Essays in biochemistry最新文献_第5页

Malate dehydrogenase: a story of diverse evolutionary radiation. 苹果酸脱氢酶：多种进化辐射的故事。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230076

Michael J Wolyniak, Robert H Frazier, Peter K Gemborys, Henry E Loehr

{"title":"Malate dehydrogenase: a story of diverse evolutionary radiation.","authors":"Michael J Wolyniak, Robert H Frazier, Peter K Gemborys, Henry E Loehr","doi":"10.1042/EBC20230076","DOIUrl":"10.1042/EBC20230076","url":null,"abstract":"Malate dehydrogenase (MDH) is a ubiquitous enzyme involved in cellular respiration across all domains of life. MDH's ubiquity allows it to act as an excellent model for considering the history of life and how the rise of aerobic respiration and eukaryogenesis influenced this evolutionary process. Here, we present the diversity of the MDH family of enzymes across bacteria, archaea, and eukarya, the relationship between MDH and lactate dehydrogenase (LDH) in the formation of a protein superfamily, and the connections between MDH and endosymbiosis in the formation of mitochondria and chloroplasts. The development of novel and powerful DNA sequencing techniques has challenged some of the conventional wisdom underlying MDH evolution and suggests a history dominated by gene duplication, horizontal gene transfer, and cryptic endosymbiosis events and adaptation to a diverse range of environments across all domains of life over evolutionary time. The data also suggest a superfamily of proteins that do not share high levels of sequential similarity but yet retain strong conservation of core function via key amino acid residues and secondary structural components. As DNA sequencing and 'big data' analysis techniques continue to improve in the life sciences, it is likely that the story of MDH will continue to refine as more examples of superfamily diversity are recovered from nature and analyzed.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"213-220"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11461315/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141174471","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

Malate dehydrogenase as a multi-purpose target for drug discovery. 苹果酸脱氢酶作为药物发现的多用途靶点。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230081

Charles S Fermaintt, Sarah A Wacker

{"title":"Malate dehydrogenase as a multi-purpose target for drug discovery.","authors":"Charles S Fermaintt, Sarah A Wacker","doi":"10.1042/EBC20230081","DOIUrl":"10.1042/EBC20230081","url":null,"abstract":"Malate dehydrogenase (MDH) enzymes play critical roles in cellular metabolism, facilitating the reversible conversion of malate to oxaloacetate using NAD+/NADH as a cofactor. The two human isoforms of MDH have roles in the citric acid cycle and the malate-aspartate shuttle, and thus both are key enzymes in aerobic respiration as well as regenerating the pool of NAD+ used in glycolysis. This review highlights the potential of MDH as a therapeutic drug target in various diseases, including metabolic and neurological disorders, cancer, and infectious diseases. The most promising molecules for targeting MDH have been examined in the context of human malignancies, where MDH is frequently overexpressed. Recent studies have led to the identification of several antagonists, some of which are broad MDH inhibitors while others have selectivity for either of the two human MDH isoforms. Other promising compounds have been studied in the context of parasitic MDH, as inhibiting the function of the enzyme could selectively kill the parasite. Research is ongoing with these chemical scaffolds to develop more effective small-molecule drug leads that would have great potential for clinical applications.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"147-160"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141178814","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

Acetylation, ADP-ribosylation and methylation of malate dehydrogenase. 苹果酸脱氢酶的乙酰化、ADP-核糖基化和甲基化。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230080

Misty L Kuhn, John F Rakus, Delphine Quenet

{"title":"Acetylation, ADP-ribosylation and methylation of malate dehydrogenase.","authors":"Misty L Kuhn, John F Rakus, Delphine Quenet","doi":"10.1042/EBC20230080","DOIUrl":"10.1042/EBC20230080","url":null,"abstract":"Metabolism within an organism is regulated by various processes, including post-translational modifications (PTMs). These types of chemical modifications alter the molecular, biochemical, and cellular properties of proteins and allow the organism to respond quickly to different environments, energy states, and stresses. Malate dehydrogenase (MDH) is a metabolic enzyme that is conserved in all domains of life and is extensively modified post-translationally. Due to the central role of MDH, its modification can alter metabolic flux, including the Krebs cycle, glycolysis, and lipid and amino acid metabolism. Despite the importance of both MDH and its extensively post-translationally modified landscape, comprehensive characterization of MDH PTMs, and their effects on MDH structure, function, and metabolic flux remains underexplored. Here, we review three types of MDH PTMs - acetylation, ADP-ribosylation, and methylation - and explore what is known in the literature and how these PTMs potentially affect the 3D structure, enzymatic activity, and interactome of MDH. Finally, we briefly discuss the potential involvement of PTMs in the dynamics of metabolons that include MDH.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"199-212"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11451102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141589986","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

Roles of the oncometabolite enantiomers of 2-hydroxyglutarate and their metabolism by diverse dehydrogenases. 2-hydroxyglutarate 对映体的作用及其在不同脱氢酶中的代谢。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230077

Ivelitza Garcia, Kathleen Cornely, Celeste N Peterson, Melanie B Berkmen

{"title":"Roles of the oncometabolite enantiomers of 2-hydroxyglutarate and their metabolism by diverse dehydrogenases.","authors":"Ivelitza Garcia, Kathleen Cornely, Celeste N Peterson, Melanie B Berkmen","doi":"10.1042/EBC20230077","DOIUrl":"10.1042/EBC20230077","url":null,"abstract":"2-Hydroxyglutarate (2HG) is an oncometabolite that can contribute to tumor progression. Two enantiomer forms, L-2HG and D-2HG, arise from independent pathways starting from the precursor α-ketoglutarate (αKG). L-2HG production occurs through the promiscuous activities of malate dehydrogenase (MDH) and lactate dehydrogenase (LDH) under acidic and/or hypoxic conditions. D-2HG frequently accumulates by gain-of-function mutations in the genes encoding two isoforms of isocitrate dehydrogenase (IDH1 and IDH2). Cognate metabolite repair enzymes, L- and D-2-hydroxyglutarate dehydrogenases, oxidize the enantiomers and cause abnormally high 2HG accumulation and disease when mutated. Elevated levels of either oncometabolite affect redox homeostasis, metabolism, and immune system functioning. Moreover, the oncometabolites inhibit several α-ketoglutarate-dependent dioxygenases resulting in epigenetic changes such as DNA and histone hypermethylation as well as deficiencies in DNA repair. L-2HG, and D-2HG in some cases, inhibit degradation of hypoxia-inducible factor (HIF1α), a transcription factor that alters gene expression to adapt to hypoxic conditions, favoring tumorigenesis. Patients with the rare disease 2-hydroxyglutaric aciduria (2HGA) have exceedingly high levels of 2HG, which is neurotoxic, causing developmental delays and brain abnormalities. D-2HG also has specific effects on collagen production and NADPH pools. Recently, D-2HG has been targeted in new chemotherapies aimed at disrupting the gain-of-function IDH1 and IDH2 mutants, resulting in successful clinical trials for several cancers.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"161-171"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141450147","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

Physiology of malate dehydrogenase and how dysregulation leads to disease. 苹果酸脱氢酶的生理学以及失调如何导致疾病。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230085

Amy D Parente, Danielle E Bolland, Kathryn L Huisinga, Joseph J Provost

{"title":"Physiology of malate dehydrogenase and how dysregulation leads to disease.","authors":"Amy D Parente, Danielle E Bolland, Kathryn L Huisinga, Joseph J Provost","doi":"10.1042/EBC20230085","DOIUrl":"10.1042/EBC20230085","url":null,"abstract":"Malate dehydrogenase (MDH) is pivotal in mammalian tissue metabolism, participating in various pathways beyond its classical roles and highlighting its adaptability to cellular demands. This enzyme is involved in maintaining redox balance, lipid synthesis, and glutamine metabolism and supports rapidly proliferating cells' energetic and biosynthetic needs. The involvement of MDH in glutamine metabolism underlines its significance in cell physiology. In contrast, its contribution to lipid metabolism highlights its role in essential biosynthetic processes necessary for cell maintenance and proliferation. The enzyme's regulatory mechanisms, such as post-translational modifications, underscore its complexity and importance in metabolic regulation, positioning MDH as a potential target in metabolic dysregulation. Furthermore, the association of MDH with various pathologies, including cancer and neurological disorders, suggests its involvement in disease progression. The overexpression of MDH isoforms MDH1 and MDH2 in cancers like breast, prostate, and pancreatic ductal adenocarcinoma, alongside structural modifications, implies their critical role in the metabolic adaptation of tumor cells. Additionally, mutations in MDH2 linked to pheochromocytomas, paragangliomas, and other metabolic diseases emphasize MDH's role in metabolic homeostasis. This review spotlights MDH's potential as a biomarker and therapeutic target, advocating for further research into its multifunctional roles and regulatory mechanisms in health and disease.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"121-134"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141497493","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

Innovate and empower: the malate dehydrogenase course-based undergraduate research experiences and community of practice. 创新和赋权：基于苹果酸脱氢酶课程的本科生研究经验和实践社区。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230074

Sue Ellen DeChenne-Peters, Nicole L Scheuermann, Amy D Parente, Jing Zhang

{"title":"Innovate and empower: the malate dehydrogenase course-based undergraduate research experiences and community of practice.","authors":"Sue Ellen DeChenne-Peters, Nicole L Scheuermann, Amy D Parente, Jing Zhang","doi":"10.1042/EBC20230074","DOIUrl":"10.1042/EBC20230074","url":null,"abstract":"College science programs exhibit high rates of student attrition, especially among Students of Color, women, members of the LGBTQ+ community, and those with disabilities. Many of the reasons students choose to leave or feel pushed out of science can be mitigated through participation in faculty-mentored research. However, faculty resources are limited, and not every student has access to faculty mentoring due to systemic or structural barriers. By bringing authentic scientific research into the classroom context, course-based undergraduate research experiences (CUREs) expand the number of students who participate in research and provide benefits similar to faculty-mentored research. Instructors also benefit from teaching CUREs. Using a systematic review of 14 manuscripts concerning the Malate Dehydrogenase CUREs Community (MCC) and malate dehydrogenase (MDH) CUREs, we demonstrate that CUREs can be implemented flexibly, are authentic research experiences, generate new scientific discoveries, and improve student outcomes. Additionally, CURE communities offer substantial advantages to faculty wishing to implement CUREs.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"253-268"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141733833","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

The structural biology and dynamics of malate dehydrogenases. 苹果酸脱氢酶的结构生物学和动力学。

IF 5.6 2区生物学

Essays in biochemistry Pub Date : 2024-10-03 DOI: 10.1042/EBC20230082

Christopher E Berndsen, Jessica K Bell

{"title":"The structural biology and dynamics of malate dehydrogenases.","authors":"Christopher E Berndsen, Jessica K Bell","doi":"10.1042/EBC20230082","DOIUrl":"10.1042/EBC20230082","url":null,"abstract":"Malate dehydrogenase (MDH) enzymes catalyze the reversible oxidoreduction of malate to oxaloacetate using NAD(P) as a cofactor. This reaction is vital for metabolism and the exchange of reducing equivalents between cellular compartments. There are more than 100 structures of MDH in the Protein Data Bank, representing species from archaea, bacteria, and eukaryotes. This conserved family of enzymes shares a common nucleotide-binding domain, substrate-binding domain, and subunits associate to form a dimeric or a tetrameric enzyme. Despite the variety of crystallization conditions and ligands in the experimental structures, the conformation and configuration of MDH are similar. The quaternary structure and active site dynamics account for most conformational differences in the experimental MDH structures. Oligomerization appears essential for activity despite each subunit having a structurally independent active site. There are two dynamic regions within the active site that influence substrate binding and possibly catalysis, with one of these regions adjoining the subunit interface. In this review, we introduce the reader to the general structural framework of MDH highlighting the conservation of certain features and pointing out unique differences that regulate MDH enzyme activity.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"57-72"},"PeriodicalIF":5.6,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141901346","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

Computational models as catalysts for investigating redoxin systems. 计算模型是研究氧化还原系统的催化剂。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-04-30 DOI: 10.1042/EBC20230036

Ché S Pillay, Johann M Rohwer

{"title":"Computational models as catalysts for investigating redoxin systems.","authors":"Ché S Pillay, Johann M Rohwer","doi":"10.1042/EBC20230036","DOIUrl":"10.1042/EBC20230036","url":null,"abstract":"Thioredoxin, glutaredoxin and peroxiredoxin systems play central roles in redox regulation, signaling and metabolism in cells. In these systems, reducing equivalents from NAD(P)H are transferred by coupled thiol-disulfide exchange reactions to redoxins which then reduce a wide array of targets. However, the characterization of redoxin activity has been unclear, with redoxins regarded as enzymes in some studies and redox metabolites in others. Consequently, redoxin activities have been quantified by enzyme kinetic parameters in vitro, and redox potentials or redox ratios within cells. By analyzing all the reactions within these systems, computational models showed that many kinetic properties attributed to redoxins were due to system-level effects. Models of cellular redoxin networks have also been used to estimate intracellular hydrogen peroxide levels, analyze redox signaling and couple omic and kinetic data to understand the regulation of these networks in disease. Computational modeling has emerged as a powerful complementary tool to traditional redoxin enzyme kinetic and cellular assays that integrates data from a number of sources into a single quantitative framework to accelerate the analysis of redoxin systems.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"27-39"},"PeriodicalIF":6.4,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734762","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

Computational methods for processing and interpreting mass spectrometry-based metabolomics. 处理和解释基于质谱的代谢组学的计算方法。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-04-30 DOI: 10.1042/EBC20230019

Leonardo Perez de Souza, Alisdair R Fernie

{"title":"Computational methods for processing and interpreting mass spectrometry-based metabolomics.","authors":"Leonardo Perez de Souza, Alisdair R Fernie","doi":"10.1042/EBC20230019","DOIUrl":"10.1042/EBC20230019","url":null,"abstract":"Metabolomics has emerged as an indispensable tool for exploring complex biological questions, providing the ability to investigate a substantial portion of the metabolome. However, the vast complexity and structural diversity intrinsic to metabolites imposes a great challenge for data analysis and interpretation. Liquid chromatography mass spectrometry (LC-MS) stands out as a versatile technique offering extensive metabolite coverage. In this mini-review, we address some of the hurdles posed by the complex nature of LC-MS data, providing a brief overview of computational tools designed to help tackling these challenges. Our focus centers on two major steps that are essential to most metabolomics investigations: the translation of raw data into quantifiable features, and the extraction of structural insights from mass spectra to facilitate metabolite identification. By exploring current computational solutions, we aim at providing a critical overview of the capabilities and constraints of mass spectrometry-based metabolomics, while introduce some of the most recent trends in data processing and analysis within the field.","PeriodicalId":11812,"journal":{"name":"Essays in biochemistry","volume":" ","pages":"5-13"},"PeriodicalIF":6.4,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11065554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138298743","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

Kinetic modelling of glycolytic oscillations. 糖酵解振荡的动力学模型。

IF 6.4 2区生物学

Essays in biochemistry Pub Date : 2024-04-30 DOI: 10.1042/EBC20230037

David D van Niekerk, Morne van Wyk, Theresa Kouril, Jacky L Snoep

引用次数: 0