Journal of Molecular Biology最新文献

{"title":"In Defense of Biochemistry: Studies of Transcriptional Regulation.","authors":"Roger D Kornberg, Andrey Feklistov","doi":"10.1016/j.jmb.2025.169299","DOIUrl":"10.1016/j.jmb.2025.169299","url":null,"abstract":"<p><p>The mechanisms of the nucleosome and the Mediator complex, central players in transcriptional regulation, are only now coming into focus. Knowledge of the nucleosome and implications for chromosome structure derive almost entirely from studies performed in vitro. Knowledge of Mediator and the transduction of regulatory information is the product of discoveries made in vitro, together with information from genetic studies in yeast and and from aberrations in human disease. The mechanism of regulatory signal transduction by Mediator is an outstanding question, and a proposal is put forward on the basis of Mediator structure.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169299"},"PeriodicalIF":4.7,"publicationDate":"2025-06-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144324079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Membrane Disruption Properties of Poly-Glycine Arginine Dipeptide Repeats Affected by Peptide Repeats Continuity and Membrane Composition","authors":"Chia-Yi Ho ,&nbsp;Yu-Jen Chang ,&nbsp;Chih-Wen Yang ,&nbsp;Orion Shih ,&nbsp;U-Ser Jeng ,&nbsp;Ing-Shouh Hwang ,&nbsp;Wan-Chen Huang ,&nbsp;Yun-Ru Chen","doi":"10.1016/j.jmb.2025.169296","DOIUrl":"10.1016/j.jmb.2025.169296","url":null,"abstract":"<div><div><em>C9ORF72</em> hexanucleotide expansion is the most common genetic mutation in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTD). This expansion can be translated into dipeptide repeats (DPRs) through repeat-associated non-ATG (RAN) translation. Arginine-rich DPRs, i.e., poly-glycine arginine (poly-GR) and poly-proline arginine (poly-PR) are considered the most toxic ones among the five types of DPRs. We recently discovered that poly-GR forms helical conformation and is able to penetrate cell membranes, leading to cytotoxicity, but the mechanism remains unclear. Here, we investigated the membrane disruption mechanism of poly-GR related to its sequence and membrane composition. To test this, we stopped its continuously repeated sequence by inserting several proline residues to disrupt its helical structure. We found that the modification reduced its cytotoxicity and membrane disruption capability. Next, we examined the influence of lipid composition on the membrane-disrupting ability of poly-GR using various liposomes. Poly-GR caused higher leakage in the negatively charged liposomes compared to the neutral or positively charged ones. Cholesterol content affected the extent of disruption, while gangliosides had no significant effect. Using small-angle x-ray scattering (SAXS), total internal reflection fluorescence (TIRF) microscopy, and atomic force microscopy (AFM), we observed the behavior of poly-GR on lipid membranes. Finally, we directly treated mouse neuroblastoma to modulate the cholesterol content and found that cholesterol depletion inhibited the internalization of poly-GR into the cells and reduced cytotoxicity. These findings reveal that the conformation of poly-GR and the lipid composition influence its membrane penetration, offering insights into potential therapeutic strategies for C9ORF72-related diseases.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169296"},"PeriodicalIF":4.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DropFit: Determination of the Critical Concentration for Protein Liquid–Liquid Phase Separation","authors":"Michaela Brezinova ,&nbsp;Samuel Toluwanimi Dada ,&nbsp;Monika Fuxreiter ,&nbsp;Michele Vendruscolo","doi":"10.1016/j.jmb.2025.169294","DOIUrl":"10.1016/j.jmb.2025.169294","url":null,"abstract":"<div><div>In the liquid–liquid phase separation of proteins, dense liquid droplets often form within the dilute phase below the critical concentration. The resulting size distribution of these precritical droplets can be described by a scale-invariant distribution, which is characterized by an increasing average as the concentration approaches from below the critical value. This phenomenon can be leveraged for the quantitative estimation of the critical concentration. Here, to facilitate applications of this approach, we present the DropFit web server (<span><span>https://www-cohsoftware.ch.cam.ac.uk/index.php/dropfit</span><svg><path></path></svg></span>). DropFit can be used to estimate the critical concentration using experimental data on the length, area, or volume of the precritical droplets, which are taken away from the critical concentration and thus be more accurate and reproducible. We anticipate that the accurate value of the critical concentration under different experimental conditions will help understand the contributions from different macromolecules to the formation of protein condensates, and to investigate the perturbations that lead to pathological processes through the disruption of membraneless organelles.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 19","pages":"Article 169294"},"PeriodicalIF":4.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Designing Structure-specific and Switchable Allosteric Effectors for GPCRs Based on the Causality and Energetics of Inherent Signaling.","authors":"Bingxue Dong, Wei-Ven Tee, Igor N Berezovsky","doi":"10.1016/j.jmb.2025.169293","DOIUrl":"10.1016/j.jmb.2025.169293","url":null,"abstract":"<p><p>The pervasiveness and versatility of G protein-coupled receptors (GPCRs) in virtually all physiological processes is based on the receptors' capability to activate intracellular signal transduction pathways in response to diverse extracellular stimuli. While the importance of GPCRs makes them the largest group of drug targets (comprising about one-third of marketed medicines), more than half of GPCRs lack preclinical drug candidates because of high structural conservatism of their orthosteric sites. Recognizing that the mechanisms of GPCR function and regulation are chiefly allosteric in nature, we explore their allosteric control and the potential for developing allosteric drugs with high specificity. First, we obtained a picture of allosteric signaling in 280 non-olfactory GPCRs in human and explored archetypal structure-based patterns and sequence-determined variations of allosteric communication. We showed how the causality of allosteric effects due to ligand binding can be quantified, using the β₂-adrenergic receptor (ADRB2) and glucagon-like peptide 1 receptor (GLP1R) as case studies. Implementing our directed design protocol for developing allosteric drug candidates, switchable agonist-antagonist pairs were obtained for GPL1R. Moreover, we showed the predictive power of our approach for identification of latent allosteric sites and the capability for de novo design of agonistic and antagonistic effectors. We also performed efficacy-based design of ligands, demonstrating on the homologous GLP1R and GIPR that the strength of allosteric signaling induced by an effector can determine specificity to a target receptor. Our computational framework not only provides a foundation for addressing the problem of \"difficult\" GPCR targets with the allosteric approach, but also allows rational design of effectors with controllable mode switching and high specificity in general. The comprehensive data on allosteric signaling in classes A, B1, B2, C, F, and T GPCRs at single-residue resolution is available in the AlloMAPS database (https://allomaps.bii.a-star.edu.sg/browse/gpcraf).</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169293"},"PeriodicalIF":4.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into Noncanonical and Diversified Functions of ABCF1: From Health to Disease","authors":"Junyi Duan ,&nbsp;Prince Saini ,&nbsp;Yick W. Fong","doi":"10.1016/j.jmb.2025.169286","DOIUrl":"10.1016/j.jmb.2025.169286","url":null,"abstract":"<div><div>The ATP-binding cassette (ABC) family is one of the largest and most ancient classes of transporters found in nearly all living organisms. However, ABCF1 lacks a transmembrane domain and therefore does not function as a transporter. Recent studies point to an unexpectedly diverse role of ABCF1 in regulating cell-essential processes from mRNA translation, innate immune response, and phagocytosis in somatic cells, to transcriptional regulation in embryonic stem cells. ABCF1’s functional plasticity is in part mediated by its disordered low-complexity domain (LCD) to enable dynamic biomolecular interactions. In this review, we discuss how ABCF1 takes advantage of the LCD to expand its functional repertoire and highlight fundamental principles of biomolecular assembly driving biological reactions. We also discuss the functions and mechanisms of ABCF1 in development and tissue homeostasis, and how dysregulation of ABCF1 contributes to diseases such as inflammatory disease and cancer.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169286"},"PeriodicalIF":4.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293157","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"ATG9 Not Just an Autophagy Related Protein","authors":"Emily Millard,&nbsp;Sharon A. Tooze","doi":"10.1016/j.jmb.2025.169288","DOIUrl":"10.1016/j.jmb.2025.169288","url":null,"abstract":"<div><div>Autophagy proteins coordinate the biogenesis of a phagophore, the formation and maturation of an autophagosome. Genetic mutations of these proteins can result in dysregulated autophagy, stalled autophagosome biogenesis, and lead to cell death. ATG9, the sole transmembrane ATG (<u>a</u>u<u>t</u>opha<u>g</u>y related) protein governs the nucleation of the phagophore. At a molecular level ATG9 has been shown to be a lipid scramblase capable of redistributing lipids across the lipid bilayer. ATG9-positive vesicles can also deliver lipid-modifying enzymes to alter the lipid composition of membranes. Both functions are required for autophagy. However, ATG proteins, including ATG9, play key molecular roles in pathways unrelated to autophagy. ATG9 has been shown to function in multiple pathways at the Golgi, plasma membrane, and lysosomes. ATG9 can also play an important role in immune signalling. The trafficking of ATG9 in ATG9-positive vesicles is essential to many of these pathways. In this review we highlight the functions of ATG9 in autophagy and autophagy-unrelated pathways, here referred to as “non-canonical functions”, and summarise the broader role of ATG9A in cell homeostasis.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 18","pages":"Article 169288"},"PeriodicalIF":4.7,"publicationDate":"2025-06-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144293153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Versatile Methodology for Efficient Large-sized DNA Delivery Between Microorganisms Without In vitro Purification","authors":"Shinya Kaneko ,&nbsp;Hiromi Fukushima ,&nbsp;Misako Nakahama ,&nbsp;Kenji Tsuge ,&nbsp;Jun Ishii ,&nbsp;Yasunori Aizawa ,&nbsp;Mitsuhiro Itaya ,&nbsp;Akihiko Kondo","doi":"10.1016/j.jmb.2025.169289","DOIUrl":"10.1016/j.jmb.2025.169289","url":null,"abstract":"<div><div>Purified DNA plasmids traditionally used for microbial transformation have been supplanted by extracellular plasmids released via host bacterial lysis, offering an alternative approach for DNA-plasmid delivery. Specifically, shuttle vector plasmids liberated from host <em>Bacillus subtilis</em> were directly employed for the transformation of chemically competent cells <em>Escherichia coli</em>, eliminating the need for biochemical purification. This unconventional DNA delivery technique, referred to as ’<u>Ce</u>ll <u>Ly</u>sis Technology to provide <u>T</u>ransformable <u>E</u>xtra-cellular <u>D</u>NA; CELyTED’, has been successfully adapted for the transformation of microorganism <em>Saccharomyces cerevisiae</em> as well. The protocol includes optimized conditions for efficient cell lysis of the donor host cells. Notably, ’ CELyTED ’ enables the introduction of large-sized DNA plasmids exceeding 50 kb into target microorganisms mitigating the potential adverse effects of physical shearing during the purification process. This simplicity in the delivery protocol makes it versatile for both prokaryotic and eukaryotic microorganisms, establishing a fundamental platform in the synthetic genome field. Our study demonstrates the feasibility of introducing large DNA plasmids into cells <em>E. coli</em> and <em>S. cerevisiae</em> using the lysate of donor host cells, showcasing the potential of ‘CELyTED ’ as a streamlined approach in genetic transformation methodologies.</div></div>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":"437 17","pages":"Article 169289"},"PeriodicalIF":4.7,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144281921","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling Protein Aggregation Kinetics from NMR Data.","authors":"Vitali Tugarinov, Francesco Torricella, Shreya Ghosh, G Marius Clore","doi":"10.1016/j.jmb.2025.169269","DOIUrl":"10.1016/j.jmb.2025.169269","url":null,"abstract":"<p><p>We provide an overview of the practical aspects of using NMR spectroscopy to follow the time course of protein fibril formation (aggregation) and quantitatively model the kinetics of aggregation processes. Following a brief survey of the theoretical foundations of the kinetics of protein aggregation and its inhibition, the modeling of aggregation kinetics, from data acquired by a series of fast two-dimensional ¹H-¹⁵N correlation NMR spectra, is described. Examples are drawn from our recent NMR-based studies of (1) the aggregation kinetics of a pathogenic huntingtin exon-1 protein whose fibrillization in neurons is responsible for Huntington's disease, and (2) the kinetics of amyloid β42 fibril formation and the mechanism of its inhibition by the chaperone Hsp104.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169269"},"PeriodicalIF":4.7,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12235721/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.","authors":"Charles E F Millard, James O Wrabl, Sarah J Brantley, Emily Grasso, Anna Schmitz, Jordan T White, Vincent J Hilser","doi":"10.1016/j.jmb.2025.169287","DOIUrl":"10.1016/j.jmb.2025.169287","url":null,"abstract":"<p><p>Allostery is the process by which perturbation at one site in a protein affects distal sites. For many years the understanding of allostery and other functions was influenced by the high-resolution, ground state structure obtained through X-ray crystallography. Ample evidence has meanwhile accumulated that this ground state structure is only one member of the biologically relevant group of conformations, known as the protein ensemble, which collectively affect the observed biological response. This review aims to; (1) focus statistical thermodynamic formalisms on quantitative description of the ensemble, (2) illustrate the functional implications of ensembles for allostery, and (3) highlight ensemble redistribution as a unifying principle underlying all biological processes. Emphasis is placed on the importance of locally unfolded regions, i.e. excited states, underpinning two theoretical treatments developed in this laboratory: a coarse-grained Ensemble Allosteric Model (EAM) and an atomic-detail model named COREX. Locally unfolded conformations are profiled with case studies of allosteric proteins that are mostly denatured (Glucocorticoid Receptor), that are mostly folded (Adenylate Kinase), and that populate alternative folded structures (Metamorphic Proteins). These examples demonstrate that redistribution of states within the thermodynamic ensemble is sufficient to explain disparate biological phenomena including allostery, epistatic effects, and responses to environmental stimuli such as temperature - often without reliance on the structural details. The coarse-grained nature of the models highlights the degeneracy of molecular mechanisms that have evolved to facilitate function, and thus draws attention to the importance of relative energy differences between states, as opposed to the specific interactions that stabilize them.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169287"},"PeriodicalIF":4.7,"publicationDate":"2025-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144273885","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ion NMR for Biomolecular Systems.","authors":"Junji Iwahara","doi":"10.1016/j.jmb.2025.169285","DOIUrl":"10.1016/j.jmb.2025.169285","url":null,"abstract":"<p><p>Counterions play a crucial role in biomolecular systems, influencing the structure and function of proteins and nucleic acids. Most counterions are not visible in experimentally determined biomolecular structures because the ions dynamically diffuse even while interacting with biomolecules. Over the past five decades, researchers have utilized ²³Na NMR to study sodium ions and their electrostatic interactions with biomolecules. Other inorganic ions as counterions of biomolecules have also been studied with ²⁵Mg, ³¹P, ³⁵Cl, and ³⁹K NMR, for example. However, investigating the dynamic properties of ions around biomolecules using NMR has been challenging. Recently, there have been significant advances in NMR studies on the behavior of various biologically relevant ions around proteins and nucleic acids. Advances in probe hardware capable of generating strong field gradients have enabled NMR-based diffusion measurements of various inorganic ions interacting with biomolecules. The diffusion data have revealed the highly mobile nature of counterions around biomolecules and quantitative information about the release of counterions upon protein-DNA association. Quantitative NMR (qNMR) approaches have been developed to determine the number of counterions accumulated around a biomolecule. Applications of the diffusion and qNMR methods appear promising since the feasibility of ion NMR has already been demonstrated for large biomolecule systems, such as ribosomes, genomic DNA, biomolecular condensates, and living organisms.</p>","PeriodicalId":369,"journal":{"name":"Journal of Molecular Biology","volume":" ","pages":"169285"},"PeriodicalIF":4.7,"publicationDate":"2025-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12266291/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144245507","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}