is stable at 4 °C; 88% of the initial activity was retained for up to five weeks. Partially purified SspCA can be obtained with ease and applied to a variety of applications. Full article

Amphotericin B has been an essential drug in the fight against leishmaniasis and fungal pathogens for decades, and has more recently gained attention for the very limited microbial resistance displayed against it. However, its toxicity has restricted its use to only the most severe cases of disease, and attempts to reduce these ill effects via formulation have had only minor success. Genetic engineering has allowed the development of superior amphotericin analogues, notably 16-descarboxyl-16-methyl amphotericin B (MeAmB), which shows a ten-fold reduction in toxicity in addition to a slight improvement in therapeutic activity. However, MeAmB is difficult to extract from its bacterial source and purify. Presented here is an alternative method of MeAmB purification. A biomimetic polymer with a high affinity for MeAmB was designed via computational modelling and synthesised. Prepared as a separation column, the polymer was able to retain the target MeAmB whilst allowing the removal of cell debris from the bacterial extract. Starting with a simple bacterial extract, the relatively simple process allowed the purification of an MeAmB salt complex at approximately 70% MeAmB, and likely higher purification from further extraction. The mean MeAmB recovery between the pre-purification extract sample and the final product was 81%. This is the first successful demonstration of extraction or purification of any amphotericin molecule with any polymeric material. The biomimetic polymer was additionally reusable and simple to fabricate, giving this technique significant advantages over traditional methods of extraction and purification of valuable compounds. Full article

Molecularly imprinted polymers (MIPs), a biomimetic artificial receptor system inspired by the human body’s antibody-antigen reactions, have gained significant attraction in the area of sensor development applications, especially in the areas of medical, pharmaceutical, food quality control, and the environment. MIPs are found to enhance the sensitivity and specificity of typical optical and electrochemical sensors severalfold with their precise binding to the analytes of choice. In this review, different polymerization chemistries, strategies used in the synthesis of MIPs, and various factors influencing the imprinting parameters to achieve high-performing MIPs are explained in depth. This review also highlights the recent developments in the field, such as MIP-based nanocomposites through nanoscale imprinting, MIP-based thin layers through surface imprinting, and other latest advancements in the sensor field. Furthermore, the role of MIPs in enhancing the sensitivity and specificity of sensors, especially optical and electrochemical sensors, is elaborated. In the later part of the review, applications of MIP-based optical and electrochemical sensors for the detection of biomarkers, enzymes, bacteria, viruses, and various emerging micropollutants like pharmaceutical drugs, pesticides, and heavy metal ions are discussed in detail. Finally, MIP’s role in bioimaging applications is elucidated with a critical assessment of the future research directions for MIP-based biomimetic systems. Full article

New bone formation starts from the initial reaction between a scaffold surface and the extracellular matrix. This research aimed to evaluate the effects of various amounts of calcium, phosphate, sodium, sulfur, and chloride ions on osteoblast-like cell differentiation using tetra-polymers of amorphous calcium phosphate (ACP), calcium sulfate hemihydrate (CSH), alginic acid, and hydroxypropyl methylcellulose. Moreover, 3D-printed scaffolds were fabricated to determine the ion distribution and cell differentiation. Various proportions of ACP/CSH were prepared in ratios of 0%, 13%, 15%, 18%, 20%, and 23%. SEM was used to observe the morphology, cell spreading, and ion complements. The scaffolds were also examined for calcium ion release. The mouse osteoblast-like cell line MC3T3-E1 was cultured to monitor the osteogenic differentiation, alkaline phosphatase (ALP) activity, total protein synthesis, osteocalcin expression (OCN), and calcium deposition. All 3D-printed scaffolds exhibited staggered filaments, except for the 0% group. The amounts of calcium, phosphate, sodium, and sulfur ions increased as the amounts of ACP/CSH increased. The 18%ACP/CSH group significantly exhibited the most ALP on days 7, 14, and 21, and the most OCN on days 14 and 21. Moreover, calcium deposition and mineralization showed the highest peak after 7 days. In conclusion, the 18%ACP/CSH group is capable of promoting osteoblast-like cell differentiation on 3D-printed scaffolds. Full article

Differences in the surface interactions of non-stoichiometric nanocrystalline B-type carbonate-substituted hydroxyapatite (n-cHAp) with the amino acids L-Lysine hydrochloride (L-LysHCl) and L-Arginine hydrochloride (L-ArgHCl) in acidic and alkaline media were determined using structural and spectroscopic analysis methods. The obtained data confirm that hydroxyapatite synthesized using our technique, which was used to develop the n-cHAp/L-LysHCl and n-cHAp/L-ArgHCl composites, is nanocrystalline. Studies of molecular composition of the samples by Fourier transform infrared spectroscopy under the change in the charge state of L-Lysine in environments with different alkalinity are consistent with the results of X-ray diffraction analysis, as evidenced by the redistribution of the modes’ intensities in the spectra that is correlated with the side chains, i.e., amide and carboxyl groups, of the amino acid. During the formation of a biomimetic composite containing L-Lysine hydrochloride and n-cHAp, the interaction occurred through bonding of the L-Lysine side chain and the hydroxyl groups of hydroxyapatite, which created an anionic form of L-Lysine at pH ≤ 5. In contrast, in biocomposites based on L-Arginine and n-cHAp, the interaction only slightly depends on pH value, and it proceeds by molecular orientation mechanisms. The X-ray diffraction and infrared spectroscopy results confirm that changes in the molecular composition of n-cHAp/L-ArgHCl biomimetic composites are caused by the electrostatic interaction between the L-ArgHCl molecule and the carbonate-substituted calcium hydroxyapatite. In this case, the bond formation was detected by Fourier transform infrared (FTIR) spectroscopy; the vibrational modes attributed to the main carbon chain and the guanidine group of L-Arginine are shifted during the interaction. The discovered interaction mechanisms between nanocrystalline carbonate-substituted hydroxyapatite that has physicochemical properties characteristic of the apatite in human dental enamel and specific amino acids are important for selecting the formation conditions of biomimetic composites and their integration with the natural dental tissue. Full article