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Mitotic bookmarking by transcription factors: be aware of redundancy Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-03-18 Miguel V. Silva, Diogo S. Castro
A recent report by shows redundant functions for the transcription factors (TFs) ESRRB and NR5A2 as mitotic bookmarkers in mouse embryonic stem (ES) cells. These occupy some of their target sites in mitotic chromatin, ensuring their robust reactivation after cell division, including markers and regulators of pluripotency.
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The RNA tether model for human chromosomal translocation fragile zones Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-03-14 Di Liu, Chih-Lin Hsieh, Michael R. Lieber
One of the two chromosomal breakage events in recurring translocations in B cell neoplasms is often due to the recombination-activating gene complex (RAG complex) releasing DNA ends before end joining. The other break occurs in a fragile zone of 20–600 bp in a non-antigen receptor gene locus, with a more complex and intriguing set of mechanistic factors underlying such narrow fragile zones. These factors
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Keeping neuronal activity in check: a novel role for α-synuclein serine-129 phosphorylation in the healthy brain Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-03-07 D, a, n, i, e, l, l, e, , E, ., , M, o, r
Phosphorylation of α-synuclein protein at serine-129 (Ser129P) is a widely used marker for disease pathology in neurodegenerative disorders termed synucleinopathies. In groundbreaking work by Ser129P was shown to facilitate the normal function of α-synuclein, bearing significant implications for the transition from a physiological to pathological state.
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Spray-type modifications: an emerging paradigm in post-translational modifications Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-03-04 Yun-Bin Lee, Hyun-Woo Rhee
A post-translational modification (PTM) occurs when a nucleophilic residue (e.g., lysine of a target protein) attacks electrophilic substrate molecules (e.g., acyl-AMP), involving writer enzymes or even occurring spontaneously. Traditionally, this phenomenon was thought to be sequence specific; however, recent research suggests that PTMs can also occur in a non-sequence-specific manner confined to
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TrkB transmembrane domain: bridging structural understanding with therapeutic strategy Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-03-02 Giray Enkavi, Mykhailo Girych, Rafael Moliner, Ilpo Vattulainen, Eero Castrén
TrkB (neuronal receptor tyrosine kinase-2, NTRK2) is the receptor for brain-derived neurotrophic factor (BDNF) and is a critical regulator of activity-dependent neuronal plasticity. The past few years have witnessed an increasing understanding of the structure and function of TrkB, including its transmembrane domain (TMD). TrkB interacts with membrane cholesterol, which bidirectionally regulates TrkB
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Glucocorticoid receptor signaling: intricacies and therapeutic opportunities Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-29 Dorien Clarisse, Laura Van Moortel, Chloé Van Leene, Kris Gevaert, Karolien De Bosscher
The glucocorticoid receptor (GR) is a major nuclear receptor (NR) drug target for the treatment of inflammatory disorders and several cancers. Despite the effectiveness of GR ligands, their systemic action triggers a plethora of side effects, limiting long-term use. Here, we discuss new concepts of and insights into GR mechanisms of action to assist in the identification of routes toward enhanced therapeutic
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Oxytocin and vasopressin signaling in health and disease Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-27 Monika Perisic, Katrina Woolcock, Anke Hering, Helen Mendel, Markus Muttenthaler
Neurohypophysial peptides are ancient and evolutionarily highly conserved neuropeptides that regulate many crucial physiological functions in vertebrates and invertebrates. The human neurohypophysial oxytocin–vasopressin (OT-VP) signaling system with its four receptors has become an attractive drug target for a variety of diseases, including cancer, pain, cardiovascular indications, and neurological
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Mitochondria in disease: changes in shapes and dynamics Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-23 Brenita C. Jenkins, Kit Neikirk, Prasanna Katti, Steven M. Claypool, Annet Kirabo, Melanie R. McReynolds, Antentor Hinton
Mitochondrial structure often determines the function of these highly dynamic, multifunctional, eukaryotic organelles, which are essential for maintaining cellular health. The dynamic nature of mitochondria is apparent in descriptions of different mitochondrial shapes [e.g., donuts, megamitochondria (MGs), and nanotunnels] and crista dynamics. This review explores the significance of dynamic alterations
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A left-handed RNA quadruplex directs gene silencing Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-16 Samuel E. Butcher
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Exploring membrane asymmetry and its effects on membrane proteins Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-13 Georg Pabst, Sandro Keller
Plasma membranes utilize free energy to maintain highly asymmetric, non-equilibrium distributions of lipids and proteins between their two leaflets. In this review we discuss recent progress in quantitative research enabled by using compositionally controlled asymmetric model membranes. Both experimental and computational studies have shed light on the nuanced mechanisms that govern the structural
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Microtubule specialization by +TIP networks: from mechanisms to functional implications Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-12 Sandro M. Meier, Michel O. Steinmetz, Yves Barral
To fulfill their actual cellular role, individual microtubules become functionally specialized through a broad range of mechanisms. The ‘search and capture’ model posits that microtubule dynamics and functions are specified by cellular targets that they capture (i.e., ), independently of the microtubule-organizing center (MTOC) they emerge from. However, work in budding yeast indicates that MTOCs may
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Enlightening epigenetics: optochemical tools illuminate the path Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-12 Kaijun Su, Olalla Vázquez
Optochemical tools have become potent instruments for understanding biological processes at the molecular level, and the past decade has witnessed their use in epigenetics and epitranscriptomics (also known as RNA epigenetics) for deciphering gene expression regulation. By using photoresponsive molecules such as photoswitches and photocages, researchers can achieve precise control over when and where
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Interlinked switch circuits of biological intelligence Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-09 Raktim Mukherjee, Saptarshi Sinha, Gary D. Luker, Pradipta Ghosh
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cAMP signaling: a remarkably regional affair Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-02 Andreas Bock, Roshanak Irannejad, John D. Scott
Louis Pasteur once famously said ‘in the fields of observation chance favors only the prepared mind’. Much of chance is being in the right place at the right time. This is particularly true in the crowded molecular environment of the cell where being in the right place is often more important than timing. Although Brownian motion argues that enzymes will eventually bump into substrates, this probability
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Advisory Board and Contents Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-01
Abstract not available
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Subscription and Copyright Information Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-02-01
Abstract not available
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Pre-twisting for improved genome modification and miRNA targeting Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-17 Rongguang Lu, Gang Chen
Two reports by Dhuri et al. and Oyaghire et al., respectively, show that, through installing chiral centers at the backbone of the artificial nucleic acid, peptide nucleic acid (PNA), enhanced miRNA targeting and genome modification can be achieved, with important implications in fighting cancers and β-thalassemia.
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Decoding anaphylatoxins: unveiling the molecular mechanisms of complement receptor activation and signaling Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-16 Francisco J. Fernández, M. Cristina Vega
Recent advances in cryo-electron microscopy (Cryo-EM) have revolutionized our understanding of the complement C5a/C3a receptors that are crucial in inflammation. A recent report by Yadav et al. has elucidated the activation, ligand binding, selectivity, and signaling bias of these receptors, thereby enhancing structure-guided drug discovery. This paves the way for more effective anti-inflammatory therapies
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Taking Me away: the function of phosphorylation on histone lysine demethylases Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-16 Nicola M. Karakatsanis, Joshua J. Hamey, Marc R. Wilkins
Histone lysine demethylases (KDMs) regulate eukaryotic gene transcription by catalysing the removal of methyl groups from histone proteins. These enzymes are intricately regulated by the kinase signalling system in response to internal and external stimuli. Here, we review the mechanisms by which kinase-mediated phosphorylation influence human histone KDM function. These include the changing of histone
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Interplay between the transcription preinitiation complex and the +1 nucleosome Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-13 Xizi Chen, Yanhui Xu
Eukaryotic transcription starts with the assembly of a preinitiation complex (PIC) on core promoters. Flanking this region is the +1 nucleosome, the first nucleosome downstream of the core promoter. While this nucleosome is rich in epigenetic marks and plays a key role in transcription regulation, how the +1 nucleosome interacts with the transcription machinery has been a long-standing question. Here
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Advances, challenges, and opportunities in structural biology Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-09 Basavraj Khanppnavar, Rachel A. North, Salvador Ventura, Yanhui Xu
Abstract not available
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Unlocking translational machinery for antitubercular drug development Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-08 Navneet Kumar, Mushtaq Ahmad Wani, Chaaya Iyengar Raje, Prabha Garg
Targeting translational factor proteins (TFPs) presents significant promise for the development of innovative antitubercular drugs. Previous insights from antibiotic binding mechanisms and recently solved 3D crystal structures of () elongation factor thermo unstable–GDP (EF-Tu–GDP), elongation factor thermo stable–EF-Tu (EF-Ts–EF-Tu), and elongation factor G–GDP (EF-G–GDP) have opened up new avenues
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Advisory Board and Contents Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-04
Abstract not available
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Subscription and Copyright Information Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-04
Abstract not available
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Guidelines for organizing accessible and inclusive research retreats Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-06 Margaret J. Fuller, Madison R. Mix, Ellen Voigt, Darren S. Hoffmann, Pamela K. Geyer
Research retreats are elements of scientific graduate training programs. Although expected to provide strong educational value, some students are reluctant to attend. Here, we identify participation barriers and provide guidelines for retreat design that minimize obstacles and establish an inclusive environment to improve attendance and enrichment for all attendees.
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The inner workings of an ancient biological clock Trends Biochem. Sci. (IF 13.8) Pub Date : 2024-01-06 Mingxu Fang, Andy LiWang, Susan S. Golden, Carrie L. Partch
Circadian clocks evolved in diverse organisms as an adaptation to the daily swings in ambient light and temperature that derive from Earth’s rotation. These timing systems, based on intracellular molecular oscillations, synchronize organisms' behavior and physiology with the 24-h environmental rhythm. The cyanobacterial clock serves as a special model for understanding circadian rhythms because it
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Creative approaches using proximity labeling to gain new biological insights Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-30 Ryan R. Milione, Bin-Bin Schell, Cameron J. Douglas, Ciaran P. Seath
At its most fundamental level, life is a collection of synchronized cellular processes driven by interactions among biomolecules. Proximity labeling has emerged as a powerful technique to capture these interactions in native settings, revealing previously unexplored elements of biology. This review highlights recent developments in proximity labeling, focusing on methods that push the fundamental technologies
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Unlocking the biosynthesis of psychedelic-inspired indolethylamines Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-29 Abhishek K. Sen, J. Andrew Jones
A recent report by describes the discovery of RmNMT, a highly active and promiscuous tryptamine -methyltransferase from the cane toad, . -dimethyltryptamine derivatives produced by this enzyme were then evaluated for their potential to serve as next-generation treatments for mental health disorders.
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Structural insights into membrane adenylyl cyclases, initiators of cAMP signaling Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-28 Dina Schuster, Basavraj Khanppnavar, Ilayda Kantarci, Ved Mehta, Volodymyr M. Korkhov
Membrane adenylyl cyclases (ACs) catalyze the conversion of ATP to the ubiquitous second messenger cAMP. As effector proteins of G protein-coupled receptors and other signaling pathways, ACs receive and amplify signals from the cell surface, translating them into biochemical reactions in the intracellular space and integrating different signaling pathways. Despite their importance in signal transduction
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Revealing eEF-2 kinase: recent structural insights into function Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-16 Andrea Piserchio, Kevin N. Dalby, Ranajeet Ghose
The α-kinase eukaryotic elongation factor 2 kinase (eEF-2K) regulates translational elongation by phosphorylating its ribosome-associated substrate, the GTPase eEF-2. eEF-2K is activated by calmodulin (CaM) through a distinctive mechanism unlike that in other CaM-dependent kinases (CAMK). We describe recent structural insights into this unique activation process and examine the effects of specific
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Why U matters: detection and functions of pseudouridine modifications in mRNAs Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-14 Rebecca Rodell, Nicolas Robalin, Nicole M. Martinez
The uridine modifications pseudouridine (Ψ), dihydrouridine, and 5-methyluridine are present in eukaryotic mRNAs. Many uridine-modifying enzymes are associated with human disease, underscoring the importance of uncovering the functions of uridine modifications in mRNAs. These modified uridines have chemical properties distinct from those of canonical uridines, which impact RNA structure and RNA–protein
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TRAPs: the ‘elevator-with-an-operator’ mechanism Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-14 James S. Davies, Michael J. Currie, Renwick C.J. Dobson, Christopher R. Horne, Rachel A. North
Tripartite ATP-independent periplasmic (TRAP) transporters are nutrient-uptake systems found in bacteria and archaea. These evolutionary divergent transporter systems couple a substrate-binding protein (SBP) to an elevator-type secondary transporter, which is a first-of-its-kind mechanism of transport. Here, we highlight breakthrough TRAP transporter structures and recent functional data that probe
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Molecular mechanisms of the RNA polymerases in plant RNA-directed DNA methylation Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-09 Guohui Xie, Xuan Du, Hongmiao Hu, Jiamu Du
In plants, two atypical DNA-dependent RNA polymerases, RNA polymerase IV (Pol IV) and Pol V, and an RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) together produce noncoding RNAs (ncRNAs) to guide the plant-specific RNA-directed DNA methylation (RdDM). Although both Pol IV and Pol V have evolved from the canonical Pol II, they have adapted to different roles in RdDM. The mechanisms of their adaptation are key
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mRNA accessibility within mRNPs as a determinant of gene expression Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-12-08 P. Cody He, Chuan He
Gene expression is a complex process requiring many control mechanisms to achieve a desired phenotype. DNA accessibility within chromatin is well established as an important determinant of gene expression. By contrast, while mRNA also associates with a complement of proteins, the exact nature of messenger ribonucleoprotein (mRNP) packaging and its functional relevance is not as clear. Recent reports
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Causes and consequences of DNA single-strand breaks Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-30 Keith W. Caldecott
DNA single-strand breaks (SSBs) are among the most common lesions arising in human cells, with tens to hundreds of thousands arising in each cell, each day. Cells have efficient mechanisms for the sensing and repair of these ubiquitous DNA lesions, but the failure of these processes to rapidly remove SSBs can lead to a variety of pathogenic outcomes. The threat posed by unrepaired SSBs is illustrated
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Hypoxia Inducible Factor pathway proteins in high-altitude mammals Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-29 Frank S. Lee
Humans and other mammals inhabit hypoxic high-altitude locales. In many of these species, genes under positive selection include ones in the Hypoxia Inducible Factor (HIF) pathway. One is PHD2 (EGLN1), which encodes for a key oxygen sensor. Another is HIF2A (EPAS1), which encodes for a PHD2-regulated transcription factor. Recent studies have provided insights into mechanisms for these high-altitude
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Elucidating the novel mechanisms of molecular chaperones by single-molecule technologies Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-16 Ayush Chandrakant Mistry, Debojyoti Chowdhury, Soham Chakraborty, Shubhasis Haldar
Molecular chaperones play central roles in sustaining protein homeostasis and preventing protein aggregation. Most studies of these systems have been performed in bulk, providing averaged measurements, though recent single-molecule approaches have provided an in-depth understanding of the molecular mechanisms of their activities and structural rearrangements during substrate recognition. Chaperone
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The ART of RNAylation: covalent RNA–protein linkage in bacteriophage infection Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-16 Sophie M. Korn, Sunny Sharma, Anna-Lena Steckelberg
Bacteriophages have been a treasure trove for the discovery of fundamental biological principles and the expansion of our enzymatic toolkit since the dawn of molecular biology. In a recent study by Wolfram-Schauerte et al. these ubiquitous bacteria-infecting viruses reveal yet another new biological concept: post-translational modification through covalent RNA–protein linkages.
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Subscription and Copyright Information Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-09
Abstract not available
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Team science: building, nurturing, and expanding research collaborations Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-10 Arun K. Shukla
Science is a collaborative endeavor, and the importance of collaborations across disciplines and boundaries is becoming clearer with the advent of new technologies. This article focuses on key aspects of initiating and sustaining new collaborations, and expanding from bilateral to multilateral efforts to create major impact through team science.
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Advisory Board and Contents Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-09
Abstract not available
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Wrapping up a special series on scientific figure development Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-09 Sannie Culbertson
Abstract not available
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Turning science into cover art Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-09 Helen Dauben, Ivan Matic, Rune Thomas Kidmose, Bjørn Panyella Pedersen, Tannishtha Saha, Michela Di Virgilio, Julie Ho Sung
Abstract not available
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Dissecting the biophysics and biology of intrinsically disordered proteins Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-08 Priya R. Banerjee, Alex S. Holehouse, Richard Kriwacki, Paul Robustelli, Hao Jiang, Alexander I. Sobolevsky, Jennifer M. Hurley, Joshua T. Mendell
Intrinsically disordered regions (IDRs) within human proteins play critical roles in cellular information processing, including signaling, transcription, stress response, DNA repair, genome organization, and RNA processing. Here, we summarize current challenges in the field and propose cutting-edge approaches to address them in physiology and disease processes, with a focus on cancer.
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Type III CRISPR-Cas: beyond the Cas10 effector complex Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-08 Gianna Stella, Luciano Marraffini
Type III CRISPR-Cas loci encode some of the most abundant, yet complex, immune systems of prokaryotes. They are composed of a Cas10 complex that uses an RNA guide to recognize transcripts from bacteriophage and plasmid invaders. Target recognition triggers three activities within this complex: ssDNA degradation, synthesis of cyclic oligoadenylates (cOA) that act as second messengers to activate CARF-domain
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UFMylation: a ubiquitin-like modification Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-07 Xingchen Zhou, Sayyed J. Mahdizadeh, Matthieu Le Gallo, Leif A. Eriksson, Eric Chevet, Elodie Lafont
Post-translational modifications (PTMs) add a major degree of complexity to the proteome and are essential controllers of protein homeostasis. Amongst the hundreds of PTMs identified, ubiquitin and ubiquitin-like (UBL) modifications are recognized as key regulators of cellular processes through their ability to affect protein–protein interactions, protein stability, and thus the functions of their
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Cryo-EM structures of functional and pathological amyloid ribonucleoprotein assemblies Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-03 Javier Garcia-Pardo, Salvador Ventura
Amyloids are implicated in neurodegenerative and systemic diseases, yet they serve important functional roles in numerous organisms. Heterogeneous nuclear ribonucleoproteins (hnRNPs) represent a large family of RNA-binding proteins (RBPs) that control central events of RNA biogenesis in normal and diseased cellular conditions. Many of these proteins contain prion-like sequences of low complexity, which
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Mini PROTACs: N-end rule-mediated degradation on the horizon Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-02 Yanfen Liu, Zhangshun Wang, Yong Cang
Heterobifunctional proteolysis-targeting chimeras (PROTACs) offer a promising cancer treatment avenue by efficiently degrading unwanted cellular proteins. A recent study from Zhang et al. demonstrated the successful utilization of the N-end rule in PROTAC design, allowing for a modular degradation rate tailored to the oncogenic driver BCR–ABL.
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Helicases clear hurdles during plant defense protein translation Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-01 Liyuan You, Cuilan Shi, Daowen Wang, Zheng Qing Fu
Plants undergo translational reprogramming when they are under attack by pathogens. recently revealed that plant helicases induced by pathogen recognition unwind RNA hairpins upstream of the main open reading frames (mORFs), thus allowing ribosomes to bypass the upstream ORFs (uORFs) and translate downstream defense proteins, a mechanism that is also found in mammals.
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Cotranslational sorting and processing of newly synthesized proteins in eukaryotes Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-11-01 Martin Gamerdinger, Elke Deuerling
Ribosomes interact with a variety of different protein biogenesis factors that guide newly synthesized proteins to their native 3D shapes and cellular localization. Depending on the type of translated substrate, a distinct set of cotranslational factors must interact with the ribosome in a timely and coordinated manner to ensure proper protein biogenesis. While cytonuclear proteins require cotranslational
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Defining the commonalities between post-transcriptional and post-translational modification communities Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-24 Zachary T. Baumer, Luke Erber, Elizabeth Jolley, Sheldon Lawrence, Chuwei Lin, Shino Murakami, Veronica Perez, Wil Prall, Cassandra Schaening-Burgos, Megan Sylvia, Sixue Chen, Brian D. Gregory
Post-transcriptional modifications of RNA (PRMs) and post-translational modifications of proteins (PTMs) are important regulatory mechanisms in biological processes and have many commonalities. However, the integration of these research areas is lacking. A recent discussion identified the priorities, areas of emphasis, and necessary technologies to advance and integrate these areas of study.
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Dynamics and logic of promoter melting Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-18 Andrey Feklistov
Despite significant progress in our understanding of promoter melting dynamics, underlying principles of the process remain elusive, with opposing views on key aspects held by many in the field. Here, I discuss the mechanistic logic behind the interplay of thermal and deterministic forces acting to create transcriptionally competent promoter complexes.
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Subscription and Copyright Information Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-13
Abstract not available
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Time-resolved serial crystallography to reveal protein structural changes Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-14 Petra Meszaros, Sebastian Westenhoff
Abstract not available
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Advisory Board and Contents Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-13
Abstract not available
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Using graphs and charts in scientific figures Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-13 Karol Buda, Katerina Cermakova, H. Courtney Hodges, Eugenio F. Fornasiero, Shahar Sukenik, Alex S. Holehouse
Abstract not available
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Confluence and convergence of Dscam and Pcdh cell-recognition codes Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-13 Haiyang Dong, Jinhuan Li, Qiang Wu, Yongfeng Jin
The ability of neurites of the same neuron to avoid each other (self-avoidance) is a conserved feature in both invertebrates and vertebrates. The key to self-avoidance is the generation of a unique subset of cell-surface proteins in individual neurons engaging in isoform-specific homophilic interactions that drive neurite repulsion rather than adhesion. Among these cell-surface proteins are fly Dscam1
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AI interprets the Central Dogma and Genetic Code Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-10-11 Alexander M. Ille, Michael B. Mathews
Generative artificial intelligence (AI) is a burgeoning field with widespread applications, including in science. Here, we explore two paradigms that provide insight into the capabilities and limitations of Chat Generative Pre-trained Transformer (ChatGPT): its ability to (i) define a core biological concept (the Central Dogma of molecular biology); and (ii) interpret the genetic code.
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Two for one: regulatory RNAs that encode small proteins Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-09-28 Jordan J. Aoyama, Gisela Storz
RNAs are commonly categorized as being either protein-coding mRNAs or noncoding RNAs. However, an increasing number of transcripts, in organisms ranging from bacteria to humans, are being found to have both coding and noncoding functions. In some cases, the sequences encoding the protein and the regulatory RNA functions are separated, while in other cases the sequences overlap. The protein and RNA
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Giant variations in giant virus genome packaging Trends Biochem. Sci. (IF 13.8) Pub Date : 2023-09-28 Paul B. Talbert, Steven Henikoff, Karim-Jean Armache
Giant viruses (Nucleocytoviricota) have a largely conserved lifecycle, yet how they cram their large genomes into viral capsids is mostly unknown. The major capsid protein and the packaging ATPase (pATPase) comprise a highly conserved morphogenesis module in giant viruses, yet some giant viruses dispense with an icosahedral capsid, and others encode multiple versions of pATPases, including conjoined