Sub-cellular biochemistry最新文献

Rapid urea permeation mediated by urea transporters (UTs) is crucial for maintaining normal physiological processes in organisms. UTs not only facilitate urea transport but also water transport, further underscoring their role in maintaining fluid balance. Advances in structural biology have led to the elucidation of high-resolution three-dimensional structures of various UTs, offering critical insights into the molecular mechanisms underlying their efficiency in transporting urea and water. UT-B displays high permeability to urea analogs, which can competitively inhibit urea permeation by obstructing the channel. However, whether UT-A is capable of transporting urea analogs remains contentious. Additionally, further investigation is required to determine if UTs can facilitate ammonia transport. Urea permeability (P_urea) in erythrocytes differs between different mammals. Carnivores exhibit high P_urea. In contrast, herbivores show much lower P_urea. Erythrocyte P_urea in omnivores was intermediate. Rodents and lagomorphs have P_urea intermediate between carnivores and omnivores. This chapter provides information about the transporter characteristics of UTs.

Prion diseases are fatal neurodegenerative disorders for which no effective therapies exist. Despite decades of drug discovery efforts, progress in developing disease-modifying treatments has been slow. However, recent advances have introduced novel therapeutic modalities targeting key aspects of prion pathology, including prion protein biogenesis, aggregation, and degradation. Advancements in diagnostic tools and highly sensitive prion detection methods are also playing a crucial role in enabling early and accurate diagnosis, which is essential for the timely application of emerging therapeutics. This chapter explores novel therapeutic modalities for prion diseases, focusing on small-molecule theranostics and compounds promoting prion protein degradation, RNA-based therapeutics, and gene therapy approaches. We critically assess the advantages and limitations of these therapeutic strategies, considering their development, efficacy, and translational potential. By leveraging these innovative modalities, the therapeutic toolbox for prion diseases is expanding, offering hope for the development of effective treatments.

The nuclear membrane of cells harbors a lamina as a critical structural component beneath itself which serves as a dynamic scaffold that maintains nuclear integrity and cellular homeostasis. The primary component of the nuclear lamina is lamins, a set of type V intermediate filament proteins, which form a meshwork to provide mechanical stability while modulating essential biological processes like DNA replication, chromatin organization, and gene expression via mechanotransduction. The clinical significance of lamins is exemplified by laminopathies, a heterogeneous group of genetic disorders arising from mutations in the genes encoding the proteins (LMNA for A-type lamins [A and C], LMNB1 for lamin B1, and LMNB2 for lamin B2) that manifest in the form of a variety of pathologies comprising muscular dystrophies, premature aging syndromes, cardiovascular abnormalities, and metabolic aberrations. Laminopathies, though rare, form the basis of many life-threatening conditions that lack potent therapeutic interventions. Lamins have also been shown to be dysregulated in a multitude of cancers, and research has uncovered a diabolical role of lamins in oncogenesis. The understanding of laminopathies and dysregulation of lamins resulting in disorders is critical in developing novel therapeutic strategies through drug repurposing and epigenetic modulation to curb the burden of the diseases.

Prion diseases (PrDs) are fatal neurodegenerative disorders characterized by the accumulation of misfolded prion protein (PrP^Sc) in the central nervous system (CNS). This pathological isoform of the cellular prion protein drives disease pathogenesis through its unique ability to propagate itself via a template-directed misfolding mechanism. The definite diagnosis of PrDs relies on the detection of PrP^Sc in the CNS by invasive procedures or postmortem examination, limiting early detection and antemortem diagnostic investigations. Real-time quaking-induced conversion (RT-QuIC) has emerged as a revolutionary diagnostic tool, allowing ultrasensitive detection of PrP^Sc in cerebrospinal fluid (CSF) and other easily accessible tissues, including the olfactory mucosa, skin, and, more recently, tears. This assay exploits the autocatalytic amplification of misfolded prions, providing high sensitivity and specificity in the detection of peripheral PrP^Sc. This chapter explores the advancements and applications of RT-QuIC in diagnosing human PrDs.

Although cellular environment represents a kind of pottage with the increased viscosity and molecular interactions, changed water activity, volume exclusion, and considerably restricted amounts of free water, most of the biomolecular research in vitro is traditionally conducted under the "physiological conditions"; i.e., in warm, slightly salted, neutral or slightly alkaline aqueous solution, where the effects of such crowded environment on the behavior of biological macromolecules are mostly ignored. Furthermore, macromolecular crowding is spatially and temporally heterogeneous, as cell contains numerous biological condensates, overcrowded liquid droplets, which, being formed in response to the changing environment, reflect complexity of the cellular molecular kitchen. This chapter represents a brief historical overview of the developments in the field of macromolecular crowding reflecting the evolution of understanding of what are the appropriate experimental conditions for gaining the most accurate information on the behavior of biological macromolecule in biological systems.

The interaction between proteins and DNA is fundamental to numerous enzymatic processes, relying on the precise recognition of specific DNA bases by DNA-binding proteins (DBPs). This interaction occurs within the densely packed environment of the cell nucleus, which contains high concentrations of biomolecules. Consequently, the limited intracellular space can impact the diffusion and association of large macromolecules. This scenario prompts the question of how the complex milieu of the cell nucleus influences the ability of DBPs to locate and bind to their target DNA sites within a large polymeric DNA substrate. In this work, we review the in silico approaches used to investigate the facilitated diffusion of DBPs along DNA and the influence of crowded environments on this process. We illustrate that the effects of crowding differ significantly from those observed in protein-protein associations and cannot be solely attributed to volume exclusion principles. Additionally, we demonstrate how the physicochemical characteristics of crowding agents impact the facilitated diffusion of DBPs, crucial for understanding the protein's search for its DNA binding motif within the densely packed nuclear environment.

The cytoskeleton is not only responsible for cell morphology and rheology, but is also involved in such functions as cell motility, intracellular transport and cell division. Key to all these roles is the suitable deployment of its labile parts, a process that occurs in a highly crowded environment. Here we consider the effects of crowding on the assembly and organization of cytoskeletal filaments, and how the cell exploits or evades these effects, as needed. Due to entropic trade-offs among different degrees of freedom, long protein filaments crowded by globular proteins spontaneously form segregated bundles. This behavior can be recruited to specific locations by proteins that nucleate filaments and can be adjusted by proteins that cross-link parallel filaments in a fashion that stabilizes polarity, spacing and register within the bundle. Alternatively, spontaneous bundling can be prevented by limiting filament growth with capping and severing proteins or by frustrating filament alignment with oblique cross-links or the formation of branches. Thus, building upon the effects of macromolecular crowding, a modest library of regulatory proteins is able to achieve versatile results.

Macromolecular crowding has significant impact on protein behavior in cellular environments, having influence on their structure, folding, and interactions. This process comes from the high concentration of macromolecules, including proteins, nucleic acids, and carbohydrates, which occupy a substantial fraction of intracellular space. Ficoll 70 and Dextran, synthetic crowding agents, are utilized by researchers to mimic these conditions in vitro. Various studies demonstrate that different crowding agents can enhance protein thermal stability and promote structural organization by stabilizing folded states and compacting denatured forms. Additionally, crowding agents like PEG have been found to exert stronger stabilizing effects on proteins compared to others like Dextran. Understanding the effects of crowding agents is important and crucial for elucidating protein dynamics in cellular contexts and has crucial implications for both fundamental biology and therapeutic applications. Continued research into the mechanisms by which these agents influence protein behavior will provide better insights into cellular biochemistry and may lead to novel strategies for drug development.

Urea transporters (UTs) are a group of membrane channel proteins that specifically facilitate the permeation of urea, which play an essential role in urea reabsorption and water conservation. There are 4 isoforms, UT-A1, UT-A2, UT-A3, UT-B, that are expressed in the kidney to maintain the urea recycle and establish the urea concentration gradient in the medulla, which is essential for the urinary concentration capacity of the kidney. Outside the kidney, widely distributed UT-B and some UT-A isoforms directly participate in regulating signaling transduction and determining cell fate by regulating osmotic pressure, arginine metabolism, and protein carbamylation in various systems. In recent years, studies on different UT knockout mouse models revealed multiple physiological roles of UTs. This chapter summarizes the physiological functions of UTs, including the blood system, urinary system, nervous system, circulatory system, digestive system, auditory system, visual system, reproductive system, and skeletal system.

Urea and urea transporters (UT) are critical to the production of concentrated urine and hence in maintaining body fluid balance. The UT-A1 urea transporter is the major and most important UT isoform in the kidney. Native UT-A1, expressed in the terminal inner medullary collecting duct (IMCD) epithelial cells, is a glycosylated protein with two glycoforms of 117 and 97 kDa. Vasopressin is the major hormone in vivo that rapidly increases urea permeability in the IMCD through increasing the phosphorylation and apical plasma membrane accumulation of UT-A1. The cell signaling pathway for vasopressin-mediated UT-A1 phosphorylation and activity involves two cAMP-dependent signaling pathways: protein kinase A (PKA) and exchange protein activated by cAMP (Epac). UT-A3 is the NH₂-terminal half of UT-A1, exhibiting similarities and dissimilarities with UT-A1. In this chapter, we will discuss UT-A1 and UT-A3 regulation by phosphorylation, ubiquitination and glycosylation.