Biochimie最新文献_第8页

CD38/NAD⁺ glycohydrolase and associated antigens in chronic lymphocytic leukaemia: From interconnected signalling pathways to therapeutic strategies. 慢性淋巴细胞白血病中的 CD38/NAD+糖水解酶和相关抗原：从相互关联的信号通路到治疗策略。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-07-14 DOI: 10.1016/j.biochi.2024.07.006

Brigitte Bauvois, Florence Nguyen-Khac, Hélène Merle-Béral, Santos A Susin

{"title":"CD38/NAD+ glycohydrolase and associated antigens in chronic lymphocytic leukaemia: From interconnected signalling pathways to therapeutic strategies.","authors":"Brigitte Bauvois, Florence Nguyen-Khac, Hélène Merle-Béral, Santos A Susin","doi":"10.1016/j.biochi.2024.07.006","DOIUrl":"10.1016/j.biochi.2024.07.006","url":null,"abstract":"Chronic lymphocytic leukaemia (CLL) is a heterogenous disease characterized by the accumulation of neoplastic CD5+/CD19+ B lymphocytes. The spreading of the leukaemia relies on the CLL cell's ability to survive in the blood and migrate to and proliferate within the bone marrow and lymphoid tissues. Some patients with CLL are either refractory to the currently available therapies or relapse after treatment; this emphasizes the need for novel therapeutic strategies that improving clinical responses and overcome drug resistance. CD38 is a marker of a poor prognosis and governs a set of survival, proliferation and migration signals that contribute to the pathophysiology of CLL. The literature data evidence a spatiotemporal association between the cell surface expression of CD38 and that of other CLL antigens, such as the B-cell receptor (BCR), CD19, CD26, CD44, the integrin very late antigen 4 (VLA4), the chemokine receptor CXCR4, the vascular endothelial growth factor receptor-2 (VEGF-R2), and the neutrophil gelatinase-associated lipocalin receptor (NGAL-R). Most of these proteins contribute to CLL cell survival, proliferation and trafficking, and cooperate with CD38 in multilayered signal transduction processes. In general, these antigens have already been validated as therapeutic targets in cancer, and a broad repertoire of specific monoclonal antibodies and derivatives are available. Here, we review the state of the art in this field and examine the therapeutic opportunities for cotargeting CD38 and its partners in CLL, e.g. by designing novel bi-/trispecific antibodies.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"135-151"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141621936","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

Behind the stoNE wall: A fervent activity for nuclear lipids. stoNE墙的背后：核脂的狂热活动。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-08-05 DOI: 10.1016/j.biochi.2024.08.002

Kseniya Samardak, Janélie Bâcle, María Moriel-Carretero

引用次数: 0

Alternate recognition by dengue protease: Proteolytic and binding assays provide functional evidence beyond an induced-fit. 登革病毒蛋白酶的替代识别：蛋白水解和结合试验提供了超越诱导拟合的功能证据。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-06-11 DOI: 10.1016/j.biochi.2024.06.002

Mira A M Behnam, Christian D Klein

{"title":"Alternate recognition by dengue protease: Proteolytic and binding assays provide functional evidence beyond an induced-fit.","authors":"Mira A M Behnam, Christian D Klein","doi":"10.1016/j.biochi.2024.06.002","DOIUrl":"10.1016/j.biochi.2024.06.002","url":null,"abstract":"Proteases are key enzymes in viral replication, and interfering with these targets is the basis for therapeutic interventions. We previously introduced a hypothesis about conformational selection in the protease of dengue virus and related flaviviruses, based on conformational plasticity noted in X-ray structures. The present work presents the first functional evidence for alternate recognition by the dengue protease, in a mechanism based primarily on conformational selection rather than induced-fit. Recognition of distinct substrates and inhibitors in proteolytic and binding assays varies to a different extent, depending on factors reported to influence the protease structure. The pH, salinity, buffer type, and temperature cause a change in binding, proteolysis, or inhibition behavior. Using representative inhibitors with distinct structural scaffolds, we identify two contrasting binding profiles to dengue protease. Noticeable effects are observed in the binding assay upon inclusion of a non-ionic detergent in comparison to the proteolytic assay. The findings highlight the impact of the selection of testing conditions on the observed ligand affinity or inhibitory potency. From a broader scope, the dengue protease presents an example, where the induced-fit paradigm appears insufficient to explain binding events with the biological target. Furthermore, this protein reveals the complexity of comparing or combining biochemical assay data obtained under different conditions. This can be particularly critical for artificial intelligence (AI) approaches in drug discovery that rely on large datasets of compounds activity, compiled from different sources using non-identical testing procedures. In such cases, mismatched results will compromise the model quality and its predictive power.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"15-27"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141319265","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

Structural descriptions of ligand interactions to RNA quadruplexes folded from the non-coding region of pseudorabies virus. 配体与伪狂犬病毒非编码区折叠的 RNA 四元体相互作用的结构描述。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-06-13 DOI: 10.1016/j.biochi.2024.06.003

Yashu Zhang, Khair Bux, Fedaa Attana, Dengguo Wei, Shozeb Haider, Gary N Parkinson

{"title":"Structural descriptions of ligand interactions to RNA quadruplexes folded from the non-coding region of pseudorabies virus.","authors":"Yashu Zhang, Khair Bux, Fedaa Attana, Dengguo Wei, Shozeb Haider, Gary N Parkinson","doi":"10.1016/j.biochi.2024.06.003","DOIUrl":"10.1016/j.biochi.2024.06.003","url":null,"abstract":"To rationalise the binding of specific ligands to RNA-quadruplex we investigated several naphthalene diimide ligands that interact with the non-coding region of Pseudorabies virus (PRV). Herein we report on the x-ray structure of the naphthalene diimide ND11 with an RNA G-quadruplex putative forming sequence from rPRV. Consistent with previously observed rPRV sequence it assembles into a bimolecular RNA G-quadruplex consisting of a pair of two tetrads stacked 3' to 5'. We observe that ND11 interacts by binding on both the externally available 5' and 3' quartets. The CUC (loop 1) is structurally altered to enhance the 5' mode of interaction. These loop residues are shifted significantly to generate a new ligand binding pocket whereas the terminal A14 residue is lifted away from the RNA G-quadruplex tetrad plane to be restacked above the bound ND11 ligand NDI core. CD analysis of this family of NDI ligands shows consistency in the spectra between the different ligands in the presence of the rPRV RNA G-quadruplex motif, reflecting a common folded topology and mode of ligand interaction. FRET melt assay confirms the strong stabilising properties of the tetrasubstituted NDI compounds and the contributions length of the substituted groups have on melt temperatures.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"28-36"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141322207","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

Direct analysis by ultra-high-resolution mass spectrometry of lipid A and phospholipids from Acinetobacter baumannii cells. 利用超高分辨率质谱法直接分析鲍曼不动杆菌细胞中的脂质 A 和磷脂。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-09-24 DOI: 10.1016/j.biochi.2024.09.012

Delphine Vergoz, Annick Schaumann, Isabelle Schmitz, Maria van Agthoven, Sara Martí, Jordi Vila, Carlos Afonso, Emmanuelle Dé, Corinne Loutelier-Bourhis, Stéphane Alexandre

{"title":"Direct analysis by ultra-high-resolution mass spectrometry of lipid A and phospholipids from Acinetobacter baumannii cells.","authors":"Delphine Vergoz, Annick Schaumann, Isabelle Schmitz, Maria van Agthoven, Sara Martí, Jordi Vila, Carlos Afonso, Emmanuelle Dé, Corinne Loutelier-Bourhis, Stéphane Alexandre","doi":"10.1016/j.biochi.2024.09.012","DOIUrl":"10.1016/j.biochi.2024.09.012","url":null,"abstract":"Acinetobacter baumannii, classified as priority number one by the World Health Organization (WHO), is an opportunistic pathogen responsible for infection and is able to develop antibiotic resistance easily. Membranes are bacteria's first line of defense against external aggression, such as antibiotics. A chemical modification of a lipid family or a change in lipid composition can lead to resistance to antibiotics. In this work, we analyzed different A. baumannii strains from various environments with different antibiotic resistance profiles, using matrix-assisted laser desorption ionization-Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FT-ICR MS). This study shows that it is possible to describe the main lipidome (phospholipids and lipid A) from the simple preparation of lysed cells, and that despite the complexity of the mixture. This ultra-high resolution mass spectrometry technique enables the separation of isobaric ion, to report a new class of lipids. Given its performance, this technique can be used to quickly and reliably characterize the lipidome of clinical strains from different environments.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"3-11"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142334286","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

New insights on pentadecanoic acid with special focus on its controversial essentiality: A mini-review. 关于十五烷酸的新见解，特别关注其有争议的本质：微型综述。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-10-10 DOI: 10.1016/j.biochi.2024.10.008

Vincent Ciesielski, Philippe Legrand, Sophie Blat, Vincent Rioux

{"title":"New insights on pentadecanoic acid with special focus on its controversial essentiality: A mini-review.","authors":"Vincent Ciesielski, Philippe Legrand, Sophie Blat, Vincent Rioux","doi":"10.1016/j.biochi.2024.10.008","DOIUrl":"10.1016/j.biochi.2024.10.008","url":null,"abstract":"Pentadecanoic acid (C15:0, PDA) is an odd and minor fatty acid that has been neglected in the literature until the last decade. Indeed, as a specific fatty acid of dairy fat, PDA was only used as a biomarker of dairy fat consumption. Lately, PDA was first correlated negatively with the incidence of metabolic syndrome disorder, then its physiological effects have been investigated as a protective fatty acid. PDA supplementation has been demonstrated as negatively correlated with elevated levels of leptin, plasminogen activator inhibitor-1 and insulin, and has been shown to exhibit sensitizing insulin effects with activation of AMPK pathway. PDA also reduced the severity of metabolic dysfunction-associated steatohepatitis (MASH), notably through reduced alanine transaminase and pro-inflammatory cytokines levels. The final effect described for PDA is its ability to display anti-inflammatory properties in several pathology models. Hence, considering these multiple effects, the presence of PDA could be associated with a healthier physiological state, this raises the question of whether the presence of PDA in the body, in adequate quantities, is needed to participate to health maintenance. PDA is not synthesized in sufficient quantities endogenously, so it must be provided by the diet, mainly through dairy fat, although other types of food can also contribute to the dietary intake of PDA. Essential fatty acids are described as not being endogenously synthesized in sufficient and required quantities to maintain physiological health. Thus, PDA might gather both conditions to be described as essential, yet further investigations on both criteria are needed to enhance knowledge on this odd chain fatty acid with promising impact as potential protective supplement nutrient.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"123-129"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142482921","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

Probing G-quadruplex-ligand binding using DNA intrinsic fluorescence. 利用 DNA 固有荧光探测 G-四叠体配体的结合。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-06-25 DOI: 10.1016/j.biochi.2024.06.009

Aleksandra Bednarz, Rebecca Torp Rosendal, Line Mørkholt Lund, Victoria Birkedal

引用次数: 0

Lipid droplets degradation mechanisms from microalgae to mammals, a comparative overview. 从微藻类到哺乳动物的脂滴降解机制比较概述。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-09-17 DOI: 10.1016/j.biochi.2024.09.006

Chems Amari, Marta Carletti, Siqi Yan, Morgane Michaud, Juliette Salvaing

{"title":"Lipid droplets degradation mechanisms from microalgae to mammals, a comparative overview.","authors":"Chems Amari, Marta Carletti, Siqi Yan, Morgane Michaud, Juliette Salvaing","doi":"10.1016/j.biochi.2024.09.006","DOIUrl":"10.1016/j.biochi.2024.09.006","url":null,"abstract":"Lipid droplets (LDs) are organelles composed of a hydrophobic core (mostly triacylglycerols and steryl esters) delineated by a lipid monolayer and found throughout the tree of life. LDs were seen for a long time as simple energy storage organelles but recent works highlighted their versatile roles in several fundamental cellular processes, particularly during stress response. LDs biogenesis occurs in the ER and their number and size can be dynamically regulated depending on their function, e.g. during development or stress. Understanding their biogenesis and degradation mechanisms is thus essential to better apprehend their roles. LDs degradation can occur in the cytosol by lipolysis or after their internalization into lytic compartments (e.g. vacuoles or lysosomes) using diverse mechanisms that depend on the considered organism, tissue, developmental stage or environmental condition. In this review, we summarize our current knowledge on the different LDs degradation pathways in several main phyla of model organisms, unicellular or pluricellular, photosynthetic or not (budding yeast, mammals, land plants and microalgae). We highlight the conservation of the main degradation pathways throughout evolution, but also the differences between organisms, or inside an organism between different organs. Finally, we discuss how this comparison can help to shed light on relationships between LDs degradation pathways and LDs functions.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"19-34"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303294","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

Specificity of lipid transfer proteins: An in vitro story. 脂质转移蛋白的特异性：一个体外故事。

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-09-19 DOI: 10.1016/j.biochi.2024.09.007

Amazigh Hamaï, Guillaume Drin

{"title":"Specificity of lipid transfer proteins: An in vitro story.","authors":"Amazigh Hamaï, Guillaume Drin","doi":"10.1016/j.biochi.2024.09.007","DOIUrl":"10.1016/j.biochi.2024.09.007","url":null,"abstract":"Lipids, which are highly diverse, are finely distributed between organelle membranes and the plasma membrane (PM) of eukaryotic cells. As a result, each compartment has its own lipid composition and molecular identity, which is essential for the functional fate of many proteins. This distribution of lipids depends on two main processes: lipid synthesis, which takes place in different subcellular regions, and the transfer of these lipids between and across membranes. This review will discuss the proteins that carry lipids throughout the cytosol, called LTPs (Lipid Transfer Proteins). More than the modes of action or biological roles of these proteins, we will focus on the in vitro strategies employed during the last 60 years to address a critical question: What are the lipid ligands of these LTPs? We will describe the extent to which these strategies, combined with structural data and investigations in cells, have made it possible to discover proteins, namely ORPs, Sec14, PITPs, STARDs, Ups/PRELIs, START-like, SMP-domain containing proteins, and bridge-like LTPs, which compose some of the main eukaryotic LTP families, and their lipid ligands. We will see how these approaches have played a central role in cell biology, showing that LTPs can connect distant metabolic branches, modulate the composition of cell membranes, and even create new subcellular compartments.","PeriodicalId":93898,"journal":{"name":"Biochimie","volume":" ","pages":"85-110"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142303197","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

Lipid remodeling in context of cellular senescence. 细胞衰老背景下的脂质重塑

Biochimie Pub Date : 2024-12-01 Epub Date: 2024-09-17 DOI: 10.1016/j.biochi.2024.09.003

Khaled Tighanimine

引用次数: 0