发布求助
文献互助 智能选刊 最新文献

Annual review of biochemistry最新文献

筛选
英文 中文
ATP-Dependent Steps in Peroxisomal Protein Import 过氧化物酶体蛋白质导入的 ATP 依赖性步骤
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-15 DOI: 10.1146/annurev-biochem-030222-111227
Harald W. Platta, Julia Jeske, Nadine Schmidt, Ralf Erdmann
{"title":"ATP-Dependent Steps in Peroxisomal Protein Import","authors":"Harald W. Platta, Julia Jeske, Nadine Schmidt, Ralf Erdmann","doi":"10.1146/annurev-biochem-030222-111227","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-111227","url":null,"abstract":"Peroxisomes are organelles that play a central role in lipid metabolism and cellular redox homeostasis. The import of peroxisomal matrix proteins by peroxisomal targeting signal (PTS) receptors is an ATP-dependent mechanism. However, the energy-dependent steps do not occur early during the binding of the receptor–cargo complex to the membrane but late, because they are linked to the peroxisomal export complex for the release of the unloaded receptor. The first ATP-demanding step is the cysteine-dependent monoubiquitination of the PTS receptors, which is required for recognition by the AAA+ peroxins. They execute the second ATP-dependent step by extracting the ubiqitinated PTS receptors from the membrane for release back to the cytosol. After deubiquitination, the PTS receptors regain import competence and can facilitate further rounds of cargo import. Here, we give a general overview and discuss recent data regarding the ATP-dependent steps in peroxisome protein import.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"22 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Leucine-Rich Repeat Kinases 富亮氨酸重复激酶
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-15 DOI: 10.1146/annurev-biochem-030122-051144
Dario R. Alessi, Suzanne R. Pfeffer
{"title":"Leucine-Rich Repeat Kinases","authors":"Dario R. Alessi, Suzanne R. Pfeffer","doi":"10.1146/annurev-biochem-030122-051144","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-051144","url":null,"abstract":"Activating mutations in leucine-rich repeat kinase 2 (LRRK2) represent the most common cause of monogenic Parkinson's disease. LRRK2 is a large multidomain protein kinase that phosphorylates a specific subset of the ∼65 human Rab GTPases, which are master regulators of the secretory and endocytic pathways. After phosphorylation by LRRK2, Rabs lose the capacity to bind cognate effector proteins and guanine nucleotide exchange factors. Moreover, the phosphorylated Rabs cannot interact with their cognate prenyl-binding retrieval proteins (also known as guanine nucleotide dissociation inhibitors) and, thus, they become trapped on membrane surfaces. Instead, they gain the capacity to bind phospho-Rab-specific effector proteins, such as RILPL1, with resulting pathological consequences. Rab proteins also act upstream of LRRK2 by controlling its activation and recruitment onto membranes. LRRK2 signaling is counteracted by the phosphoprotein phosphatase PPM1H, which selectively dephosphorylates phospho-Rab proteins. We present here our current understanding of the structure, biochemical properties, and cell biology of LRRK2 and its related paralog LRRK1 and discuss how this information guides the generation of LRRK2 inhibitors for the potential benefit of patients.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"300 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular Machines that Facilitate Bacterial Outer Membrane Protein Biogenesis 促进细菌外膜蛋白质生物生成的分子机器
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-11 DOI: 10.1146/annurev-biochem-030122-033754
Matthew Thomas Doyle, Harris D. Bernstein
{"title":"Molecular Machines that Facilitate Bacterial Outer Membrane Protein Biogenesis","authors":"Matthew Thomas Doyle, Harris D. Bernstein","doi":"10.1146/annurev-biochem-030122-033754","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-033754","url":null,"abstract":"Almost all outer membrane proteins (OMPs) in Gram-negative bacteria contain a β-barrel domain that spans the outer membrane (OM). To reach the OM, OMPs must be translocated across the inner membrane by the Sec machinery, transported across the crowded periplasmic space through the assistance of molecular chaperones, and finally assembled (folded and inserted into the OM) by the β-barrel assembly machine. In this review, we discuss how considerable new insights into the contributions of these factors to OMP biogenesis have emerged in recent years through the development of novel experimental, computational, and predictive methods. In addition, we describe recent evidence that molecular machines that were thought to function independently might interact to form dynamic intermembrane supercomplexes. Finally, we discuss new results that suggest that OMPs are inserted primarily near the middle of the cell and packed into supramolecular structures (OMP islands) that are distributed throughout the OM.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"12 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Bis(monoacylglycero)-phosphate Hypothesis: From Lysosomal Function to Therapeutic Avenues 双（单酰基甘油）-磷酸假说：从溶酶体功能到治疗途径
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-11 DOI: 10.1146/annurev-biochem-092823-113814
Uche N. Medoh, Monther Abu-Remaileh
{"title":"The Bis(monoacylglycero)-phosphate Hypothesis: From Lysosomal Function to Therapeutic Avenues","authors":"Uche N. Medoh, Monther Abu-Remaileh","doi":"10.1146/annurev-biochem-092823-113814","DOIUrl":"https://doi.org/10.1146/annurev-biochem-092823-113814","url":null,"abstract":"Lysosomes catabolize and recycle lipids and other biological molecules to maintain cellular homeostasis in diverse nutrient environments. Lysosomal lipid catabolism relies on the stimulatory activity of bis(monoacylglycero)phosphate (BMP), an enigmatic lipid whose levels are altered across myriad lysosome-associated diseases. Here, we review the discovery of BMP over half a century ago and its structural properties that facilitate the activation of lipid hydrolases and recruitment of their coactivators. We further discuss the current, yet incomplete, understanding of BMP catabolism and anabolism. To conclude, we discuss its role in lysosome-associated diseases and the potential for modulating its levels by pharmacologically activating and inhibiting the BMP synthase to therapeutically target lysosomal storage disorders, drug-induced phospholipidosis, Alzheimer's disease, Parkinson's disease, frontotemporal dementia, cancer, and viral infection.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"25 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Cool Look at Positive-Strand RNA Virus Replication Organelles: New Insights from Cryo–Electron Microscopy 正链 RNA 病毒复制细胞器的酷炫外观：冷冻电子显微镜的新发现
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-052521-115736
Nina L. de Beijer, Eric J. Snijder, Montserrat Bárcena
{"title":"A Cool Look at Positive-Strand RNA Virus Replication Organelles: New Insights from Cryo–Electron Microscopy","authors":"Nina L. de Beijer, Eric J. Snijder, Montserrat Bárcena","doi":"10.1146/annurev-biochem-052521-115736","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052521-115736","url":null,"abstract":"Positive-strand RNA viruses encompass a variety of established and emerging eukaryotic pathogens. Their genome replication is confined to specialized cytoplasmic membrane compartments known as replication organelles (ROs). These ROs derive from host membranes, transformed into distinct structures such as invaginated spherules or intricate membrane networks including single- and/or double-membrane vesicles. ROs play a vital role in orchestrating viral RNA synthesis and evading detection by innate immune sensors of the host. In recent years, groundbreaking cryo–electron microscopy studies conducted with several prototypic viruses have significantly advanced our understanding of RO structure and function. Notably, these studies unveiled the presence of crown-shaped multimeric viral protein complexes that seem to actively participate in viral RNA synthesis and regulate the release of newly synthesized RNA into the cytosol for translation and packaging. These findings have shed light on novel viral functions and fascinating macromolecular complexes that delineate promising new avenues for future research.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"68 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Replication and Transcription of Human Mitochondrial DNA 人类线粒体 DNA 的复制和转录
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-052621-092014
Maria Falkenberg, Nils-Göran Larsson, Claes M. Gustafsson
{"title":"Replication and Transcription of Human Mitochondrial DNA","authors":"Maria Falkenberg, Nils-Göran Larsson, Claes M. Gustafsson","doi":"10.1146/annurev-biochem-052621-092014","DOIUrl":"https://doi.org/10.1146/annurev-biochem-052621-092014","url":null,"abstract":"Mammalian mitochondrial DNA (mtDNA) is replicated and transcribed by phage-like DNA and RNA polymerases, and our understanding of these processes has progressed substantially over the last several decades. Molecular mechanisms have been elucidated by biochemistry and structural biology and essential in vivo roles established by cell biology and mouse genetics. Single molecules of mtDNA are packaged by mitochondrial transcription factor A into mitochondrial nucleoids, and their level of compaction influences the initiation of both replication and transcription. Mutations affecting the molecular machineries replicating and transcribing mtDNA are important causes of human mitochondrial disease, reflecting the critical role of the genome in oxidative phosphorylation system biogenesis. Mechanisms controlling mtDNA replication and transcription still need to be clarified, and future research in this area is likely to open novel therapeutic possibilities for treating mitochondrial dysfunction.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"300 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598798","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Replication–Transcription Conflicts: A Perpetual War on the Chromosome 复制-转录冲突：染色体上的持久战
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-115809
Kaitlyn R. Browning, Houra Merrikh
{"title":"Replication–Transcription Conflicts: A Perpetual War on the Chromosome","authors":"Kaitlyn R. Browning, Houra Merrikh","doi":"10.1146/annurev-biochem-030222-115809","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-115809","url":null,"abstract":"DNA replication and transcription occur in all living cells across all domains of life. Both essential processes occur simultaneously on the same template, leading to conflicts between the macromolecular machines that perform these functions. Numerous studies over the past few decades demonstrate that this is an inevitable problem in both prokaryotic and eukaryotic cells. We have learned that conflicts lead to replication fork reversal, breaks in the DNA, R-loop formation, topological stress, and mutagenesis, and they can ultimately impact evolution. Recent studies have also provided insight into the various mechanisms that mitigate, resolve, and allow tolerance of conflicts and how conflicts result in divergent pathological consequences across divergent species. In this review, we summarize current knowledge regarding the outcomes of encounters between replication and transcription machineries and explore how these clashes are dealt with across species.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"39 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
How Natural Enzymes and Synthetic Ribozymes Generate Methylated Nucleotides in RNA 天然酶和合成核糖酶如何在 RNA 中生成甲基化核苷酸
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-112310
Claudia Höbartner, Katherine E. Bohnsack, Markus T. Bohnsack
{"title":"How Natural Enzymes and Synthetic Ribozymes Generate Methylated Nucleotides in RNA","authors":"Claudia Höbartner, Katherine E. Bohnsack, Markus T. Bohnsack","doi":"10.1146/annurev-biochem-030222-112310","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-112310","url":null,"abstract":"Methylation of RNA nucleotides represents an important layer of gene expression regulation, and perturbation of the RNA methylome is associated with pathophysiology. In cells, RNA methylations are installed by RNA methyltransferases (RNMTs) that are specialized to catalyze particular types of methylation (ribose or different base positions). Furthermore, RNMTs must specifically recognize their appropriate target RNAs within the RNA-dense cellular environment. Some RNMTs are catalytically active alone and achieve target specificity via recognition of sequence motifs and/or RNA structures. Others function together with protein cofactors that can influence stability, <jats:italic>S</jats:italic>-adenosyl-L-methionine binding, and RNA affinity as well as aiding specific recruitment and catalytic activity. Association of RNMTs with guide RNAs represents an alternative mechanism to direct site-specific methylation by an RNMT that lacks intrinsic specificity. Recently, ribozyme-catalyzed methylation of RNA has been achieved in vitro, and here, we compare these different strategies for RNA methylation from structural and mechanistic perspectives.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"57 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The Art and Science of Molecular Docking 分子对接的艺术与科学
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030222-120000
Joseph M. Paggi, Ayush Pandit, Ron O. Dror
{"title":"The Art and Science of Molecular Docking","authors":"Joseph M. Paggi, Ayush Pandit, Ron O. Dror","doi":"10.1146/annurev-biochem-030222-120000","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030222-120000","url":null,"abstract":"Molecular docking has become an essential part of a structural biologist's and medicinal chemist's toolkits. Given a chemical compound and the three-dimensional structure of a molecular target—for example, a protein—docking methods fit the compound into the target, predicting the compound's bound structure and binding energy. Docking can be used to discover novel ligands for a target by screening large virtual compound libraries. Docking can also provide a useful starting point for structure-based ligand optimization or for investigating a ligand's mechanism of action. Advances in computational methods, including both physics-based and machine learning approaches, as well as in complementary experimental techniques, are making docking an even more powerful tool. We review how docking works and how it can drive drug discovery and biological research. We also describe its current limitations and ongoing efforts to overcome them.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"103 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140599105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Natural and Engineered Guide RNA–directed Transposition with CRISPR-Associated Tn7-like Transposons 利用 CRISPR 相关 Tn7 类转座子进行天然和工程化的引导 RNA 定向转座
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-10 DOI: 10.1146/annurev-biochem-030122-041908
Shan-Chi Hsieh, Joseph E. Peters
{"title":"Natural and Engineered Guide RNA–directed Transposition with CRISPR-Associated Tn7-like Transposons","authors":"Shan-Chi Hsieh, Joseph E. Peters","doi":"10.1146/annurev-biochem-030122-041908","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-041908","url":null,"abstract":"CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated nuclease) defense systems have been naturally coopted for guide RNA–directed transposition on multiple occasions. In all cases, cooption occurred with diverse elements related to the bacterial transposon Tn7. Tn7 tightly controls transposition; the transposase is activated only when special targets are recognized by dedicated target-site selection proteins. Tn7 and the Tn7-like elements that coopted CRISPR–Cas systems evolved complementary targeting pathways: one that recognizes a highly conserved site in the chromosome and a second pathway that targets mobile plasmids capable of cell-to-cell transfer. Tn7 and Tn7-like elements deliver a single integration into the site they recognize and also control the orientation of the integration event, providing future potential for use as programmable gene-integration tools. Early work has shown that guide RNA–directed transposition systems can be adapted to diverse hosts, even within microbial communities, suggesting great potential for engineering these systems as powerful gene-editing tools.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"59 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140598805","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：604180095
Book学术官方微信
小红书