Methods in enzymology最新文献_第3页

Characterization of amyloid-like metal-amino acid assemblies with remarkable catalytic activity. 具有显著催化活性的淀粉样金属-氨基酸组合体的特征。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-02-07 DOI: 10.1016/bs.mie.2024.01.018

Om Shanker Tiwari, Ehud Gazit

{"title":"Characterization of amyloid-like metal-amino acid assemblies with remarkable catalytic activity.","authors":"Om Shanker Tiwari, Ehud Gazit","doi":"10.1016/bs.mie.2024.01.018","DOIUrl":"10.1016/bs.mie.2024.01.018","url":null,"abstract":"While enzymes are potentially useful in various applications, their limited operational stability and production costs have led to an extensive search for stable catalytic agents that will retain the efficiency, specificity, and environmental-friendliness of natural enzymes. Despite extensive efforts, there is still an unmet need for improved enzyme mimics and novel concepts to discover and optimize such agents. Inspired by the catalytic activity of amyloids and the formation of amyloid-like assemblies by metabolites, our group pioneered the development of novel metabolite-metal co-assemblies (bio-nanozymes) that produce nanomaterials mimicking the catalytic function of common metalloenzymes that are being used for various technological applications. In addition to their notable activity, bio-nanozymes are remarkably safe as they are purely composed of amino acids and minerals that are harmless to the environment. The bio-nanozymes exhibit high efficiency and exceptional robustness, even under extreme conditions of temperature, pH, and salinity that are impractical for enzymes. Our group has recently also demonstrated the formation of ordered amino acid co-assemblies showing selective and preferential interactions comparable to the organization of residues in folded proteins. The identified bio-nanozymes can be used in various applications including environmental remediation, synthesis of new materials, and green energy.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"697 ","pages":"181-209"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Structural studies of catalytic peptides using molecular dynamics simulations. 利用分子动力学模拟对催化肽进行结构研究。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-02-06 DOI: 10.1016/bs.mie.2024.01.019

Parth Rathee, Sreerag N Moorkkannur, Rajeev Prabhakar

{"title":"Structural studies of catalytic peptides using molecular dynamics simulations.","authors":"Parth Rathee, Sreerag N Moorkkannur, Rajeev Prabhakar","doi":"10.1016/bs.mie.2024.01.019","DOIUrl":"10.1016/bs.mie.2024.01.019","url":null,"abstract":"Many self-assembling peptides can form amyloid like structures with different sizes and morphologies. Driven by non-covalent interactions, their aggregation can occur through distinct pathways. Additionally, they can bind metal ions to create enzyme like active sites that allow them to catalyze diverse reactions. Due to the non-crystalline nature of amyloids, it is quite challenging to elucidate their structures using experimental spectroscopic techniques. In this aspect, molecular dynamics (MD) simulations provide a useful tool to derive structures of these macromolecules in solution. They can be further validated by comparing with experimentally measured structural parameters. However, these simulations require a multi-step process starting from the selection of the initial structure to the analysis of MD trajectories. There are multiple force fields, parametrization protocols, equilibration processes, software and analysis tools available for this process. Therefore, it is complicated for non-experts to select the most relevant tools and perform these simulations effectively. In this chapter, a systematic methodology that covers all major aspects of modeling of catalytic peptides is provided in a user-friendly manner. It will be helpful for researchers in this critical area of research.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"697 ","pages":"151-180"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141180261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

Bioinformatic analysis of microbial type terpene synthase genes in plants. 植物中微生物型萜烯合成酶基因的生物信息学分析。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-03-12 DOI: 10.1016/bs.mie.2024.02.014

Xinlu Chen, Jin Han, Feng Chen

引用次数: 0

Structural biology of terpene synthases. 萜烯合成酶的结构生物学。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-03-31 DOI: 10.1016/bs.mie.2024.03.012

Baiying Xing, Zhenyu Lei, Zhaoye Bai, Guowei Zang, Yuxian Wang, Chenyu Zhang, Minren Chen, Yucheng Zhou, Jiahao Ding, Donghui Yang, Ming Ma

引用次数: 0

Vanadium haloperoxidases as noncanonical terpene synthases. 作为非典型萜烯合成酶的钒卤过氧化物酶

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-04-17 DOI: 10.1016/bs.mie.2024.03.024

Jackson T Baumgartner, Lia I Lozano Salazar, Lukas A Varga, Gabriel H Lefebre, Shaun M K McKinnie

引用次数: 0

Processing serial synchrotron crystallography diffraction data with DIALS.

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-10-29 DOI: 10.1016/bs.mie.2024.10.004

James Beilsten-Edmands, James M Parkhurst, Graeme Winter, Gwyndaf Evans

引用次数: 0

Discovery, isolation, and characterization of diazeniumdiolate siderophores. 发现、分离和鉴定重氮二硫酸盐苷元。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-07-20 DOI: 10.1016/bs.mie.2024.06.006

Melanie Susman, Jin Yan, Christina Makris, Alison Butler

引用次数: 0

The production of siderophore analogues using precursor-directed biosynthesis. 利用前体定向生物合成法生产苷酸类似物。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-07-23 DOI: 10.1016/bs.mie.2024.06.009

Tomas Richardson-Sanchez, Thomas J Telfer, Cho Z Soe, Kate P Nolan, Michael P Gotsbacher, Rachel Codd

{"title":"The production of siderophore analogues using precursor-directed biosynthesis.","authors":"Tomas Richardson-Sanchez, Thomas J Telfer, Cho Z Soe, Kate P Nolan, Michael P Gotsbacher, Rachel Codd","doi":"10.1016/bs.mie.2024.06.009","DOIUrl":"https://doi.org/10.1016/bs.mie.2024.06.009","url":null,"abstract":"Siderophores are low-molecular-weight organic bacterial and fungal secondary metabolites that form high affinity complexes with Fe(III). These Fe(III)-siderophore complexes are part of the siderophore-mediated Fe(III) uptake mechanism, which is the most widespread strategy used by microbes to access sufficient iron for growth. Microbial competition for limited iron is met by biosynthetic gene clusters that encode for the biosynthesis of siderophores with variable molecular scaffolds and iron binding motifs. Some classes of siderophores have well understood biosynthetic pathways, which opens opportunities to further expand structural and property diversity using precursor-directed biosynthesis (PDB). PDB involves augmenting culture medium with non-native substrates to compete against native substrates during metabolite assembly. This chapter provides background information and technical details of conducting a PDB experiment towards producing a range of different analogues of the archetypal hydroxamic acid siderophore desferrioxamine B. This includes processes to semi-purify the culture supernatant and the use of liquid chromatography-tandem mass spectrometry for downstream analysis of analogues and groups of constitutional isomers.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"702 ","pages":"121-145"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142000399","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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

RADD: A real-time FRET-based biochemical assay for DNA deaminase studies. RADD：基于实时 FRET 的 DNA 脱氨酶生化测定。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-08-27 DOI: 10.1016/bs.mie.2024.08.001

Christopher A Belica, Patricia C Hernandez, Michael A Carpenter, Yanjun Chen, William L Brown, Reuben S Harris, Hideki Aihara

引用次数: 0

The MitoLuc assay for the analysis of the mechanism of mitochondrial protein import. 用于分析线粒体蛋白质导入机制的 MitoLuc 分析法。

4区生物学

Methods in enzymology Pub Date : 2024-01-01 Epub Date: 2024-08-22 DOI: 10.1016/bs.mie.2024.07.033

Hope I Needs, Youmian Yan, Natalie M Niemi, Ian Collinson

{"title":"The MitoLuc assay for the analysis of the mechanism of mitochondrial protein import.","authors":"Hope I Needs, Youmian Yan, Natalie M Niemi, Ian Collinson","doi":"10.1016/bs.mie.2024.07.033","DOIUrl":"10.1016/bs.mie.2024.07.033","url":null,"abstract":"The NanoLuc split luciferase assay has proven to be a powerful tool for the analysis of protein translocation. Its flexibility has enabled in vivo, ex vivo, and in vitro studies-including systems reconstituting protein transport from pure components. The assay has been particularly useful in the characterization of bacterial secretion and mitochondrial protein import. In the latter case, MitoLuc has been developed for the investigation of the TIM23-pathway via import into the matrix of isolated yeast mitochondria. Subsequent analysis identified three distinct phases of import, rather than in a single continuous step. The assay has also been developed to monitor import into the mitochondrial matrix of intact cultured cells. This latter innovation has laid the foundations for further analysis of the import process in humans, including the consequences of interactions with cytosolic factors and neighboring organelles. The versatility of the MitoLuc assay is conducive for its adaptation to also monitor import into the inter-membrane space (MIA-pathway), and into the inner-membrane via the TIM22- and TIM23-complexes. Here, we present detailed protocols for the application of MitoLuc to mitochondria isolated from yeast and to those within cultured human cells.","PeriodicalId":18662,"journal":{"name":"Methods in enzymology","volume":"706 ","pages":"407-436"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142504061","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"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