Enzymes最新文献_第9页

Sphingolipids: From structural components to signaling hubs. 鞘磷脂：从结构成分到信号中枢。

Enzymes Pub Date : 2023-01-01 Epub Date: 2023-08-28 DOI: 10.1016/bs.enz.2023.07.003

Batoul M Issleny, Rama Jamjoum, Saurav Majumder, Johnny Stiban

{"title":"Sphingolipids: From structural components to signaling hubs.","authors":"Batoul M Issleny, Rama Jamjoum, Saurav Majumder, Johnny Stiban","doi":"10.1016/bs.enz.2023.07.003","DOIUrl":"10.1016/bs.enz.2023.07.003","url":null,"abstract":"In late November 2019, Prof. Lina M. Obeid passed away from cancer, a disease she spent her life researching and studying its intricate molecular underpinnings. Along with her husband, Prof. Yusuf A. Hannun, Obeid laid down the foundations of sphingolipid biochemistry and oversaw its remarkable evolution over the years. Lipids are a class of macromolecules that are primarily associated with cellular architecture. In fact, lipids constitute the perimeter of the cell in such a way that without them, there cannot be cells. Hence, much of the early research on lipids identified the function of this class of biological molecules as merely structural. Nevertheless, unlike proteins, carbohydrates, and nucleic acids, lipids are elaborately diverse as they are not made up of monomers in polymeric forms. This diversity in structure is clearly mirrored by functional pleiotropy. In this chapter, we focus on a major subset of lipids, sphingolipids, and explore their historic rise from merely inert structural components of plasma membranes to lively and necessary signaling molecules that transmit various signals and control many cellular processes. We will emphasize the works of Lina Obeid since she was an integral pillar of the sphingolipid research world.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"171-201"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mitochondrial AAA+ proteases. 线粒体AAA+蛋白酶。

Enzymes Pub Date : 2023-01-01 Epub Date: 2023-10-13 DOI: 10.1016/bs.enz.2023.09.002

Yuichi Matsushima

引用次数: 0

Conserved mechanisms of NuRD function in hematopoetic gene expression. NuRD在造血基因表达中功能的保守机制。

Enzymes Pub Date : 2023-01-01 Epub Date: 2023-08-30 DOI: 10.1016/bs.enz.2023.07.006

Jonathan Lenz, Alexander Brehm

{"title":"Conserved mechanisms of NuRD function in hematopoetic gene expression.","authors":"Jonathan Lenz, Alexander Brehm","doi":"10.1016/bs.enz.2023.07.006","DOIUrl":"https://doi.org/10.1016/bs.enz.2023.07.006","url":null,"abstract":"The Nucleosome Remodeling and Deacetylating Complex (NuRD) is ubiquitously expressed in all metazoans. It combines nucleosome remodeling and histone deacetylating activities to generate inaccessible chromatin structures and to repress gene transcription. NuRD is involved in the generation and maintenance of a wide variety of lineage-specific gene expression programs during differentiation and in differentiated cells. A close cooperation with a large number of lineage-specific transcription factors is key to allow NuRD to function in many distinct differentiation contexts. The molecular nature of this interplay between transcription factors and NuRD is complex and not well understood. This review uses hematopoiesis as a paradigm to highlight recent advances in our understanding of how transcription factors and NuRD cooperate at the molecular level during differentiation. A comparison of vertebrate and invertebrate systems serves to identify the conserved and fundamental concepts guiding functional interactions between transcription factors and NuRD. We also discuss how the transcription factor-NuRD axis constitutes a potential therapeutic target for the treatment of hemoglobinopathies.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"53 ","pages":"7-32"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41146415","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

History of advances in enzyme kinetic methods: From minutes to milliseconds. 酶动力学方法的发展史：从几分钟到几毫秒。

Enzymes Pub Date : 2023-01-01 Epub Date: 2023-08-08 DOI: 10.1016/bs.enz.2023.07.005

Kenneth A Johnson

{"title":"History of advances in enzyme kinetic methods: From minutes to milliseconds.","authors":"Kenneth A Johnson","doi":"10.1016/bs.enz.2023.07.005","DOIUrl":"10.1016/bs.enz.2023.07.005","url":null,"abstract":"The last review on transient-state kinetic methods in The Enzymes was published three decades ago (Johnson, K.A., 1992. The Enzymes, XX, 1-61). In that review the foundations were laid out for the logic behind the design and interpretation of experiments. In the intervening years the instrumentation has improved mainly in providing better sample economy and shorter dead times. More significantly, in 1992 we were just introducing methods for fitting data based on numerical integration of rate equations, but the software was slow and difficult to use. Today, advances in numerical integration methods for data fitting have led to fast and dynamic software, making it easy to fit data without simplifying approximations. This approach overcomes multiple disadvantages of traditional data fitting based on equations derived by analytical integration of rate equations, requiring simplifying approximations. Mechanism-based fitting using computer simulation resolves mechanisms by accounting for the concentration dependence of the rates and amplitudes of the reaction to find a set of intrinsic rate constants that reproduce the experimental data, including details about how the experiment was performed in modeling the data. Rather than discuss how to design and interpret rapid-quench and stopped-flow experiments individually, we now focus on how to fit them simultaneously so that the quench-flow data anchor the interpretation of fluorescence signals. Computer simulation streamlines the fitting of multiple experiments globally to yield a single unifying model to account for all available data.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"54 ","pages":"107-134"},"PeriodicalIF":0.0,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72015663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Overview of DNA damage and double-strand breaks. DNA损伤和双链断裂概述。

Enzymes Pub Date : 2022-01-01 Epub Date: 2022-10-07 DOI: 10.1016/bs.enz.2022.08.001

Fuyuhiko Tamanoi, Kenichi Yoshikawa

引用次数: 0

Damages of DNA in tritiated water. 氚化水中DNA的损伤。

Enzymes Pub Date : 2022-01-01 Epub Date: 2022-10-05 DOI: 10.1016/bs.enz.2022.08.009

Yuji Hatano, Hiroaki Nakamura, Susumu Fujiwara, Seiki Saito, Takahiro Kenmotsu

{"title":"Damages of DNA in tritiated water.","authors":"Yuji Hatano, Hiroaki Nakamura, Susumu Fujiwara, Seiki Saito, Takahiro Kenmotsu","doi":"10.1016/bs.enz.2022.08.009","DOIUrl":"https://doi.org/10.1016/bs.enz.2022.08.009","url":null,"abstract":"Tritium is a radioisotope of hydrogen emitting low energy β-rays in disintegration to 3He. DNA molecules are damaged mainly by β-ray irradiation, and additional damages can be induced by break of chemical bond by nuclear transmutation to inert 3He. Deep knowledges of the mechanisms underlying DNA damages lead to better understanding of biological effects of tritium. This chapter reviews recent experimental and computer simulation activities on quantitative evaluation of damage rates by β-ray irradiation and nuclear transmutation. The rate of DNA double-strand breaks in tritiated water has been examined using a single molecule observation method. The effects of β-ray irradiation were not noticeable at the level of tritium concentration of ∼kBq/cm3, while the irradiation effects were clear at tritium concentrations of ∼MBq/cm3. The factors affecting on the DSB rate are discussed. A new image processing method for the automatic measurement of DNA length using OpenCV and deep learning is also introduced. The effects of tritium transmutation on hydrogen bonds acting between the two main strands of DNA have been examined using molecular dynamics simulations. The study showed that the collapsing of DNA structure by the transmutation can be quantitatively evaluated using the root mean square deviation of atomic positions.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"51 ","pages":"131-152"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40682355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mechanical force induced DNA double-strand breaks: Ultrasound. 机械力诱导DNA双链断裂:超声。

Enzymes Pub Date : 2022-01-01 Epub Date: 2022-09-27 DOI: 10.1016/bs.enz.2022.08.004

Yue Ma, Iwaki Akiyama

引用次数: 0

Auger electrons and DNA double-strand breaks studied by using iodine-containing chemicals. 利用含碘化学物质研究俄歇电子和DNA双链断裂。

Enzymes Pub Date : 2022-01-01 Epub Date: 2022-09-27 DOI: 10.1016/bs.enz.2022.08.007

Yuya Higashi, Yue Ma, Kotaro Matsumoto, Ayumi Shiro, Hiroyuki Saitoh, Tetsuya Kawachi, Fuyuhiko Tamanoi

{"title":"Auger electrons and DNA double-strand breaks studied by using iodine-containing chemicals.","authors":"Yuya Higashi, Yue Ma, Kotaro Matsumoto, Ayumi Shiro, Hiroyuki Saitoh, Tetsuya Kawachi, Fuyuhiko Tamanoi","doi":"10.1016/bs.enz.2022.08.007","DOIUrl":"https://doi.org/10.1016/bs.enz.2022.08.007","url":null,"abstract":"Irradiation of high Z elements such as iodine, gold, gadolinium with monochromatic X-rays causes photoelectric effects that include the release of Auger electrons. Decay of radioactive iodine such as I-123 and I-125 also results in multiple events and some involve the generation of Auger electrons. These electrons have low energy and travel only a short distance but have a strong effect on DNA damage including the generation of double-strand breaks. In this chapter, we focus on iodine and discuss various studies that used iodine-containing chemicals to generate Auger electrons and cause DNA double-strand breaks. First, DNA synthesis precursors containing iodine were used to place iodine on DNA. DNA binding dyes such as iodine Hoechst were investigated for Auger electron generation and DNA breaks. More recently, iodine containing nanoparticles were developed. We describe our study using tumor spheroids loaded with iodine nanoparticles and synchrotron-generated monochromatic X-rays. This study led to the demonstration that an optimum effect on DNA double-strand break formation is observed with a 33.2keV X-ray which is just above the K-edge energy of iodine.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"51 ","pages":"101-115"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40667370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chromatin organization and DNA damage. 染色质组织和DNA损伤。

Enzymes Pub Date : 2022-01-01 Epub Date: 2022-09-27 DOI: 10.1016/bs.enz.2022.08.003

Katsuhiko Minami, Shiori Iida, Kazuhiro Maeshima

{"title":"Chromatin organization and DNA damage.","authors":"Katsuhiko Minami, Shiori Iida, Kazuhiro Maeshima","doi":"10.1016/bs.enz.2022.08.003","DOIUrl":"https://doi.org/10.1016/bs.enz.2022.08.003","url":null,"abstract":"Genomic DNA is organized three-dimensionally in the nucleus as chromatin. Recent accumulating evidence has demonstrated that chromatin organizes into numerous dynamic domains in higher eukaryotic cells, which act as functional units of the genome. These compacted domains facilitate DNA replication and gene regulation. Undamaged chromatin is critical for healthy cells to function and divide. However, the cellular genome is constantly threatened by many sources of DNA damage (e.g., radiation). How do cells maintain their genome integrity when subjected to DNA damage? This chapter describes how the compact state of chromatin safeguards the genome from radiation damage and chemical attacks. Together with recent genomics data, our finding suggests that DNA compaction, such as chromatin domain formation, plays a critical role in maintaining genome integrity. But does the formation of such domains limit DNA accessibility inside the domain and hinder the recruitment of repair machinery to the damaged site(s) during DNA repair? To approach this issue, we first describe a sensitive imaging method to detect changes in chromatin states in living cells (single-nucleosome imaging/tracking). We then use this method to explain how cells can overcome potential recruiting difficulties; cells can decompact chromatin domains following DNA damage and temporarily increase chromatin motion (∼DNA accessibility) to perform efficient DNA repair. We also speculate on how chromatin compaction affects DNA damage-resistance in the clinical setting.","PeriodicalId":39097,"journal":{"name":"Enzymes","volume":"51 ","pages":"29-51"},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40682356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Quantitative evaluation of DNA double-strand breaks (DSBs) through single-molecule observation. 通过单分子观察定量评价DNA双链断裂(DSBs)。

Enzymes Pub Date : 2022-01-01 Epub Date: 2022-10-03 DOI: 10.1016/bs.enz.2022.08.002

Kenichi Yoshikawa

引用次数: 0