Search Results (718)

Bombyx mori silk fibroin is a promising biopolymer with notable mechanical strength, biocompatibility, and potential for diverse biomedical applications, such as tissue engineering scaffolds, and drug delivery. These properties are intrinsically linked to the structural characteristics of silk fibroin, making it essential to understand its molecular stability under varying environmental conditions. This study employed molecular dynamics simulations to examine the structural stability of silk I and silk II conformations of silk fibroin under changes in temperature (298 K to 378 K) and pressure (0.1 MPa to 700 MPa). Key parameters, including Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), and Radius of Gyration (R_g) were analyzed, along with non-bonded interactions such as van der Waals and electrostatic potential energy. Our findings demonstrate that both temperature and pressure exert a destabilizing effect on silk fibroin, with silk I exhibiting a higher susceptibility to destabilization compared to silk II. Additionally, pressure elevated the van der Waals energy in silk I, while temperature led to a reduction. In contrast, electrostatic potential energy remained unaffected by these environmental conditions, highlighting stable long-range interactions throughout the study. Silk II’s tightly packed β-sheet structure offers greater resilience to environmental changes, while the more flexible α-helices in silk I make it more susceptible to structural perturbations. These findings provide valuable insights into the atomic-level behavior of silk fibroin, contributing to a deeper understanding of its potential for applications in environments where mechanical or thermal stress is a factor. The study underscores the importance of computational approaches in exploring protein stability and supports the continued development of silk fibroin for biomedical and engineering applications. Full article

Over the years, pulses and cereals have been identified as promising sources of plant proteins. The intensive production of these crops and concerns about food security and malnutrition worldwide have intensified research into their separation. While wet extraction remains the standard protein isolation method, the search for more sustainable extraction methods is still ongoing. Two dry fractionation techniques, air classification and tribo-electrostatic separation, have been discussed in this review. This review highlights the design aspects of air classifiers including the cut-off point and flow rate, and for electrostatic separators, factors such as charger materials, the nature of the flow in charger tubes, and the strength of the electric field potential have been discussed in detail. Our analysis revealed that cascading the two techniques should help enhance the concentration and purity of the separated fractions. While limitations such as low purity and low yield exist, current research studies are focused on overcoming such drawbacks. Dry fractionation exhibits potential as a sustainable processing method while also preserving the native functionality of the proteins, making it easier to incorporate the fractions in commercial scale processes. Full article

In the present work, we studied the interactions of three types of iron oxide nanoparticles (IONPs) with human serum albumin (HSA) by fluorescence and UV-Vis spectroscopy. The determined binding parameters of the reactions and the thermodynamic parameters, including ΔHo, ΔSo, and ΔGo indicated that electrostatic forces play a major role in the interaction of IONPs with HSA. These measurements indicate a fluorescent quenching mechanism based on IONPs-HSA static complex formation. Our study shows that the interaction between HSA and IONPs depends on the nanoparticle structure. The interaction between IONPs and HSA was found to be spontaneous, exothermic, and entropy-driven. HSA was shown to interact moderately with IONPs obtained with plant extracts of Uncaria tomentosa L. (IONP@UT) and Clinopodium vulgare L. (IONP@CV), and firmly with IONPs prepared with Ganoderma lingzhi (Reishi) extract (IONP@GL), via ground-state association. Analysis by modified Stern-Volmer approximation indicates that the quenching mechanism is static. Our study significantly improves our understanding of the mechanisms of interaction, distribution, and transport involved in the interaction between proteins and IONPs. It provides crucial insights into the functional perturbations of albumin binding capacity and the effects of IONPs on the stability and structural modifications of plasma carrier proteins. Full article

GTP-binding proteins are essential molecular switches that regulate a wide range of cellular processes. Their function relies on the specific recognition and binding of guanine within their binding pockets. This study aims to elucidate the molecular determinants underlying this recognition. A large-scale data mining of the Protein Data Bank yielded 298 GTP-binding protein complexes, which provided a structural foundation for a systematic analysis of the intermolecular interactions that are responsible for the molecular recognition of guanine in proteins. It was found that multiple modes of non-bonded interactions including hydrogen bonding, cation–π interactions, and π–π stacking interactions are employed by GTP-binding proteins for binding. Subsequently, the strengths of non-bonded interaction energies between guanine and its surrounding protein residues were quantified by means of the double-hybrid DFT method B2PLYP-D3/cc-pVDZ. Hydrogen bonds, particularly those involving the N2 and O6 atoms of guanine, confer specificity to guanine recognition. Cation–π interactions between the guanine ring and basic residues (Lys and Arg) provide significant electrostatic stabilization. π–π stacking interactions with aromatic residues (Phe, Tyr, and Trp) further contribute to the overall binding affinity. This synergistic interplay of multiple interaction modes enables GTP-binding proteins to achieve high specificity and stability in guanine recognition, ultimately underpinning their crucial roles in cellular signaling and regulation. Notably, the NKXD motif, while historically considered crucial for guanine binding in GTP-binding proteins, is not universally required. Our study revealed significant variability in hydrogen bonding patterns, with many proteins lacking the NKXD motif but still effectively binding guanine through alternative arrangements of interacting residues. Full article

The angiotensin-converting enzyme-2 (ACE2) is a transmembrane glycoprotein, consisting of two segments: a large carboxypeptidase catalytic domain and a small transmembrane collectrin-like segment. This protein plays an essential role in blood pressure regulation, transforming the peptides angiotensin-I and angiotensin-II (vasoconstrictors) into angiotensin-1-9 and angiotensin-1-7 (vasodilators). During the COVID-19 pandemic, ACE2 became best known as the receptor of the S-protein of SARS-CoV-2 coronavirus. The purpose of the following research is to reconstruct the 3D structure of the catalytic domain of the rabbit enzyme rACE2 using its primary amino acid sequence, and then to compare it with the human analog hACE2. For this purpose, we have calculated the electric properties and thermodynamic stability of the two protein globules employing computer programs for protein electrostatics. The analysis of the amino acid content and sequence demonstrates an 85% identity between the two polypeptide chains. The 3D alignment of the catalytic domains of the two enzymes shows coincidence of the α-helix segments, and a small difference in two unstructured segments of the chain. The electric charge of the catalytic domain of rACE2, determined by 70 positively chargeable amino acid residues, 114 negatively chargeable ones, and two positive charges of the Zn²⁺ atom in the active center exceeds that of hACE2 by one positively and four negatively chargeable groups; however, in 3D conformation, their isoelectric points pI 5.21 coincide. The surface electrostatic potential is similarly distributed on the surface of the two catalytic globules, but it strongly depends on the pH of the extracellular medium: it is almost positive at pH 5.0 but strongly negative at pH 7.4. The pH dependence of the electrostatic component of the free energy discloses that the 3D structure of the two enzymes is maximally stable at pH 6.5. The high similarity in the 3D structure, as well as in the electrostatic and thermodynamic properties, suggests that rabbit can be successfully used as an animal model to study blood pressure regulation and coronavirus infection, and the results can be extrapolated to humans. Full article

Clinical genomics sequencing is rapidly expanding the number of variants that need to be functionally elucidated. Interpreting genetic variants (i.e., mutations) usually begins by identifying how they affect protein-coding sequences. Still, the three-dimensional (3D) protein molecule is rarely considered for large-scale variant analysis, nor in analyses of how proteins interact with each other and their environment. We propose a standardized approach to scoring protein surface property changes as a new dimension for functionally and mechanistically interpreting genomic variants. Further, it directs hypothesis generation for functional genomics research to learn more about the encoded protein’s function. We developed a novel method leveraging 3D structures and time-dependent simulations to score and statistically evaluate protein surface property changes. We evaluated positive controls composed of eight thermophilic versus mesophilic orthologs and variants that experimentally change the protein’s solubility, which all showed large and statistically significant differences in charge distribution (p < 0.01). We scored static 3D structures and dynamic ensembles for 43 independent variants (23 pathogenic and 20 uninterpreted) across four proteins. Focusing on the potassium ion channel, KCNK9, the average local surface potential shifts were 0.41 k_BT/ec with an average p-value of 1 × 10⁻². In contrast, dynamic ensemble shifts averaged 1.15 k_BT/ec with an average p-value of 1 × 10⁻⁵, enabling the identification of changes far from mutated sites. This study demonstrates that an objective assessment of how mutations affect electrostatic distributions of protein surfaces can aid in interpreting genomic variants discovered through clinical genomic sequencing. Full article

Calcium-chelated polysaccharides have been increasingly considered as promising calcium supplements. In this study, degraded fucoidans (DFs) with different molecular weights (Mws) were prepared after UV/H₂O₂ treatment; their calcium-chelating capacities and intestinal absorption properties were also investigated. The results showed that the calcium-chelating capacities of DFs were improved with a decrease in Mw. This was mainly ascribed to the increased carboxyl content, which was caused by free-radical-mediated degradation. Meanwhile, the conformation of DF changed from a rod-like chain to a shorter and softer chain. The thermodynamic analysis demonstrated that DF binding to calcium was spontaneously driven by electrostatic interactions. Additionally, DF-Ca chelates with lower Mw showed favorable transport properties across a Caco-2 cell monolayer and could effectively accelerate the calcium influx through intestinal enterocytes. Furthermore, these chelates also exhibited a protective effect on the epithelial barrier by alleviating damage to tight junction proteins. These findings provide an effective free-radical-related approach for the development of polysaccharide-based calcium supplements with improved intestinal calcium transport ability. Full article

The diffusional dynamics and vibrational spectroscopy of molecular hydrogen (H₂) in myoglobin (Mb) is characterized. Hydrogen has been implicated in a number of physiologically relevant processes, including cellular aging or inflammation. Here, the internal diffusion through the protein matrix was characterized, and the vibrational spectroscopy was investigated using conventional empirical energy functions and improved models able to describe higher-order electrostatic moments of the ligand. Depending on the energy function used, H₂ can occupy the same internal defects as already found for Xe or CO (Xe1 to Xe4 and B-state). Furthermore, four additional sites were found, some of which had been discovered in earlier simulation studies. Simulations using a model based on a Morse oscillator and distributed charges to correctly describe the molecular quadrupole moment of H₂ indicate that the vibrational spectroscopy of the ligand depends on the docking site it occupies. This is consistent with the findings for CO in Mb from experiments and simulations. For H₂, the maxima of the absorption spectra cover ∼20 cm⁻¹ which are indicative of a pronounced Stark effect of the surrounding protein matrix on the vibrational spectroscopy of the ligand. Electronic structure calculations show that H₂ forms a stable complex with the heme iron (stabilized by ∼−12 kcal/mol), but splitting of H₂ is unlikely due to a high activation energy (∼50 kcal/mol). Full article

The impact of heat treatment, pH and phytic acid (PA) concentration on the aggregation behavior and digestibility of whey protein isolate (WPI) was investigated. The experimental results indicated that below the isoelectric point of WPI, heat treatment and elevated PA levels significantly increased turbidity and particle size, leading to the aggregation of WPI molecules. No new chemical bonds were formed and the thermodynamic parameters ΔH < 0, ΔS > 0 and ΔG < 0 suggested that the interaction between PA and WPI was primarily a spontaneous electrostatic interaction driven by enthalpy. After the small intestine stage, increasing phytic acid levels resulted in a significant decrease in hydrolysis degree from 16.2 ± 1.5% (PA0) to 10.9 ± 1.4% (0.5% PA). Conversely, above isoelectric point of WPI, there was no significant correlation between the presence of PA and the aggregation behavior or digestion characteristics of WPI. These results were attributed to steric hindrance caused by PA-WPI condensates, which prevented protease binding to hydrolysis sites on WPI. In summary, the effect of PA on protein aggregation behavior and digestive characteristics was not simply dependent on its presence but largely on the aggregation degree of PA-WPI induced by heat treatment, pH and PA concentration. The findings obtained here suggested that phytic acid may be utilized as an agent to modulate the digestion characteristics of proteins according to production requirements. Additionally, the agglomerates formed by heating phytic acid and protein below the isoelectric point could also be utilized for nutrient delivery. Full article

The industrial application of pea protein is limited due to its poor gelation properties. This study aimed to evaluate the effects of psyllium husk powder (PHP) on improving the rheological, textural, and structural properties of heat-induced pea protein isolate (PPI) gel. Scanning electron microscopy (SEM), intermolecular forces analysis, the quantification of the surface hydrophobicity and free amino groups, and Fourier transform infrared spectroscopy (FTIR) were conducted to reveal the inner structures of PPI-PHP composite gels, conformational changes, and molecular interactions during gelation, thereby clarifying the underlying mechanism. The results showed that moderate levels of PHP (0.5–2.0%) improved the textural properties, water holding capacity (WHC), whiteness, and viscoelasticity of PPI gel in a dose-dependent manner, with the WHC (92.60 ± 1.01%) and hardness (1.19 ± 0.02 N) peaking at 2.0%. PHP significantly increased surface hydrophobicity and enhanced hydrophobic interactions, hydrogen bonding, and electrostatic interactions in PPI-PHP composite gels. Moreover, the electrostatic repulsion between anionic PHP and negatively charged PPI in a neutral environment prevented the rapid and random aggregation of proteins, thereby promoting the formation of a well-organized gel network with more β-sheet structures. However, the self-aggregation of excessive PHP (3.0%) weakened molecular interactions and disrupted the continuity of protein networks, slightly reducing the gel strength. Overall, PHP emerged as an effective natural gel enhancer for the production of pea protein gel products. This study provides technical support for the development of innovative plant protein-based foods with strong gel properties and enriched dietary fiber content. Full article

Validation of the data deposited in the Protein Data Bank is of the upmost importance, since many other databases, data mining processes, and artificial intelligence tools are strictly grounded on them. The present paper is divided into two parts. The first part describes and analyzes validation methods that have been designed and used by the structural biology community. Everything began with the Ramachandran plot, with its allowed and disallowed types of backbone conformations, and evolved in different directions, with the inclusion of additional stereochemical features, distributions’ analyses of structural moieties, and scrutiny of structure factor amplitudes across the reciprocal lattice. The second part of the paper is focused on the largely unexplored problem of the high number of false positives amongst the sodium(I) cations observed in protein crystal structures. It is demonstrated that these false positives, which are atoms wrongly identified with sodium, can be identified by using electrostatic considerations and it is anticipated that this approach can be extended to other alkali and alkaline earth cations or to monoatomic anions. In the end, I think a global initiative, accessible to all volunteers and possibly overseen by the Protein Data Bank, should take the place of the numerous web servers and software applications by providing the community with a select few reliable and widely accepted tools. Full article

The deposition of amyloid β-protein (Aβ) in the brain is the main pathogenesis of Alzheimer’s disease (AD). The development of potent inhibitors against Aβ aggregation is one of the effective strategies to combat AD. Endogenous transthyretin (TTR) can inhibit Aβ fibrillization via hydrophobic interactions, but its weak inhibitory potency hinders its application in AD therapy. Here, different recombinant TTRs were designed by cationic surface charge engineering. Compared with TTR, all positively charged recombinant TTRs showed enhanced capability in inhibiting Aβ aggregation, especially the recombinant protein obtained by mutating the acidic amino acid in TTR to arginine (TTR-nR) exhibited excellent inhibitory effect. Among them, TTR-7R remarkably increased the inhibitory potency against Aβ, which could effectively inhibit Aβ₄₀ fibrillization at a very low concentration (0.5 μM). In addition, TTR-7R increased cultured cell viability from 62% to 89%, scavenged amyloid plaques in AD nematodes, and prolonged nematode lifespan by 5 d at 2 μM. Thermodynamic studies demonstrated that TTR-7R, enriching in positive charges, presented hydrophobic interactions and enhanced electrostatic interactions with Aβ₄₀, leading to a significantly enhanced inhibitory capacity of TTR-7R. The research provided insights into the development of efficient recombinant protein inhibitors for AD treatment. Full article

Background: Proteins are commonly used in the healthcare industry to treat various health conditions, and most proteins are sensitive to physical and chemical changes. Lyophilization, also known as freeze-drying, involves sublimating water in the form of ice from a substance at low pressure, forming a freeze-dried powder that increases its shelf life. Extreme pressure and varying temperatures in the freeze-drying process may damage the protein’s structural integrity. Lyoprotectants are commonly used to protect protein conformations. It is important to choose a suitable lyoprotectant to ensure optimal effectiveness. Method: Twenty articles screened from Scopus, Web of Science, and PubMed were included in this review that discussed potential lyoprotectants and their effectiveness with different protein models. Results: Lyoprotectants were categorized into sugars, polyols, surfactants, and amino acids. Lyoprotectants can exhibit significant protective effects towards proteins, either singularly or in combination with another lyoprotectant. They exert various interactions with the protein to stabilize it, such as hydrogen bonding, hydrophobic interactions, electrostatic interactions, and osmoprotection. Conclusions: This review concludes that disaccharides are the most effective lyoprotectants, while other groups of lyoprotectants are best used in combination with other lyoprotectants. Full article

Background: The issue of human mental health is gaining more and more attention nowadays. However, most mental disorders are treated with antipsychotic drugs that cause weight gain and metabolic disorders, which include olanzapine (OLZ). The search for and development of natural compounds for the prevention of obesity when taking antipsychotic drugs is an urgent task. The biopolymer chitosan (Chi) and its derivatives have lipid-lowering and anti-diabetic properties, which makes them potential therapeutic substances for use in the treatment of metabolic disorders. The purpose of this work was to analyze the effect of the natural biopolymer Chi, its derivative N-succinyl chitosan (SuChi), and Orlistat (ORL) as a control on the effects caused by the intake of OLZ in a mouse model. Methods: Mice were fed with pearl barley porridge mixed with OLZ or combinations OLZ + Chi, OLZ + SuChi, or OLZ + ORL for 2 months. The weight, lipid profile, blood chemokines, expression of genes associated with appetite regulation, and behavior of the mice were analyzed in dynamics. Results: For the first time, data were obtained on the effects of Chi and SuChi on metabolic changes during the co-administration of antipsychotics. Oral OLZ increased body weight, food and water intake, and glucose, triglyceride, and cholesterol levels in blood. ORL and SuChi better normalized lipid metabolism than Chi, decreasing triglyceride and cholesterol levels. OLZ decreased the production of all chemokines tested at the 4th week of treatment and increased CXCL1, CXCL13, and CCL22 chemokine levels at the 7th week. All of the supplements corrected the level of CXCL1, CXCL13, and CCL22 chemokines but did not recover suppressed chemokines. SuChi and ORL stimulated the expression of satiety associated proopiomelanocortin (POMC) and suppressed the appetite-stimulating Agouti-related protein (AgRP) genes. All supplements improved the locomotion of mice. Conclusions: Taken collectively, we found that SuChi more than Chi possessed an activity close to that of ORL, preventing metabolic disorders in mice fed with OLZ. As OLZ carries positive charge and SuChi is negatively charged, we hypothesized that SuChi’s protective effect can be explained by electrostatic interaction between OLZ byproducts and SuChi in the gastrointestinal tract. Full article

The combination of paclitaxel (PTX) with other chemotherapy drugs (e.g., gemcitabine, GEM) or genetic drugs (e.g., siRNA) has been shown to enhance therapeutic efficacy against tumors, reduce individual drug dosages, and prevent drug resistance associated with single-drug treatments. However, the varying solubility of chemotherapy drugs and genetic drugs presents a challenge in co-delivering these agents. In this study, nanoparticles loaded with PTX were prepared using the biodegradable polymer material poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (PHBHHx). These nanoparticles were surface-modified with target proteins (Affibody molecules) and RALA cationic peptides to create core-shell structured microspheres with targeted and cationic functionalization. A three-drug co-delivery system (PTX@PHBHHx-ARP/siRNA_GEM) were developed by electrostatically adsorbing siRNA chains containing GEM onto the microsphere surface. The encapsulation efficiency of PTX in the nanodrug was found to be 81.02%, with a drug loading of 5.09%. The chemogene adsorption capacity of siRNA_GEM was determined to be 97.3%. Morphological and size characterization of the nanodrug revealed that PTX@PHBHHx-ARP/siRNA_GEM is a rough-surfaced microsphere with a particle size of approximately 150 nm. This nanodrug exhibited targeting capabilities toward BT474 cells with HER2 overexpression while showing limited targeting ability toward MCF-7 cells with low HER2 expression. Results from the MTT assay demonstrated that PTX@PHBHHx-ARP/siRNA_GEM exhibits high cytotoxicity and excellent combination therapy efficacy compared to physically mixed PTX/GEM/siRNA. Additionally, Western blot analysis confirmed that siRNA-mediated reduction of Bcl-2 expression significantly enhanced cell apoptosis mediated by PTX or GEM in tumor cells, thereby increasing cell sensitivity to PTX and GEM. This study presents a novel targeted nanosystem for the co-delivery of chemotherapy drugs and genetic drugs. Full article