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Annual review of biochemistry最新文献

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Reading and Writing the Human Glycocode 读写人类糖码
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-26 DOI: 10.1146/annurev-biochem-030122-044347
Noortje de Haan, Mathias I. Nielsen, Hans H. Wandall
{"title":"Reading and Writing the Human Glycocode","authors":"Noortje de Haan, Mathias I. Nielsen, Hans H. Wandall","doi":"10.1146/annurev-biochem-030122-044347","DOIUrl":"https://doi.org/10.1146/annurev-biochem-030122-044347","url":null,"abstract":"The complex carbohydrate structures decorating human proteins and lipids, also called glycans, are abundantly present at cell surfaces and in the secretome. Glycosylation is vital for biological processes including cell–cell recognition, immune responses, and signaling pathways. Therefore, the structural and functional characterization of the human glycome is gaining more and more interest in basic biochemistry research and in the context of developing new therapies, diagnostic tools, and biotechnology applications. For glycomics to reach its full potential in these fields, it is critical to appreciate the specific factors defining the function of the human glycome. Here, we review the glycosyltransferases (the writers) that form the glycome and the glycan-binding proteins (the readers) with an essential role in decoding glycan functions. While abundantly present throughout different cells and tissues, the function of specific glycosylation features is highly dependent on their context. In this review, we highlight the relevance of studying the glycome in the context of specific carrier proteins, cell types, and subcellular locations. With this, we hope to contribute to a richer understanding of the glycome and a more systematic approach to identifying the roles of glycosylation in human physiology.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"15 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140806292","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
Soluble Human Lectins at the Host–Microbe Interface 宿主-微生物界面上的可溶性人类凝集素
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2024-04-19 DOI: 10.1146/annurev-biochem-062917-012322
Amanda L. Peiffer, A.E. Dugan, L.L. Kiessling
{"title":"Soluble Human Lectins at the Host–Microbe Interface","authors":"Amanda L. Peiffer, A.E. Dugan, L.L. Kiessling","doi":"10.1146/annurev-biochem-062917-012322","DOIUrl":"https://doi.org/10.1146/annurev-biochem-062917-012322","url":null,"abstract":"Human lectins are integral to maintaining microbial homeostasis on the skin, in the blood, and at mucosal barriers. These proteins can recognize microbial glycans and inform the host about its microbial status. In accordance with their roles, their production can vary with tissue type. They also can have unique structural and biochemical properties, and they can influence microbial colonization at sites proximal and distal to their tissue of origin. In line with their classification as innate immune proteins, soluble lectins have long been studied in the context of acute infectious disease, but only recently have we begun to appreciate their roles in maintaining commensal microbial communities (i.e., the human microbiota). This review provides an overview of soluble lectins that operate at host–microbe interfaces, their glycan recognition properties, and their roles in physiological and pathological mechanisms.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"33 1","pages":""},"PeriodicalIF":16.6,"publicationDate":"2024-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140626315","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
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
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
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