Sub-cellular biochemistry最新文献_第7页

Plant Golgi and GECCO: The Universality of ER-Golgi Interface. 植物高尔基与GECCO: er -高尔基界面的普适性。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-06936-8_10

Yoko Ito, Tomohiro Uemura

{"title":"Plant Golgi and GECCO: The Universality of ER-Golgi Interface.","authors":"Yoko Ito, Tomohiro Uemura","doi":"10.1007/978-3-032-06936-8_10","DOIUrl":"10.1007/978-3-032-06936-8_10","url":null,"abstract":"In spite of its highly conserved molecular constituents, the Golgi apparatus shows diverse morphologies depending on the organism and cell type. In particular, in plant cells, the distribution and dynamics of the Golgi differ considerably from that seen in their mammalian or yeast counterparts. The architecture of the ER-Golgi interface, the first transfer station of the whole secretory traffic, has also been thought to differ between plants and the better-known mammalian system that possesses the ER-Golgi intermediate compartment (ERGIC). However, detailed observations with plant cells gave rise to the identification of GECCO, the ER-Golgi intermediate that is likely to correspond to the mammalian ERGIC. The existence of compartments that are seemingly different, but still share common features across multiple eukaryotic kingdoms, highlights the universality of the ER-Golgi interface. In this chapter, after summarizing the characteristics of the plant Golgi, we will introduce the findings about GECCO by comparing plants with mammals and yeast. In addition, we will discuss the universal identity of the ER-Golgi intermediate compartments in order to transcend the morphological diversity for a deeper understanding of the ER-Golgi interface.","PeriodicalId":21991,"journal":{"name":"Sub-cellular biochemistry","volume":"110 ","pages":"245-265"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145522886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fibrin as a Versatile Fibrous Biopolymer. 纤维蛋白是一种多用途的纤维生物聚合物。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-05273-5_13

John W Weisel, Rustem I Litvinov

{"title":"Fibrin as a Versatile Fibrous Biopolymer.","authors":"John W Weisel, Rustem I Litvinov","doi":"10.1007/978-3-032-05273-5_13","DOIUrl":"10.1007/978-3-032-05273-5_13","url":null,"abstract":"Fibrin is a fibrous biopolymer that plays a crucial role in hemostasis, thrombosis, wound healing, and various other biological functions and pathological conditions. The X-ray crystallographic structure of fibrinogen, along with computational reconstructions of missing regions and extensive biochemical and biophysical studies, has provided significant insights into the molecular mechanisms of fibrin formation, its structural organization, and its biological and mechanical properties. Upon cleavage of fibrinopeptides by thrombin, the blood protein fibrinogen is converted into fibrin monomers, which then interact through \"knobs\" exposed by the removal of fibrinopeptides in the central region and \"holes\" that are constitutively available at the ends of the molecules. The result is half-staggered, double-stranded oligomers that elongate into protofibrils, which then aggregate laterally to form fibers, and branch to create a three-dimensional network. Much has been learned about how the structure of fibrin contributes to the mechanical properties of the clot, including changes in fiber orientation, stretching, buckling, and the forced unfolding of molecular domains. Recent research into the mechanical stability of fibrin has enhanced our understanding of its rupture resistance, which is relevant to thrombotic embolization and mechanical thrombectomy. The fibrinolytic system, in which plasminogen, along with tissue-type plasminogen activator, binds to fibrin and is activated to plasmin, leads to the digestion of fibrin at specific lysine residues. Fibrin has been utilized in hemostatic fibrin sealants and as a biomaterial in tissue engineering and regenerative medicine. Despite significant advances in our understanding of these interconnected processes, much remains unknown about the molecular mechanisms underlying fibrin's biological functions, particularly concerning the molecular origins of its mechanical properties and the more complex structure and properties of hemostatic clots and pathological thrombi and their clinical implications.","PeriodicalId":21991,"journal":{"name":"Sub-cellular biochemistry","volume":"113 ","pages":"413-473"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146012315","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils. 序列预测、结构建模和线圈塑性的挑战。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-05273-5_1

Christopher W Wood, Guto G Rhys, Evangelia Notari

{"title":"Sequence Prediction, Structural Modelling and the Challenges of Plasticity in Coiled Coils.","authors":"Christopher W Wood, Guto G Rhys, Evangelia Notari","doi":"10.1007/978-3-032-05273-5_1","DOIUrl":"10.1007/978-3-032-05273-5_1","url":null,"abstract":"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.","PeriodicalId":21991,"journal":{"name":"Sub-cellular biochemistry","volume":"113 ","pages":"1-34"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146011631","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Designability of α-Helical Protein Filaments. α-螺旋蛋白细丝的可设计性。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-05273-5_15

Abhinaba Das, Vincent Conticello

{"title":"Designability of α-Helical Protein Filaments.","authors":"Abhinaba Das, Vincent Conticello","doi":"10.1007/978-3-032-05273-5_15","DOIUrl":"10.1007/978-3-032-05273-5_15","url":null,"abstract":"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.","PeriodicalId":21991,"journal":{"name":"Sub-cellular biochemistry","volume":"113 ","pages":"493-520"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146012383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Golgi Membrane-Associated Degradation (GOMED), a New Intracellular Proteolysis Mechanism. 高尔基膜相关降解（GOMED），一种新的细胞内蛋白水解机制。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-16833-7_14

Shigeomi Shimizu, Shinya Honda, Satoru Torii, Satoko Arakawa, Masatsune Tsujioka, Hirofumi Yamaguchi, Hajime Tajima Sakurai

引用次数: 0

Applications of Carbonic Anhydrase Inhibitors in Neurological Disorders, Mechanisms and Therapeutic Potential. 碳酸酐酶抑制剂在神经系统疾病中的应用、机制和治疗潜力。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-23172-7_7

Neera Raghav, Rashmi Pundeer

引用次数: 0

Physics and Life at Interfaces: Momentum Conservation and Albert Einstein's Thermodynamics in 2D. 界面上的物理和生命：动量守恒和爱因斯坦的二维热力学。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-24159-7_9

Matthias F Schneider, Andreas Gruhn

引用次数: 0

Correction to: From (Epi)genetics-to-Precision (E2P): Non-protein Coding RNAs (ncRNAs) a Step-toward Precision Medicine. 更正：从（Epi）遗传学到精确（E2P）：非蛋白编码rna （ncRNAs）迈向精确医学的一步。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-08530-6_9

Nadia M Hamdy, Ahmed S Sultan, John Frederick Kennedy

引用次数: 0

Mapping Non-Coding Epimutations in Breast Cancer: Advancing Epigenetics Towards Precision Medicine. 在乳腺癌中定位非编码表观突变：向精准医学推进表观遗传学。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-08530-6_3

Mohamed E Abdel Aziz, Heba Momtaz, Basel Mohamed, Mariam Amr, Alhassan Soliman Wadan, Shaimaa Abdel-Ghany, Borros Arneth, Hussein Sabit

{"title":"Mapping Non-Coding Epimutations in Breast Cancer: Advancing Epigenetics Towards Precision Medicine.","authors":"Mohamed E Abdel Aziz, Heba Momtaz, Basel Mohamed, Mariam Amr, Alhassan Soliman Wadan, Shaimaa Abdel-Ghany, Borros Arneth, Hussein Sabit","doi":"10.1007/978-3-032-08530-6_3","DOIUrl":"10.1007/978-3-032-08530-6_3","url":null,"abstract":"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.","PeriodicalId":21991,"journal":{"name":"Sub-cellular biochemistry","volume":"114 ","pages":"123-182"},"PeriodicalIF":0.0,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145889433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Insights into the Structure of Intermediate Filaments. 对中间细丝结构的洞察。

Sub-cellular biochemistry Pub Date : 2026-01-01 DOI: 10.1007/978-3-032-05273-5_6

Matthias Eibauer, Ohad Medalia

引用次数: 0