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Evolutionary Dynamics and Molecular Mechanisms of HORMA Domain Protein Signaling. HORMA结构域蛋白信号的进化动力学和分子机制。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-01-18 DOI: 10.1146/annurev-biochem-090920-103246
Yajie Gu, Arshad Desai, Kevin D Corbett
{"title":"Evolutionary Dynamics and Molecular Mechanisms of HORMA Domain Protein Signaling.","authors":"Yajie Gu,&nbsp;Arshad Desai,&nbsp;Kevin D Corbett","doi":"10.1146/annurev-biochem-090920-103246","DOIUrl":"https://doi.org/10.1146/annurev-biochem-090920-103246","url":null,"abstract":"<p><p>Controlled assembly and disassembly of multi-protein complexes is central to cellular signaling. Proteins of the widespread and functionally diverse HORMA family nucleate assembly of signaling complexes by binding short peptide motifs through a distinctive safety-belt mechanism. HORMA proteins are now understood as key signaling proteins across kingdoms, serving as infection sensors in a bacterial immune system and playing central roles in eukaryotic cell cycle, genome stability, sexual reproduction, and cellular homeostasis pathways. Here, we describe how HORMA proteins' unique ability to adopt multiple conformational states underlies their functions in these diverse contexts. We also outline how a dedicated AAA+ ATPase regulator, Pch2/TRIP13, manipulates HORMA proteins' conformational states to activate or inactivate signaling in different cellular contexts. The emergence of Pch2/TRIP13 as a lynchpin for HORMA protein action in multiple genome-maintenance pathways accounts for its frequent misregulation in human cancers and highlights TRIP13 as a novel therapeutic target.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"541-569"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39829358","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: 15
Encapsulins. 密封剂。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-040320-102858
Tobias W Giessen
{"title":"Encapsulins.","authors":"Tobias W Giessen","doi":"10.1146/annurev-biochem-040320-102858","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-102858","url":null,"abstract":"<p><p>Subcellular compartmentalization is a defining feature of all cells. In prokaryotes, compartmentalization is generally achieved via protein-based strategies. The two main classes of microbial protein compartments are bacterial microcompartments and encapsulin nanocompartments. Encapsulins self-assemble into proteinaceous shells with diameters between 24 and 42 nm and are defined by the viral HK97-fold of their shell protein. Encapsulins have the ability to encapsulate dedicated cargo proteins, including ferritin-like proteins, peroxidases, and desulfurases. Encapsulation is mediated by targeting sequences present in all cargo proteins. Encapsulins are found in many bacterial and archaeal phyla and have been suggested to play roles in iron storage, stress resistance, sulfur metabolism, and natural product biosynthesis. Phylogenetic analyses indicate that they share a common ancestor with viral capsid proteins. Many pathogens encode encapsulins, and recent evidence suggests that they may contribute toward pathogenicity. The existing information on encapsulin structure, biochemistry, biological function, and biomedical relevance is reviewed here.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"353-380"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9944552/pdf/nihms-1869567.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10750512","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 14
The Structural Dynamics of Translation. 翻译的结构动力学。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-071921-122857
Andrei A Korostelev
{"title":"The Structural Dynamics of Translation.","authors":"Andrei A Korostelev","doi":"10.1146/annurev-biochem-071921-122857","DOIUrl":"https://doi.org/10.1146/annurev-biochem-071921-122857","url":null,"abstract":"<p><p>Accurate protein synthesis (translation) relies on translation factors that rectify ribosome fluctuations into a unidirectional process. Understanding this process requires structural characterization of the ribosome and translation-factor dynamics. In the 2000s, crystallographic studies determined high-resolution structures of ribosomes stalled with translation factors, providing a starting point for visualizing translation. Recent progress in single-particle cryogenic electron microscopy (cryo-EM) has enabled near-atomic resolution of numerous structures sampled in heterogeneous complexes (ensembles). Ensemble and time-resolved cryo-EM have now revealed unprecedented views of ribosome transitions in the three principal stages of translation: initiation, elongation, and termination. This review focuses on how translation factors help achieve high accuracy and efficiency of translation by monitoring distinct ribosome conformations and by differentially shifting the equilibria of ribosome rearrangements for cognate and near-cognate substrates.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"245-267"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10389292/pdf/nihms-1920330.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9890319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 13
The Initiation of Eukaryotic DNA Replication. 真核生物DNA复制的起始。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-03-23 DOI: 10.1146/annurev-biochem-072321-110228
Alessandro Costa, John F X Diffley
{"title":"The Initiation of Eukaryotic DNA Replication.","authors":"Alessandro Costa,&nbsp;John F X Diffley","doi":"10.1146/annurev-biochem-072321-110228","DOIUrl":"https://doi.org/10.1146/annurev-biochem-072321-110228","url":null,"abstract":"<p><p>DNA replication in eukaryotic cells initiates from large numbers of sites called replication origins. Initiation of replication from these origins must be tightly controlled to ensure the entire genome is precisely duplicated in each cell cycle. This is accomplished through the regulation of the first two steps in replication: loading and activation of the replicative DNA helicase. Here we describe what is known about the mechanism and regulation of these two reactions from a genetic, biochemical, and structural perspective, focusing on recent progress using proteins from budding yeast.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"107-131"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40316866","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: 35
Lipoproteins in the Central Nervous System: From Biology to Pathobiology. 中枢神经系统中的脂蛋白：从生物学到病理生物学
IF 12.1 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-03-18 DOI: 10.1146/annurev-biochem-032620-104801
Ana-Caroline Raulin, Yuka A Martens, Guojun Bu
{"title":"Lipoproteins in the Central Nervous System: From Biology to Pathobiology.","authors":"Ana-Caroline Raulin, Yuka A Martens, Guojun Bu","doi":"10.1146/annurev-biochem-032620-104801","DOIUrl":"10.1146/annurev-biochem-032620-104801","url":null,"abstract":"<p><p>The brain, as one of the most lipid-rich organs, heavily relies on lipid transport and distribution to maintain homeostasis and neuronal function. Lipid transport mediated by lipoprotein particles, which are complex structures composed of apolipoproteins and lipids, has been thoroughly characterized in the periphery. Although lipoproteins in the central nervous system (CNS) were reported over half a century ago, the identification of <i>APOE4</i> as the strongest genetic risk factor for Alzheimer's disease has accelerated investigation of the biology and pathobiology of lipoproteins in the CNS. This review provides an overview of the different components of lipoprotein particles, in particular apolipoproteins, and their involvements in both physiological functions and pathological mechanisms in the CNS.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":"91 ","pages":"731-759"},"PeriodicalIF":12.1,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9634960/pdf/nihms-1844218.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9743352","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily. DMSO还原酶超家族中酶的新化学多样性和潜在应用。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 Epub Date: 2022-03-23 DOI: 10.1146/annurev-biochem-032620-110804
Chi Chip Le, Minwoo Bae, Sina Kiamehr, Emily P Balskus
{"title":"Emerging Chemical Diversity and Potential Applications of Enzymes in the DMSO Reductase Superfamily.","authors":"Chi Chip Le,&nbsp;Minwoo Bae,&nbsp;Sina Kiamehr,&nbsp;Emily P Balskus","doi":"10.1146/annurev-biochem-032620-110804","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-110804","url":null,"abstract":"<p><p>Molybdenum- and tungsten-dependent proteins catalyze essential processes in living organisms and biogeochemical cycles. Among these enzymes, members of the dimethyl sulfoxide (DMSO) reductase superfamily are considered the most diverse, facilitating a wide range of chemical transformations that can be categorized as oxygen atom installation, removal, and transfer. Importantly, DMSO reductase enzymes provide high efficiency and excellent selectivity while operating under mild conditions without conventional oxidants such as oxygen or peroxides. Despite the potential utility of these enzymes as biocatalysts, such applications have not been fully explored. In addition, the vast majority of DMSO reductase enzymes still remain uncharacterized. In this review, we describe the reactivities, proposed mechanisms, and potential synthetic applications of selected enzymes in the DMSO reductase superfamily. We also highlight emerging opportunities to discover new chemical activity and current challenges in studying and engineering proteins in the DMSO reductase superfamily.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"475-504"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40316864","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: 4
In Vitro Genetic Code Reprogramming for the Expansion of Usable Noncanonical Amino Acids. 扩增可用非规范氨基酸的体外遗传密码重编程。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-06-21 DOI: 10.1146/annurev-biochem-040320-103817
Takayuki Katoh, Hiroaki Suga
{"title":"In Vitro Genetic Code Reprogramming for the Expansion of Usable Noncanonical Amino Acids.","authors":"Takayuki Katoh,&nbsp;Hiroaki Suga","doi":"10.1146/annurev-biochem-040320-103817","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-103817","url":null,"abstract":"<p><p>Genetic code reprogramming has enabled us to ribosomally incorporate various nonproteinogenic amino acids (npAAs) into peptides in vitro. The repertoire of usable npAAs has been expanded to include not only l-α-amino acids with noncanonical sidechains but also those with noncanonical backbones. Despite successful single incorporation of npAAs, multiple and consecutive incorporations often suffer from low efficiency or are even unsuccessful. To overcome this stumbling block, engineering approaches have been used to modify ribosomes, EF-Tu, and tRNAs. Here, we provide an overview of these in vitro methods that are aimed at optimal expansion of the npAA repertoire and their applications for the development of de novo bioactive peptides containing various npAAs.</p>","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":"221-243"},"PeriodicalIF":16.6,"publicationDate":"2022-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40151104","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: 5
Kinetic Proofreading. 动能校对。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-04-01 DOI: 10.1146/annurev-biochem-040320-103630
Hinrich Boeger
{"title":"Kinetic Proofreading.","authors":"Hinrich Boeger","doi":"10.1146/annurev-biochem-040320-103630","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-103630","url":null,"abstract":"Biochemistry and molecular biology rely on the recognition of structural complementarity between molecules. Molecular interactions must be both quickly reversible, i.e., tenuous, and specific. How the cell reconciles these conflicting demands is the subject of this article. The problem and its theoretical solution are discussed within the wider theoretical context of the thermodynamics of stochastic processes (stochastic thermodynamics). The solution-an irreversible reaction cycle that decreases internal error at the expense of entropy export into the environment-is shown to be widely employed by biological processes that transmit genetic and regulatory information. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42335189","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: 6
Validating Small Molecule Chemical Probes for Biological Discovery. 用于生物发现的小分子化学探针的验证。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-04-01 DOI: 10.1146/annurev-biochem-032620-105344
Victoria Vu, Magdalena M. Szewczyk, David Y. Nie, C. Arrowsmith, D. Barsyte-Lovejoy
{"title":"Validating Small Molecule Chemical Probes for Biological Discovery.","authors":"Victoria Vu, Magdalena M. Szewczyk, David Y. Nie, C. Arrowsmith, D. Barsyte-Lovejoy","doi":"10.1146/annurev-biochem-032620-105344","DOIUrl":"https://doi.org/10.1146/annurev-biochem-032620-105344","url":null,"abstract":"Small molecule chemical probes are valuable tools for interrogating protein biological functions and relevance as a therapeutic target. Rigorous validation of chemical probe parameters such as cellular potency and selectivity is critical to unequivocally linking biological and phenotypic data resulting from treatment with a chemical probe to the function of a specific target protein. A variety of modern technologies are available to evaluate cellular potency and selectivity, target engagement, and functional response biomarkers of chemical probe compounds. Here, we review these technologies and the rationales behind using them for the characterization and validation of chemical probes. In addition, large-scale phenotypic characterization of chemical probes through chemical genetic screening is increasingly leading to a wealth of information on the cellular pharmacology and disease involvement of potential therapeutic targets. Extensive compound validation approaches and integration of phenotypic information will lay foundations for further use of chemical probes in biological discovery. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47671355","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: 8
Metalloproteomics for Biomedical Research: Methodology and Applications. 生物医学研究的金属代谢组学：方法论和应用。
IF 16.6 1区 生物学
Annual review of biochemistry Pub Date : 2022-02-18 DOI: 10.1146/annurev-biochem-040320-104628
Ying Zhou, Hongyan Li, Hongzhe Sun
{"title":"Metalloproteomics for Biomedical Research: Methodology and Applications.","authors":"Ying Zhou, Hongyan Li, Hongzhe Sun","doi":"10.1146/annurev-biochem-040320-104628","DOIUrl":"https://doi.org/10.1146/annurev-biochem-040320-104628","url":null,"abstract":"Metals are essential components in life processes and participate in many important biological processes. Dysregulation of metal homeostasis is correlated with many diseases. Metals are also frequently incorporated into diagnosis and therapeutics. Understanding of metal homeostasis under (patho)physiological conditions and the molecular mechanisms of action of metallodrugs in biological systems has positive impacts on human health. As an emerging interdisciplinary area of research, metalloproteomics involves investigating metal-protein interactions in biological systems at a proteome-wide scale, has received growing attention, and has been implemented into metal-related research. In this review, we summarize the recent advances in metalloproteomics methodologies and applications. We also highlight emerging single-cell metalloproteomics, including time-resolved inductively coupled plasma mass spectrometry, mass cytometry, and secondary ion mass spectrometry. Finally, we discuss future perspectives in metalloproteomics, aiming to attract more original research to develop more advanced methodologies, which could be utilized rapidly by biochemists or biologists to expand our knowledge of how metal functions in biology and medicine. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.","PeriodicalId":7980,"journal":{"name":"Annual review of biochemistry","volume":" ","pages":""},"PeriodicalIF":16.6,"publicationDate":"2022-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47684630","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: 13
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