Critical Reviews in Biochemistry and Molecular Biology最新文献_第2页

The biogenesis of potassium transporters: implications of disease-associated mutations. 钾转运体的生物生成：疾病相关突变的影响。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-06-01 Epub Date: 2024-07-01 DOI: 10.1080/10409238.2024.2369986

Morgan Kok, Jeffrey L Brodsky

{"title":"The biogenesis of potassium transporters: implications of disease-associated mutations.","authors":"Morgan Kok, Jeffrey L Brodsky","doi":"10.1080/10409238.2024.2369986","DOIUrl":"10.1080/10409238.2024.2369986","url":null,"abstract":"The concentration of intracellular and extracellular potassium is tightly regulated due to the action of various ion transporters, channels, and pumps, which reside primarily in the kidney. Yet, potassium transporters and cotransporters play vital roles in all organs and cell types. Perhaps not surprisingly, defects in the biogenesis, function, and/or regulation of these proteins are linked to range of catastrophic human diseases, but to date, few drugs have been approved to treat these maladies. In this review, we discuss the structure, function, and activity of a group of potassium-chloride cotransporters, the KCCs, as well as the related sodium-potassium-chloride cotransporters, the NKCCs. Diseases associated with each of the four KCCs and two NKCCs are also discussed. Particular emphasis is placed on how these complex membrane proteins fold and mature in the endoplasmic reticulum, how non-native forms of the cotransporters are destroyed in the cell, and which cellular factors oversee their maturation and transport to the cell surface. When known, we also outline how the levels and activities of each cotransporter are regulated. Open questions in the field and avenues for future investigations are further outlined.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"154-198"},"PeriodicalIF":6.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11444911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141466780","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}

引用次数: 0

Pioneer factors: nature or nurture? 先驱因素：天性还是后天培养？

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-06-01 Epub Date: 2024-05-22 DOI: 10.1080/10409238.2024.2355885

Shane Stoeber, Holly Godin, Cheng Xu, Lu Bai

引用次数: 0

Mitochondrial sirtuin 3 and role of natural compounds: the effect of post-translational modifications on cellular metabolism. 线粒体 sirtuin 3 和天然化合物的作用：翻译后修饰对细胞代谢的影响。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-06-01 Epub Date: 2024-07-11 DOI: 10.1080/10409238.2024.2377094

Francesca Oppedisano, Salvatore Nesci, Anna Spagnoletta

{"title":"Mitochondrial sirtuin 3 and role of natural compounds: the effect of post-translational modifications on cellular metabolism.","authors":"Francesca Oppedisano, Salvatore Nesci, Anna Spagnoletta","doi":"10.1080/10409238.2024.2377094","DOIUrl":"10.1080/10409238.2024.2377094","url":null,"abstract":"Sirtuins (SIRTs) are a family of proteins with enzymatic activity. In particular, they are a family of class III NAD+-dependent histone deacetylases and ADP-ribosyltransferases. NAD+-dependent deac(et)ylase activities catalyzed by sirtuin include ac(et)ylation, propionylation, butyrylation, crotonylation, manylation, and succinylation. Specifically, human SIRT3 is a 399 amino acid protein with two functional domains: a large Rossmann folding motif and NAD+ binding, and a small complex helix and zinc-binding motif. SIRT3 is widely expressed in mitochondria-rich tissues and is involved in maintaining mitochondrial integrity, homeostasis, and function. Moreover, SIRT3 regulates related diseases, such as aging, hepatic, kidney, neurodegenerative and cardiovascular disease, metabolic diseases, and cancer development. In particular, one of the most significant and damaging post-translational modifications is irreversible protein oxidation, i.e. carbonylation. This process is induced explicitly by increased ROS production due to mitochondrial dysfunction. SIRT3 is carbonylated by 4-hydroxynonenal at the level of Cys280. The carbonylation induces conformational changes in the active site, resulting in allosteric inhibition of SIRT3 activity and loss of the ability to deacetylate and regulate antioxidant enzyme activity. Phytochemicals and, in particular, polyphenols, thanks to their strong antioxidant activity, are natural compounds with a positive regulatory action on SIRT3 in various pathologies. Indeed, the enzymatic SIRT3 activity is modulated, for example, by different natural polyphenol classes, including resveratrol and the bergamot polyphenolic fraction. Thus, this review aims to elucidate the mechanisms by which phytochemicals can interact with SIRT3, resulting in post-translational modifications that regulate cellular metabolism.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"199-220"},"PeriodicalIF":6.2,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589869","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}

引用次数: 0

Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli. 大肠杆菌单链 DNA 结合蛋白原型的分子研究。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-02-01 Epub Date: 2024-05-21 DOI: 10.1080/10409238.2024.2330372

Nina J Bonde, Alexander G Kozlov, Michael M Cox, Timothy M Lohman, James L Keck

引用次数: 0

Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques. 利用生化和模拟技术探究蛋白质赖氨酸甲基转移酶的催化机理。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-02-01 Epub Date: 2024-03-07 DOI: 10.1080/10409238.2024.2318547

Philipp Schnee, Jürgen Pleiss, Albert Jeltsch

{"title":"Approaching the catalytic mechanism of protein lysine methyltransferases by biochemical and simulation techniques.","authors":"Philipp Schnee, Jürgen Pleiss, Albert Jeltsch","doi":"10.1080/10409238.2024.2318547","DOIUrl":"10.1080/10409238.2024.2318547","url":null,"abstract":"Protein lysine methyltransferases (PKMTs) transfer up to three methyl groups to the side chains of lysine residues in proteins and fulfill important regulatory functions by controlling protein stability, localization and protein/protein interactions. The methylation reactions are highly regulated, and aberrant methylation of proteins is associated with several types of diseases including neurologic disorders, cardiovascular diseases, and various types of cancer. This review describes novel insights into the catalytic machinery of various PKMTs achieved by the combined application of biochemical experiments and simulation approaches during the last years, focusing on clinically relevant and well-studied enzymes of this group like DOT1L, SMYD1-3, SET7/9, G9a/GLP, SETD2, SUV420H2, NSD1/2, different MLLs and EZH2. Biochemical experiments have unraveled many mechanistic features of PKMTs concerning their substrate and product specificity, processivity and the effects of somatic mutations observed in PKMTs in cancer cells. Structural data additionally provided information about the substrate recognition, enzyme-substrate complex formation, and allowed for simulations of the substrate peptide interaction and mechanism of PKMTs with atomistic resolution by molecular dynamics and hybrid quantum mechanics/molecular mechanics methods. These simulation technologies uncovered important mechanistic details of the PKMT reaction mechanism including the processes responsible for the deprotonation of the target lysine residue, essential conformational changes of the PKMT upon substrate binding, but also rationalized regulatory principles like PKMT autoinhibition. Further developments are discussed that could bring us closer to a mechanistic understanding of catalysis of this important class of enzymes in the near future. The results described here illustrate the power of the investigation of enzyme mechanisms by the combined application of biochemical experiments and simulation technologies.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"20-68"},"PeriodicalIF":6.2,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140048996","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}

引用次数: 0

Collaborators or competitors: the communication between RNA polymerase II and the nucleosome during eukaryotic transcription. 合作者还是竞争者：真核生物转录过程中 RNA 聚合酶 II 与核小体之间的交流。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-02-01 Epub Date: 2024-01-30 DOI: 10.1080/10409238.2024.2306365

Haley A Hardtke, Y Jessie Zhang

{"title":"Collaborators or competitors: the communication between RNA polymerase II and the nucleosome during eukaryotic transcription.","authors":"Haley A Hardtke, Y Jessie Zhang","doi":"10.1080/10409238.2024.2306365","DOIUrl":"10.1080/10409238.2024.2306365","url":null,"abstract":"Decades of scientific research have been devoted to unraveling the intricacies of eukaryotic transcription since the groundbreaking discovery of eukaryotic RNA polymerases in the late 1960s. RNA polymerase II, the polymerase responsible for mRNA synthesis, has always attracted the most attention. Despite its structural resemblance to its bacterial counterpart, eukaryotic RNA polymerase II faces a unique challenge in progressing transcription due to the presence of nucleosomes that package DNA in the nuclei. In this review, we delve into the impact of RNA polymerase II and histone signaling on the progression of eukaryotic transcription. We explore the pivotal points of interactions that bridge the RNA polymerase II and histone signaling systems. Finally, we present an analysis of recent cryo-electron microscopy structures, which captured RNA polymerase II-nucleosome complexes at different stages of the transcription cycle. The combination of the signaling crosstalk and the direct visualization of RNA polymerase II-nucleosome complexes provides a deeper understanding of the communication between these two major players in eukaryotic transcription.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"1-19"},"PeriodicalIF":6.2,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11209794/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139575508","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}

引用次数: 0

Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. 表观基因组编辑的定向 DNA（脱）甲基化：调节基因表达的新视角。

IF 6.2 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2024-02-01 Epub Date: 2024-03-05 DOI: 10.1080/10409238.2024.2320659

Karishma Seem, Simardeep Kaur, Suresh Kumar, Trilochan Mohapatra

{"title":"Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression.","authors":"Karishma Seem, Simardeep Kaur, Suresh Kumar, Trilochan Mohapatra","doi":"10.1080/10409238.2024.2320659","DOIUrl":"10.1080/10409238.2024.2320659","url":null,"abstract":"Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"69-98"},"PeriodicalIF":6.2,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140027605","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}

引用次数: 0

Insights into the metabolism, signaling, and physiological effects of 2’,3’-cyclic nucleotide monophosphates in bacteria 洞察细菌中 2',3'-环核苷酸单磷酸的代谢、信号传递和生理效应

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2023-12-08 DOI: 10.1080/10409238.2023.2290473

Nick J. Marotta, Emily E. Weinert

引用次数: 0

Platelet protein synthesis, regulation, and post-translational modifications: mechanics and function. 血小板蛋白质合成、调节和翻译后修饰：力学与功能。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2023-12-01 Epub Date: 2023-06-22 DOI: 10.1080/10409238.2023.2224532

Gerald Soslau

{"title":"Platelet protein synthesis, regulation, and post-translational modifications: mechanics and function.","authors":"Gerald Soslau","doi":"10.1080/10409238.2023.2224532","DOIUrl":"10.1080/10409238.2023.2224532","url":null,"abstract":"Dogma had been firmly entrenched in the minds of the scientific community that the anucleate mammalian platelet was incapable of protein biosynthesis since their identification in the late 1880s. These beliefs were not challenged until the 1960s when several reports demonstrated that platelets possessed the capacity to biosynthesize proteins. Even then, many still dismissed the synthesis as trivial and unimportant for at least another two decades. Research in the field expanded after the 1980s and numerous reports have since been published that now clearly demonstrate the potential significance of platelet protein synthesis under normal, pathological, and activating conditions. It is now clear that the platelet proteome is not a static entity but can be altered slowly or rapidly in response to external signals to support physiological requirements to maintain hemostasis and other biological processes. All the necessary biological components to support protein synthesis have been identified in platelets along with post-transcriptional processing of mRNAs, regulators of translation, and post-translational modifications such as glycosylation. The last comprehensive review of the subject appeared in 2009 and much work has been conducted since that time. The current review of the field will briefly incorporate the information covered in earlier reviews and then bring the reader up to date with more recent findings.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"99-117"},"PeriodicalIF":6.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9677281","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}

引用次数: 0

Hemoglobin wonders: a fascinating gas transporter dive into molluscs. 血红蛋白奇观：软体动物中令人着迷的气体运输工具。

IF 6.5 2区生物学

Critical Reviews in Biochemistry and Molecular Biology Pub Date : 2023-12-01 Epub Date: 2024-02-02 DOI: 10.1080/10409238.2023.2299381

Weifeng Zhang, Yang Zhang, Xizhi Shi, Shi Wang, Yongbo Bao

{"title":"Hemoglobin wonders: a fascinating gas transporter dive into molluscs.","authors":"Weifeng Zhang, Yang Zhang, Xizhi Shi, Shi Wang, Yongbo Bao","doi":"10.1080/10409238.2023.2299381","DOIUrl":"10.1080/10409238.2023.2299381","url":null,"abstract":"Hemoglobin (Hb) has been identified in at least 14 molluscan taxa so far. Research spanning over 130 years on molluscan Hbs focuses on their genes, protein structures, functions, and evolution. Molluscan Hbs are categorized into single-, two-, and multiple-domain chains, including red blood cell, gill, and extracellular Hbs, based on the number of globin domains and their respective locations. These Hbs exhibit variation in assembly, ranging from monomeric and dimeric to higher-order multimeric forms. Typically, molluscan Hbs display moderately high oxygen affinity, weak cooperativity, and varying pH sensitivity. Hb's potential role in antimicrobial pathways could augment the immune defense of bivalves, which may be a complement to their lack of adaptive immunity. The role of Hb as a respiratory protein in bivalves likely originated from the substitution of hemocyanin. Molluscan Hbs demonstrate adaptive evolution in response to environmental changes via various strategies (e.g. increasing Hb types, multimerization, and amino acid residue substitutions at key sites), enhancing or altering functional properties for habitat adaptation. Concurrently, an increase in Hb assembly diversity, coupled with a downward trend in oxygen affinity, is observed during molluscan differentiation and evolution. Hb in Protobranchia, Heteroconchia, and Pteriomorphia bivalves originated from separate ancestors, with Protobranchia inheriting a relative ancient molluscan Hb gene. In bivalves, extracellular Hbs share a common origin, while gill Hbs likely emerged from convergent evolution. In summary, research on molluscan Hbs offers valuable insights into the origins, biological variations, and adaptive evolution of animal Hbs.","PeriodicalId":10794,"journal":{"name":"Critical Reviews in Biochemistry and Molecular Biology","volume":" ","pages":"132-157"},"PeriodicalIF":6.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139377328","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}

引用次数: 0