Search Results (60)

To address the problem of serious gas channeling during CO₂ flooding in low-permeability reservoirs, which leads to poor oil recovery, this study developed a CO₂-resistant gel using a novel CO₂-responsive polymer (ADA) for gas channel control. The ADA polymer was synthesized via free-radical copolymerization of acrylamide (AM), dimethylaminopropyl methacrylamide (DMAPMA), and 2-acrylamido-2-methylpropanesulfonic acid (AMPS), which introduced protonatable tertiary-amine groups and sulfonate moieties into the polymer backbone. Comprehensive characterizations confirmed the designed structure and adequate thermal stability of the ADA polymer. Rheological tests demonstrated that the ADA polymer solution exhibits significant CO₂-triggered viscosity enhancement and excellent shear resistance. When crosslinked with phenolic resin, the resulting ADA gel showed outstanding CO₂ tolerance under simulated reservoir conditions (110 °C, 10 MPa). After 600 s of CO₂ exposure, the ADA gel retained over 99% of its initial viscosity, whereas a conventional HPAM-based industrial gel degraded to 61% of its original viscosity. The CO₂-resistance mechanism involves protonation of tertiary amines to form quaternary ammonium salts, which electrostatically interact with sulfonate groups, creating a reinforced dual-crosslinked network that effectively protects the gel from H⁺ ion attack. Core flooding experiments confirmed its ability to enhance oil recovery by plugging high-permeability channels and diverting flow, achieving a final recovery of up to 48.5% in heterogeneous cores. This work provides a novel gel system for improving sweep efficiency and storage security during CO₂ flooding in low-permeability reservoirs. Full article

Tröger’s base (TB) polymers have received increasing attention as a novel class of polymers with intrinsic microporosity, particularly for applications in gas separation. In this study, TB was quaternized with hydrophobic long chains to create a microphase-separated structure to enhance gas separation performance. On one hand, the tertiary amine structure of TB enabled facile grafting modification through the Menshutkin reaction. On the other hand, microphase-separated channels were created in the quaternized Tröger’s base (QTB) membrane due to the polarity differences between the hydrophilicity of the quaternary ammonium groups and hydrophobicity of iodoalkanes, providing channels for gas transport within the membrane and thereby improving permeability selectivity. The successful synthesis of QTB membranes was confirmed by FTIR and ¹H NMR spectroscopy, while AFM and SAXS analyses validated the microphase-separated morphology. To investigate the impact of microphase separation on oxygen permeability and selectivity, different iodoalkanes and various concentrations of iodobutane were grafted onto the TB backbone. Among the prepared membranes, QTB-C₄-70% membrane exhibited the highest in O₂ permeability. Gas separation performance under different O₂ pressures and temperatures revealed that O₂ permeability decreased slightly with increasing pressure, indicating good pressure stability of the membrane. With increasing temperature, the permeability increased while the selectivity decreased. These findings demonstrated that microphase-separated QTB membranes offer a viable strategy for creating effective materials for gas separation. Full article

Background: Recombinant monoclonal antibodies (mAbs) represent the fastest-growing sector of the biopharmaceutical industry, with their efficient expression being a key technological factor for scalability. Objectives: In this study we compared the performance of two bicistronic vectors, which alternate the positions of the light and heavy chain coding genes, employing a wild-type Encephalomyocarditis virus (EMCV) IRES functional element to drive expression of the second gene. Methods: Using two neutralizing anti-SARS-CoV-2 IgG1 antibodies as model molecules, we conducted transient transfections in the commercially available ExpiCHO^TM platform. Following protein A affinity purification and quantification, vectors positioning the light chain as the first cistron consistently yielded higher expression levels than those with the heavy chain upstream. To confirm the quality attributes of the mAbs, we applied a comprehensive analytical workflow, including SDS-PAGE and Western blot for molecular mass and purity, circular dichroism for secondary structure, intrinsic tryptophan fluorescence for tertiary structure, and SEC-HPLC for quaternary structure and aggregate detection. Additionally, we assessed binding affinity to the target using spot blot and surface plasmon resonance, analyzed N-glycosylation profiles by HILIC-HPLC and mass spectrometry, and examined molecular structure by transmission electron microscopy. Results and Conclusions: Together, these results provide insight into the impact of gene positioning within bicistronic vectors on mAb expression efficiency and quality, supporting optimization strategies for scalable recombinant antibody production. Full article

Methods such as AlphaFold have revolutionized protein structure prediction, making quantitative prediction of the thermodynamic stability of individual proteins and their complexes one of the next frontiers in computational protein modeling. Here, we develop methods for using protein language models (PLMs) with protein mutational datasets related to protein tertiary and quaternary stability. First, we demonstrate that fine-tuning of a ProtT5 PLM enables accurate prediction of the largest protein mutant stability dataset available. Next, we show that mutational impacts on protein function can be captured by fine-tuning PLMs, using green fluorescent protein (GFP) brightness as a readout of folding and stability. In our final case study, we observe that PLMs can also be extended to protein complexes by identifying mutations that are stabilizing or destabilizing. Finally, we confirmed that state-of-the-art simulation methods (free energy perturbation) can refine the accuracy of predictions made by PLMs. This study highlights the versatility of PLMs and demonstrates their application towards the prediction of protein and complex stability. Full article

Metal ions and ligand binding are crucial in various biological processes, and their rational design can be used to develop novel therapeutic drugs and diagnostic tools. Metal atoms are soluble in biological fluids due to their ability to easily lose electrons and form positively charged ions. Because of their electron deficiency, they can interact with electron-rich biomolecules like proteins and DNA, and potentially participate in catalytic mechanisms or stabilize their tertiary or quaternary structures. Antibacterial resistance has become a major global concern and requires novel strategies to combat resistance mechanisms in infectious microbes. Full article

It is now known that diet or food is one of the environmental factors that can induce or contribute to autoimmunity. In a healthy person with a normal functioning immune system, food substances encounter no resistance and are allowed passage through the immune barriers without triggering immune reactivity. However, clinicians are becoming increasingly aware that modern food-processing methods can increase or decrease the immune reactivity of foods, including allergic reactions. Immune reactions to undigested food antigens could result in the production of IgE antibodies, which are involved in immediate immune reactivity, and in IgG and IgA antibodies, which are involved in delayed immune reactivity. Currently, measurements of these antibodies are generally only performed against antigens derived from raw foods. However, testing for food reactivity based only on raw food consumption is inaccurate because people eat both raw and cooked foods. Even home-cooked foods undergo different kinds of preparation or processing. Food processing can change the structure of raw food materials into secondary, tertiary, and quaternary structures that can have different reactive properties. This can affect the body’s normal oral tolerance of food, causing the immune system to mistakenly identify food as a harmful foreign substance and react to it immunologically, leading to food immune reactivity. This abnormal reaction to food molecules can lead to the production of antibodies against not just target food antigens but also the body’s own tissues, which can have significant implications in autoimmunity induction due to cross-reactivity and the other mechanisms discussed here. We hope that this present review will stimulate further research on the role of modified food antigens in the induction of autoimmunity based on some or all of the key points discussed in this review. Full article

First believed to be a simple intermediary between the information encoded in deoxyribonucleic acid and that functionally displayed in proteins, ribonucleic acid (RNA) is now known to have many functions through its abundance and intricate, ubiquitous, diverse, and dynamic structure. About 70–90% of the human genome is transcribed into protein-coding and noncoding RNAs as main determinants along with regulatory sequences of cellular to populational biological diversity. From the nucleotide sequence or primary structure, through Watson–Crick pairing self-folding or secondary structure, to compaction via longer distance Watson–Crick and non-Watson–Crick interactions or tertiary structure, and interactions with RNA or other biopolymers or quaternary structure, or with metabolites and biomolecules or quinary structure, RNA structure plays a critical role in RNA’s lifecycle from transcription to decay and many cellular processes. In contrast to the success of 3-dimensional protein structure prediction using AlphaFold, RNA tertiary and beyond structures prediction remains challenging. However, approaches involving machine learning and artificial intelligence, sequencing of RNA and its modifications, and structural analyses at the single-cell and intact tissue levels, among others, provide an optimistic outlook for the continued development and refinement of RNA-based applications. Here, we highlight those in gene therapy. Full article

Eukaryotic cells tether the nucleoskeleton to the cytoskeleton via a conserved molecular bridge, called the LINC complex. The core of the LINC complex comprises SUN-domain and KASH-domain proteins that directly associate within the nuclear envelope lumen. Intra- and inter-chain disulphide bonds, along with KASH-domain protein interactions, both contribute to the tertiary and quaternary structure of vertebrate SUN-domain proteins. The significance of these bonds and the role of PDIs (protein disulphide isomerases) in LINC complex biology remains unclear. Reducing and non-reducing SDS-PAGE analyses revealed a prevalence of SUN2 homodimers in non-tumorigenic breast epithelia MCF10A cells, but not in the invasive triple-negative breast cancer MDA-MB-231 cell line. Furthermore, super-resolution microscopy revealed SUN2 staining alterations in MCF10A, but not in MDA-MB-231 nuclei, upon reducing agent exposure. While PDIA1 levels were similar in both cell lines, pharmacological inhibition of PDI activity in MDA-MB-231 cells led to SUN-domain protein down-regulation, as well as Nesprin-2 displacement from the nucleus. This inhibition also caused changes in perinuclear cytoskeletal architecture and lamin downregulation, and increased the invasiveness of PDI-inhibited MDA-MB-231 cells in space-restrictive in vitro environments, compared to untreated cells. These results emphasise the key roles of PDIs in regulating LINC complex biology, cellular architecture, biomechanics, and invasion. Full article

This study prepared silicon oxide anode materials with nitrogen-doped carbon matrices (SiO_x/C–N) through silicon-containing polyester thermal carbonization. Melamine was introduced as a nitrogen source during the experiment. This nitrogen doping process resulted in a porous structure in the carbon matrices, a fact confirmed by scanning electron microscopy (SEM). Pyridinic and quaternary nitrogen, but mainly tertiary nitrogen, were generated, as shown via X-ray photoelectron spectroscopy (XPS). Electrochemical tests confirmed that, as anode materials for a lithium-ion battery, SiO_x/C–N provided better cycle stability, improved rate capability, and lower Li⁺ diffusion resistance. The best performance showed an activated capacity at 493.5 mAh/g, preserved at 432.8 mAh/g after the 100th cycle, with 87.7% total Columbic efficiency. Those without nitrogen doping gave 1126.7 mAh/g, 249.0 mAh/g, and 22.1%, respectively. The most noteworthy point was that, after 100 cycles, anodes without nitrogen doping were pulverized into fine powders (SEM); meanwhile, in the case of anodes with nitrogen doping, powders of a larger size (0.5–1.0 µm) formed, with the accumulation of surrounding cavities. We suggest that the formation of more prominent powders may have resulted from the more substantial nitrogen-doped carbon matrices, which prevented the anode from further breaking down to a smaller size. The volume expansion stress decreased when the powders decreased to nanosize, which is why the nanosized silicon anode materials showed better cycling stability. When the anodes were cracked into powders with a determined diameter, the stress from volume expansion decreased to a level at which the powders could preserve their shape, and the breakage of the powders was stopped. Hence, the diameters of the final reserved powders are contingent on the strength of the matrix. As reported, nitrogen-doped carbon matrices are more robust than those not doped with nitrogen. Thus, in our research, anodes with nitrogen-doped carbon matrices presented more large-diameter powders, as SEM confirmed. Anodes with nitrogen doping will not be further broken at a larger diameter. At this point, the SEI film will not show continuous breakage and formation compared to the anode without doping. This was validated by the lower deposition content of the SEI-film-related elements (phosphorous and fluorine) in the cycled anodes with nitrogen doping. The anode without nitrogen doping presented higher content, meaning that the SEI films were broken many times during lithiation/delithiation (EDS mapping). Full article

Object retrieval systems measure the degree of similarity of the shape of 3D models. They search for the elements of the 3D model databases that resemble the query model. In structural bioinformatics, the query model is a protein tertiary/quaternary structure and the objective is to find similarly shaped molecules in the Protein Data Bank. With the ever-growing size of the PDB, a direct atomic coordinate comparison with all its members is impractical. To overcome this problem, the shape of the molecules can be encoded by fixed-length feature vectors. The distance of a protein to the entire PDB can be measured in this low-dimensional domain in linear time. The state-of-the-art approaches utilize Zernike–Canterakis moments for the shape encoding and supply the retrieval process with geometric data of the input structures. The BioZernike descriptors are a standard utility of the PDB since 2020. However, when trying to calculate the ZC moments locally, the issue of the deficiency of libraries readily available for use in custom programs (i.e., without relying on external binaries) is encountered, in particular programs written in Python. Here, a fast and well-documented Python implementation of the Pozo–Koehl algorithm is presented. In contrast to the more popular algorithm by Novotni and Klein, which is based on the voxelized volume, the PK algorithm produces ZC moments directly from the triangular surface meshes of 3D models. In particular, it can accept the molecular surfaces of proteins as its input. In the presented PK-Zernike library, owing to Numba’s just-in-time compilation, a mesh with 50,000 facets is processed by a single thread in a second at the moment order 20. Since this is the first time the PK algorithm is used in structural bioinformatics, it is employed in a novel, simple, but efficient protein structure retrieval pipeline. The elimination of the outlying chain fragments via a fast PCA-based subroutine improves the discrimination ability, allowing for this pipeline to achieve an 0.961 area under the ROC curve in the BioZernike validation suite (0.997 for the assemblies). The correlation between the results of the proposed approach and of the 3D Surfer program attains values up to 0.99. Full article

Hemoglobin is the main protein of red blood cells that provides oxygen transport to all cells of the human body. The ability of hemoglobin to bind the main low-molecular-weight thiol of the cell glutathione, both covalently and noncovalently, is not only an important part of the antioxidant protection of red blood cells, but also affects its affinity for oxygen in both cases. In this study, the properties of oxyhemoglobin in complex with reduced glutathione (GSH) and properties of glutathionylated hemoglobin bound to glutathione via an SS bond were characterized. For this purpose, the methods of circular dichroism, Raman spectroscopy, infrared spectroscopy, tryptophan fluorescence, differential scanning fluorimetry, and molecular modeling were used. It was found that the glutathionylation of oxyhemoglobin caused changes in the secondary structure of the protein, reducing the alpha helicity, but did not affect the heme environment, tryptophan fluorescence, and the thermostability of the protein. In the noncovalent complex of oxyhemoglobin with reduced glutathione, the secondary structure of hemoglobin remained almost unchanged; however, changes in the heme environment and the microenvironment of tryptophans, as well as a decrease in the protein’s thermal stability, were observed. Thus, the formation of a noncovalent complex of hemoglobin with glutathione makes a more significant effect on the tertiary and quaternary structure of hemoglobin than glutathionylation, which mainly affects the secondary structure of the protein. The obtained data are important for understanding the functioning of glutathionylated hemoglobin, which is a marker of oxidative stress, and hemoglobin in complex with GSH, which appears to deposit GSH and release it during deoxygenation to increase the antioxidant protection of cells. Full article

An experimental laboratory set of samples of composite heterogeneous anion-exchange membranes was obtained by us for the development of our original method of polycondensation filling. Anion-exchange membranes were prepared on plasma-treated and non-plasma-treated polyester fiber fabrics. The fabric was treated with low-temperature argon plasma at a power of 400 W for 10 min at a pressure of 5 × 10⁻⁵ mbar. On the surface and bulk of the polyester fiber, a polyfunctional anionite of mixed basicity was synthesized and formed. The anion-exchange membrane contained secondary and tertiary amino groups and quaternary ammonium groups, which were obtained from polyethylene polyamines and epichlorohydrins. At the stage of the chemical synthesis of the anion matrix, oxidized nanoparticles (~1.5 wt.%) of silicon, nickel, and iron were added to the monomerization composition. The use of ion-plasma processing of fibers in combination with the introduction of oxidized nanoparticles at the synthesis stage makes it possible to influence the speed and depth of the synthesis and curing processes; this changes the formation of the surface morphology and the internal structure of the ion-exchange polymer matrix, as well as the hydrophobic/hydrophilic balance and—as a result—the different operational characteristics of anion-exchange membranes. Full article

The traditional concept of the primary, secondary, tertiary and later quaternary economy is based on several structurally divided and related tasks and processes in processing raw materials and earth resources. Gradually, a new concept of the functioning of the economy was created, called “circular economy” or “circular economy”. Its basis is the transformation of linear economic processes managing the use of raw materials to create a sustainable economic growth model. The circular economy transforms economic activity associated with the consumption of limited resources into the more efficient reuse of resources. Based on the above, the presented article aims, based on theoretical and empirical analysis, to identify the potential of processing and using non-energy raw material—recycled aggregate—in the construction industry and to propose a concept for information modeling of the parameters of sustainable construction using this non-energy raw material per the principles of the circular economy. The solution to this research problem is realized through theoretical analysis and comparison of approaches to the circular economy, reuse of non-energy raw materials in the construction industry and analysis for the creation of a concept based on the use of information needed for sustainable construction planning through building information modeling (BIM). Based on my research, my results will be presented, the applicability of which is verified through a case study. The object of the case study is the construction of a new building, which will represent a set of five similar constructions interconnected by underground floors (garages, technical facilities of buildings) and communication spaces (corridor, hall). The priority of the construction of the centre is to build a sustainable building, i.e., to implement the work using sustainable methods with the greatest possible use of sustainable materials and procedures, which will reduce the impact on the ecosystem and support the goals of the circular economy. Traditional, natural raw materials will be replaced by recycled secondary raw materials within individual constructions and elements. When choosing suitable raw materials, the design of the BIM library of sustainable elements will help. The BIM library will act as a link between manufacturers and BIM digital replicas of real building products and components. Full article

Interpreting biological phenomena at the molecular and cellular levels reveals the ways in which information that is specific to living organisms is processed: from the genetic record contained in a strand of DNA, to the translation process, and then to the construction of proteins that carry the flow and processing of information as well as reveal evolutionary mechanisms. The processing of a surprisingly small amount of information, i.e., in the range of 1 GB, contains the record of human DNA that is used in the construction of the highly complex system that is the human body. This shows that what is important is not the quantity of information but rather its skillful use—in other words, this facilitates proper processing. This paper describes the quantitative relations that characterize information during the successive steps of the “biological dogma”, illustrating a transition from the recording of information in a DNA strand to the production of proteins exhibiting a defined specificity. It is this that is encoded in the form of information and that determines the unique activity, i.e., the measure of a protein’s “intelligence”. In a situation of information deficit at the transformation stage of a primary protein structure to a tertiary or quaternary structure, a particular role is served by the environment as a supplier of complementary information, thus leading to the achievement of a structure that guarantees the fulfillment of a specified function. Its quantitative evaluation is possible via using a “fuzzy oil drop” (FOD), particularly with respect to its modified version. This can be achieved when taking into account the participation of an environment other than water in the construction of a specific 3D structure (FOD-M). The next step of information processing on the higher organizational level is the construction of the proteome, where the interrelationship between different functional tasks and organism requirements can be generally characterized by homeostasis. An open system that maintains the stability of all components can be achieved exclusively in a condition of automatic control that is realized by negative feedback loops. This suggests a hypothesis of proteome construction that is based on the system of negative feedback loops. The purpose of this paper is the analysis of information flow in organisms with a particular emphasis on the role of proteins in this process. This paper also presents a model introducing the component of changed conditions and its influence on the protein folding process—since the specificity of proteins is coded in their structure. Full article

Allostery arises when a ligand-induced change in shape of a binding site of a protein is coupled to a tertiary/quaternary conformational change with a consequent modulation of functional properties. The two-state allosteric model of Monod, Wyman and Changeux [J. Mol. Biol. 1965; 12, 88–118] is an elegant and effective theory to account for protein regulation and control. Tetrameric hemoglobin (Hb), the oxygen transporter of all vertebrates, has been for decades the ideal system to test for the validity of the MWC theory. The small ligands affecting Hb’s behavior (organic phosphates, protons, bicarbonate) are produced by the red blood cell during metabolism. By binding to specific sites, these messengers make Hb sensing the environment and reacting consequently. HbI and HbIV from trout and human HbA are classical cooperative models, being similar yet different. They share many fundamental features, starting with the globin fold and the quaternary assembly, and reversible cooperative O₂ binding. Nevertheless, they differ in ligand affinity, binding of allosteric effectors, and stability of the quaternary assembly. Here, we recollect essential functional properties and correlate them to the tertiary and quaternary structures available in the protein databank to infer on the molecular basis of the evolution of oxygen transporters. Full article