Biophysical reviews最新文献

The COVID-19 pandemic has significantly impacted global health; key questions remain regarding its effects on male reproductive function. Male infertility represents both a biomedical challenge and a societal concern. Our review considers COVID-19's biophysical mechanisms affecting the male reproductive system and focuses on the prognostic implication. Current evidence highlights two primary pathways of SARS-CoV-2 impact: hyperthermia and oxidative stress. The first pathway, as reported, significantly increases sperm aneuploidy and, as a result, has adverse effects on spermatogenesis and causes sperm DNA breaks. The second pathway of coronavirus impact on infertility is oxidative stress. During it, the level of formation of reactive oxygen species (ROS) increases and damages sperm membrane by lipid peroxidation. These mechanisms are interrelated, as fever-induced oxidative stress may alter redox-active metal homeostasis, further exacerbating cellular damage. Understanding these pathogenic processes enables targeted therapeutic development and preventive strategies for COVID-19-related male reproductive dysfunction.

Gelation of blood plasma is key to normal hemostasis. The regulation of coagulation in blood flow has been studied for several decades, but the key problems in the field remain unresolved. Understanding the major mechanisms governing coagulation under flow conditions is important for the development of new diagnostic tools, therapeutic agents, and novel strategies addressing pathological states associated with both hypo- and hypercoagulation. In this review, we highlight the general features of plasma coagulation under flow conditions, including its spatiotemporal dynamics and threshold dependence on the key parameters. A short overview of in vitro and in silico models and important breakthroughs that became possible with their combination is followed by a brief introduction into the analysis of the balance between convection, diffusion, and reactions using Peclet and Damköhler numbers. We highlight the major unresolved challenges in the field and share an overall perspective of the future directions that might help to clarify the important questions that emerged during the last decade of intensive research.

This review focuses on spectral shift analysis as a tool to study macromolecular interactions and describes its current place among the available biophysical methods. NanoTemper's Dianthus platform facilitates a plate-based, microfluidics-free, mass-independent, and immobilisation-free high-throughput screening platform for protein-ligand, protein-protein, and protein-nucleic acid interactions, as well as ternary complexes, for example in proteolysis targeting chimera (PROTAC) design. In addition to spectral shift, the Dianthus offers an orthogonal method, temperature-related intensity change (TRIC). Both methods are presented alongside fluorescent labelling techniques. Specific examples with practical tips for spectral shift methods for diverse binding partners are provided. Finally, current and future applications of spectral shift methods in the drug discovery process are discussed in the context of high-throughput screening, fragment-based drug discovery, and hit-to-lead optimisation.

The applications of immobilized enzymes in industry are progressively increasing. Methodological aspects of engineering enzymology are largely determined by immobilization approaches. Using enzymes as biocatalysts provides advantages such as mild reaction conditions, environmental biodegradability, and high catalytic efficiency. Nevertheless, the extreme conditions often found in industrial settings can destabilize enzymes, reducing their operational durability in manufacturing applications. Immobilization of enzymes is a common practice, mainly in order to minimize enzyme costs on the process economics by making it possible to reuse the enzyme many times and also minimize the operation cost as the immobilization technique may be modify the enzyme behavior, thus reducing the enzyme and product costs significantly. Many techniques have been used previously for enzyme immobilization, such as adsorption, entrapment, encapsulation, covalent binding, and cross-linking. This review provides a comparative analysis of covalent and non-covalent methods of enzyme immobilization, and briefly outlines the main issues and prospects of their practical use in both analytical practice and industrial biotechnology and medicine. These techniques alter enzyme characteristics by modifying the surrounding microenvironment and adjusting the extent of multipoint binding. As a result, analyzing the enzyme's structural changes after attachment to the support surface is essential. Advanced nanoscale characterization tools play a vital role in examining surface-immobilized enzymes, providing key qualitative and quantitative insights, such as morphological visualization, into their behavior. Such analytical techniques are critical for evaluating the success of immobilization methods and guiding the design of future enzyme stabilization strategies. Special attention is paid to computer methods of analysis of immobilized enzymes. Importantly, while simulations have been primarily performed to rationalize the molecular aspects of the immobilization event, their use to predict adequate protocols that can control its impact on the enzyme properties is, up to date, mostly missing. Artificial intelligence and machine learning have been also successfully applied for optimization of the immobilization process and predictive modeling of unmeasured parameters. Using advanced analytics, they optimize biocatalytic processes by analyzing experimental data, forecasting immobilization parameters, and developing high-performance enzyme designs. Thus, this review summarizes various new immobilization techniques, limitations, prospects and applications of immobilized enzymes.

Enzymatic biosensors have been lately gaining popularity in various areas of human life, from medicine to agriculture, owing to their effectiveness and selectivity towards the tested substances. Bioluminescent enzymatic biosensors attract special attention because of the light produced by the enzyme reaction. Researchers designing bioluminescent enzymatic sensors face a number of challenges, mainly associated with the low stability and/or sensitivity of the enzymes used as a biological recognition element of the biosensor. Herein we describe strategies of improving the analytical performance of bioluminescent enzymatic biosensors based on luciferase enzymes. We, first, discuss the increase in biosensors' sensitivity by optimizing the composition of the biological recognition element, including enzyme and substrate variations and addition of nanoparticles or stabilizing agents. Then, we provide insights into improving the stability of luciferases by immobilization or by the presence of chaperones and via directed mutagenesis. And the last section deals with projections for the future. We give special consideration to results of using these approaches in developing biosensors based on bioluminescent enzyme systems of fireflies and bacteria. Yet, the approaches described in the review are universal and can be effectively used to develop other enzymatic biosensors.

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Investigation of a protein, such as an enzyme, requires an experimental method for assessing the activity of the protein, that is, some parameter related to its function. Determining protein activity is particularly important for understanding protein function under different conditions, as well as for designing new proteins or comparing proteins from different organisms. Antifreeze protein activity is a very specific type of activity and is very difficult to measure. One of the reasons is technical difficulties, since it is challenging to conduct experiments with aqueous solutions at sub-zero or near-zero temperatures. Another reason is that the mechanism of antifreeze proteins in different organisms is not fully understood, so the property most directly related to their primary physiological activity remains unclear. It is currently believed that antifreeze proteins may perform three functions: (1) influence the freezing point of water and melting point of ice, (2) affect the size of ice crystals or their growth process, and (3) inhibit ice nucleators within the cell or solution. Although all these functions are obviously related to each other, different methods are used to study them. These methods, aimed at assessing the various properties of antifreeze proteins, can be conditionally divided into three groups. In this paper, we reviewed the main methods for studying the activity of antifreeze proteins described in the literature.

Alzheimer's disease (AD) is the most prevalent form of age-related dementia. A pathological hallmark of AD is the accumulation in the brain of amyloid-β (Aβ) peptides, which aggregate at neuronal contact points into ordered fibrils and cords, ultimately shaping into senile plaques. Various Aβ isoforms are present in healthy human brains across all age groups, where they appear to participate in neuronal signaling pathways and exhibit neuroprotective properties at normal physiological concentrations. Aβ peptides are products of stepwise proteolytic degradation of the amyloid precursor protein (APP), a membrane-bound single-span glycoprotein, by β- and γ-secretases. The APP gene contains numerous familial mutations connected to early-onset AD, most of them occurring in the transmembrane and juxtamembrane regions. The proteolytic processing of APP into Aβ is controlled by several factors, including its subcellular localization, membrane lipid composition, and potentially its association with cholesterol- and sphingolipid-enriched lipid rafts. Interestingly, structurally and functionally resembling type I membrane receptors, APP has been suggested to play a role in cholesterol sensing in the neuronal membrane rafts. By this means, APP might engage in cell signaling processes, support iron equilibrium in neurons, participate in inflammatory responses, and modulate synaptic plasticity. This concise review summarizes key findings from biophysical and structural studies investigating the interactions of APP and its proteolytic fragments with plasma membrane components, particularly cholesterol and its derivatives. These interactions are viewed in the context of both normal physiological development and AD pathogenesis.

X-ray crystallography has been pivotal in elucidating the structural basis of ribosome function and in informing antibiotic design, from early challenges in purifying and crystallizing these mega-Dalton assemblies to recent advances integrating synchrotron radiation and X-ray free-electron lasers for high-resolution and time-resolved studies. Methodological innovations - including stress-induced lattice packing, extremophile ribosome sources, optimization of the purification procedure and vapor-diffusion screens - have yielded crystals diffracting up to 2.4 Å. Progress in phasing strategies, from multiple isomorphous replacement and multiwavelength anomalous dispersion/single-wavelength anomalous dispersion to cryogenic electron microscopy-guided molecular replacement and serial femtosecond crystallography, has overcome the phase problem for large complexes. Landmark structures of prokaryotic and eukaryotic ribosomes have elucidated the architectural principles underlying peptide bond formation and messenger RNA decoding, leading to inhibitor discovery. Despite the rise of cryogenic electron microscopy, crystallography remains indispensable for mechanistic insights and rational drug design targeting ribosomal sites.

Water is an active participant of biochemical and physiological processes in living systems. This review explores the emerging recognition of water as structural biomarker, which gives knowledge about its biological environment studying water mobility by means of dielectric and nuclear magnetic resonance (NMR) techniques. Recent advances in the broadband dielectric spectroscopy (BDS) and NMR technique have deepened our understanding of water's behavior under confinement, hydration, and interactions with biomacromolecules and biological interfaces. These methods reveal pronounced deviations of water dynamic structure in biosystems from its bulk state, indicating manyfold specific interaction of water with its local environment. Microwave dielectric spectroscopy, particularly through analysis of γ-dispersion, captures disruptions in water hydrogen-bond network caused by interactions with ions, macromolecules, and cellular structures. Complementary NMR diffusion and relaxation studies enable precise characterization of water mobility and confinement effects. Evidence from biological tissues, cells, and model systems, including red blood cells, protein and polysaccharide hydrogels demonstrates how water's dielectric and NMR signatures can serve as indicators of biological systems stability and functionality. This review revisits a hypothesis proposed nearly 50 years ago, that water dynamical structure in biological systems is intimately connected with chemical composition and architecture of supramolecular and cellular structures in norm and pathology. Ultimately, dielectric and NMR assessments of water represent a powerful, yet underutilized, approach to non-invasive diagnostics and real-time biomonitoring. Recognizing water as a responsive probe of biological status opens new frontiers in the understanding of fundamental phenomena in living systems and their rational use in modern health and technological applications.

The nucleus is a highly compartmentalized organelle and this spatial organization reflects gene-regulatory environments. Chromatin exists in two distinct forms: transcriptionally active, euchromatin and silenced, compacted heterochromatin. The spatial organization of chromatin along with its transcriptional activity is governed by biomolecular assemblies (BAs). Gene regulatory assemblies form and operate through highly dynamic protein-protein and protein-DNA interactions often established via their recruitment by non-coding RNAs. The formation of BAs is essential for retaining diffusible regulatory proteins at specific genomic regions, enabling local confinement and precise gene regulation. Phase separation, particularly in the form of liquid-liquid condensation, is suggested to play a crucial role in transcriptional regulation, serving as a key driver of biomolecular assembly formation. However, some studies indicate that phase separation may also be a non-essential byproduct of the crowded nuclear environment or may not be involved in certain BAs. Despite extensive investigations into these macromolecular crowding phenomena, the precise mechanisms underlying both the formation of gene-regulatory BAs and how these localized protein concentrations function to regulate chromatin structure and gene expression remain unclear. This review highlights progress made in elucidating the mechanisms of chromatin-modifying BAs, highlighting how super-resolution microscopy and single-molecule technologies are proving essential for probing these nuclear structures in situ, within their native cellular context.