Sub-cellular biochemistry最新文献

Helix-helix interactions are mediated through highly designable interfaces within tertiary and quaternary structures of proteins and protein assemblies. The structural regularity of these interfaces suggests that ordered self-assembled structures could be constructed from implementation of these interactions between appropriately designed helical protomers. This review summarizes the current understanding of helix-helix interactions within different classes of naturally occurring α-helical protein filaments. The implications of this structural information for the de novo design of synthetic filamentous nanomaterials will be discussed with reference to examples in which these principles have been successfully implemented. A specific case study will focus on the designability of cross-α helical filaments, a recently discovered structural class in which the helical protomers are arranged in a perpendicular orientation with respect to the protofilament axis. This discussion will include an evaluation of the frequency of occurrence of cross-α interfaces in the PDB, the effectiveness of structural prediction from sequence information, and the potential for de novo design of interfaces that promote cross-α interactions.

The coiled coil is one of the most widespread and versatile protein folding motifs and is involved in a vast array of biological functions. The study and design of these assemblies have been shaped by the development of specialised computational tools. This review charts the landscape of these in silico methods, beginning with the foundational sequence-based algorithms for coiled-coil prediction and classification, before moving to the powerful parametric methods that enable the generation of idealised, atomic-resolution structural models. We argue that while indispensable, these tools can promote a view of coiled coils as static, singular structures. Challenging this, we highlight the structural plasticity of coiled coils, the remarkable and increasingly evident ability of these assemblies to adopt multiple distinct conformations and dynamically switch between states. To understand the energetic and mechanistic principles governing this complex behaviour, we explore the crucial role of molecular dynamics (MD) simulations in providing atomistic insights that are inaccessible to static modelling. Finally, we look forward, considering how the next generation of coiled-coil bioinformatics must evolve to address these challenges to take advantage of the opportunities presented by the current explosion in genomic sequence data and the proliferation of AI-predicted protein structures.

Breast cancer remains a leading cause of cancer-related morbidity and mortality in women worldwide. While extensive research has focused on mutations in protein-coding genes, emerging evidence underscores the pivotal role of the noncoding genome-including long noncoding RNAs (lncRNAs), microRNAs (miRNAs), circular RNAs (circRNAs), and piwi-interacting RNAs (piRNAs)-in tumorigenesis, progression, and therapeutic resistance. These noncoding RNAs (ncRNAs) are regulated through diverse epigenetic mechanisms such as DNA methylation, histone modifications, and N6-methyladenosine (m6A) RNA methylation. Aberrant epigenetic modifications in noncoding regions can silence tumor suppressors or activate oncogenes, thereby reprogramming cellular behavior and contributing to breast cancer heterogeneity. High-throughput techniques like whole-genome bisulfite sequencing (WGBS), ATAC-seq, and ChIP-seq have facilitated the discovery of noncoding epimutations with clinical significance. Moreover, ncRNA-based epigenetic alterations are increasingly explored as diagnostic biomarkers, prognostic indicators, and therapeutic targets, particularly in subtype-specific contexts such as triple-negative breast cancer (TNBC) and HER2-positive tumors. Despite advances, challenges remain in interpreting functional noncoding elements and translating findings into clinical interventions. This chapter provides a comprehensive examination of the noncoding epigenome in breast cancer, highlighting current methodologies, molecular mechanisms, and translational potential while also identifying future directions needed to leverage noncoding epigenetics for personalized cancer care.

Fibrillar collagens are the most abundant structural proteins in vertebrates, forming the backbone of connective tissues such as skin, bone, tendon, and cartilage. In bony fish (teleosts), fibrillar collagens exhibit unique genetic and biochemical properties that reflect a complex evolutionary history of this taxonomic group and its adaptation to diverse aquatic environments-from tropical to polar habitats. This review summarises the current understanding of the genetic organisation and biochemical characteristics of fibrillar collagens in bony fish. They show significant differences in amino acid composition to mammalian collagens, especially in cold-adapted species, where collagens display lower thermal stability and reduced hydroxyproline content relative to their mammalian counterparts.Advances in genomic, transcriptomic, and proteomic profiling have provided new perspectives on the molecular diversity and tissue-specific roles of collagen chains in teleosts. Furthermore, the biomedical potential of fish-derived collagens is receiving growing attention, particularly in biomaterials, wound healing, tissue engineering, and drug delivery systems, owing to their biocompatibility, low immunogenicity, and ease of extraction from byproducts of the fishing industry.By looking at molecular, structural, and applied perspectives, this review highlights the relevance of bony fish collagens as a subject of fundamental biological interest and as a valuable resource for biotechnological and biomedical innovation.

Intermediate filaments (IFs) are central to the mechanical integrity of metazoan cells and play critical roles in various fundamental cellular and multicellular processes, including cell motility, signal transduction, and wound healing. To perform their functions, IF proteins self-assemble into nanoscale biopolymers, each exhibiting unique properties that are finely tuned to their specific roles across different tissue types. However, the 3D structure of IFs has remained largely unresolved due to their intrinsic flexibility and polymorphism. This chapter reviews recent advances in the structural analysis of IFs, with a focus on vimentin IFs (VIFs), which are featuring a helical tube with a central luminal fiber. We discuss how AlphaFold-based modeling, chemical cross-linking data, and cryo-electron microscopy (cryo-EM) reconstructions have been integrated to generate a detailed structural model of VIFs, highlighting key features such as the helical symmetry of the filaments and the nature of the luminal fiber. Additionally, we explore potential sources of IF polymorphism and their implications for the analysis of IF structures.

In lower organisms (bacteria, fungi, yeast), some species that express the enzyme urease take up urea from the surrounding medium as a source of nitrogen, by energy-dependent urea transporters. In contrast, in mammals, urea is an endproduct of nitrogen metabolism, and the energy-dependent urea transports are associated with either the need to excrete nitrogen efficiently, in the case of excess nitrogen intake, or the need to conserve nitrogen and re-use it, in the case of low nitrogen supply.Three different energy-dependent urea transports have been characterized functionally in the mammalian kidney. One responsible for urea secretion in the straight segment of the proximal tubule (proximal straight tubule, PST), another for urea reabsorption in the upper third of the inner medullary collecting duct (IMCD), and one in the very late portion of the IMCD. But intriguingly, up to now, none of the membrane transporters responsible for these transports has been characterized molecularly.This review describes these urea transports functionally and proposes a candidate transporter responsible for urea secretion in the PST. Based on the study of knockout mice, SLC6A18 has been characterized as a glycine transporter, but several previous observations suggest that it may also serve another function. SLC6A18 is very likely a urea/glycine, sodium-dependent antiport. These observations are described in detail.Energy-dependent urea transport is suspected to also take place in two other organs that express facilitated urea transporters; in the testis, urea secretion could initiate a flux of fluid in seminiferous tubules to ensure sperm transport into the lumen; in the bladder, urea secretion could reclaim urea that is at permanent risk of dissipation, due to the large urea concentration difference between urine and blood and the high expression of the facilitated transporter UT-B on the basal membrane of the urothelium.The energy-dependent secretion of urea in the PST has a number of consequences. (1) It allows a better efficiency of urea excretion and thus may prevent some toxicity of urea. (2) It provides a much better understanding of the urine concentrating mechanism. (3) It explains how urea may influence glomerular filtration rate, indirectly.

Urea transporters (UTs) facilitate the rapid transport of urea from the extracellular space to the intracellular space through a selective transport mechanism driven by urea concentration gradients. Advances in Cryo-electron microscopy and X-ray crystallography have enabled us to solve the homotrimer structures of UT-A and UT-B, which share a common feature comprising two homologous domains surrounding a continuous transmembrane pore, indicating that UTs transport urea via a channel-like mechanism. By analyzing the structures of ligand-protein complexes, results from molecular dynamics simulations, and functional data on urea analogues and small molecule permeation inhibitors, we can gain a deeper understanding of the conservation and specificity of the urea channel architecture, and clearly recognize how urea is transported by UTs and the mechanisms of small molecule inhibition. This will provide an important structural basis for drug design and development.

Urea is generated by the urea cycle enzymes, which are mainly in the liver but are also ubiquitously expressed at low levels in other tissues of mammals. Urea is then eliminated through fluids, especially urine. Urea also serves as a readily available nitrogen source for the growth of many organisms, including plants and bacteria. Urea transporters are recognized as the primary membrane proteins responsible for urea transport in organisms. However, an increasing body of studies has identified additional membrane proteins in animals, plants, and microbes that exhibit urea transport capabilities or potential. The contribution of these membrane proteins to the maintenance of physiological homeostasis and their interactions with urea transporters remains to be fully elucidated. In this chapter, transport, characteristics, regulation, as well as cellular localization of non-urea-transporter membrane proteins facilitating urea transport, are reviewed to highlight their roles in physiology and pathophysiology. Specifically, the mammalian aquaporins AQP3, AQP6, AQP7, AQP8, AQP9, AQP10, and a sodium-glucose transporter (SGLT1) in the kidney are permeable to urea. In plants, tonoplast intrinsic proteins (TIPs), a member of aquaporin family, and the DUR3 orthologue, potentially play roles in low- and high-affinity urea transport, respectively. Two urea transporters pH-independent (Yut) and pH-dependent transporters (ureI) in bacteria are known to play roles in disease conditions.

Urea transporters (UTs) UT-As (encoded by Slc14A2) and UT-B (encoded by Slc14A1), are important members of the solute carrier family. They are a group of membrane channel proteins that are selectively permeable to urea. Slc14A1 is considered the key gene determining the Kidd blood group system, and its variants can lead to the loss of Jk antigens, resulting in transfusion-related complications. Additionally, studies have shown that Slc14A1 is closely associated with cancer development and progression, with its expression level and promoter methylation status potentially serving as biomarkers for cancer progression and prognosis. Recent research suggests that UT-B functional deficiency may cause neurodegenerative diseases by accumulating urea in the brain, thereby affecting neuronal function and viability. Mutations of Slc14A2 are linked to hypertension and metabolic syndrome, due to its essential role in maintaining urea homeostasis. This chapter aims to introduce the clinical significance of UT-B and UT-A and highlight their potential roles as diagnostic and therapeutic targets.

Prion diseases are rare yet devastating neurodegenerative disorders that result from the misfolding of the cellular prion protein, PrP^C, into its infectious and pathogenic isoform, PrP^Sc. These diseases are marked by progressive neuronal damage, leading to irreversible cognitive and motor impairments and, ultimately, death. Despite extensive research into their underlying mechanisms, effective treatments for prion diseases remain elusive. Such a lack of effective therapies mainly arises from several challenges, including delayed diagnosis and the complex and poorly understood biology of prion neurotoxicity.This chapter provides an in-depth exploration of current and emerging therapeutic strategies to treat prion diseases. One promising approach involves using small molecules to inhibit prion replication by destabilizing PrP^Sc or modulating PrP^C homeostasis, possibly avoiding previously observed strain-dependent drug resistance. In parallel, immunotherapeutic approaches, including passive and active immunization, have shown potential in targeting prions. However, challenges related to brain penetration and potential neurotoxicity remain significant hurdles to their successful clinical application. Developing advanced genetic tools, such as RNA interference (RNAi) and CRISPR-based technologies, has opened up new avenues for therapeutic intervention. These approaches selectively target and reduce PrP^C expression, thereby preventing the formation and accumulation of PrP^Sc. The chapter also highlights the progress in clinical trials, such as the PrProfile trial for ION717, which tests a novel treatment based on an antisense oligonucleotide (ASO). As we look toward the future, the chapter underscores the need for a multifaceted approach to treating prion diseases. Furthermore, early detection methods, innovative drug delivery systems, and collaborative interdisciplinary research efforts will be essential for translating scientific discoveries into practical clinical breakthroughs.