Karen N. Allen – författare

Computational Approaches to Natural Products Discovery, Volume 720 provides descriptions of the latest techniques in computational methods for the study of natural products. Techniques covered are related to genome mining, natural product biosynthesis, natural product evolution, and natural product structure. Chapters in this new release cover Prediction of natural product bioactivity from BGC sequence to guide genome mining efforts, Genome mining for resistance genes to identify bioactive natural products with ARTS, Predicting lasso peptide structure with LassoPred, Predicting lanthipeptide structure with Rosetta, Using lsaBGC to investigate BGC Evolution, and an Analysis of BGC evolution with CORASON.Provides descriptions of computational methods for natural product discovery by experts in the fieldDiscusses challenges in natural product discoveryIncludes methods that address multiple steps in the natural product discovery pipeline

Biorthogonal Tagging, Volume 731 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters such as Staudinger Ligations and Related Reactions: Scope and Applications in Chemical Biology, Strain-Promoted Bioorthogonal Cycloadditions to Investigate Sialyltransferases Promiscuity Towards Unnatural Sialic Acids, Practical Guidelines for the Bioorthogonal AMI-Isonitrile Ligation, Nitrones and Other Dipoles in Bioorthogonal Chemistry Applications, 1,2-Aminothiol-Specific Conjugation for Dual-Color Fluorescent Labeling via Ultrafast TAMMs, Genetic Incorporation of Bicyclononyne for Cell-Surface Protein Labeling via Tetrazine Ligation, and much more.Additional chapters cover Genetic Code Expansion for Single Noncanonical Amino Acid Incorporation into SARS-CoV-2 Omicron Spike on Amber-Free Lentiviral Particles, Bioorthogonal Click-Chemistry Labeling and Visualization of Dual Noncanonical Amino Acid-Incorporated HIV-1 Env on Intact Virions, Studying Bacterial Glycans with Azidosugars and Bioorthogonal Chemistry, Bioorthogonal Tagging of DNA and RNA, Efficient Labeling of Pathogenic Fungal Chitin with Bioorthogonal Probes, and many more timely topics.Provides the latest information on Biorthogonal TaggingOffers outstanding and original reviews on a range of Enzymology research topicsServes as an indispensable reference for researchers and students alike

Mucins, Volume 732 serves as a valuable resource for researchers aiming to investigate mucin biology in greater depth, offering a wide range of experimental approaches and analytical strategies. Topics in this new release cover Enrichment/isolation, glycoproteomics, Mucinase cleavage characterization and usage in glycoproteomics, Fluorescent protein-based FRET substrates for activity screening of mucinases, Development of clinical lectin assays based on MS glycomic discovery, Enzymatic selective sulfation of synthetic mucins, cryoEM, Cell-based mucin arrays and glycoengineering, CRISPR screens to characterize and identify glycan-binding proteins, and much more.Additional sections cover MD Simulations, Interactions with pathogenic bacteria, Interactions with microbiota, Covalent crosslinking of mucins, Liquid Glycan and Liquid Lectin Array-based exploration of musin recognition, Quantification of mucins, Mucins in IBD, Investigations of mucins and innate immunity, Generating synthetic mucin glycopeptides, and Microscopy and imaging.Covers a wide range of cutting-edge methodologies for studying mucins and glycoproteinsIntegrates basic science with clinical and translational research applicationsFeatures contributions from leading experts across multiple scientific disciplines

This volume surveys cutting-edge machine learning-based approaches for the study of enzyme catalysis, dynamics, and design. It brings together computational and experimental approaches that integrate molecular simulation, machine learning, and high-throughput data to interrogate enzymatic catalysis at multiple scales. The chapters in the volume highlight how data-driven frameworks complement physics-based models to advance mechanistic understanding and enable rational enzyme engineering.Discussion of cutting-edge machine learning approaches for both computational and experimental studies of enzymes.Integration of physics-based simulations with data-driven models to characterize enzymatic mechanisms.Methodological frameworks for enzyme discovery and rational protein engineering.

Lipids and Membranes: Metabolism, Lipidation, and Lipid-Protein Interactions, Volume 729 provides a broad snapshot of state-of-the-art methods for studying biological lipids and biomembranes. Sections in this new release cover De novo chemoenzymatic construction of lipid membranes, Photoaffinity labeling for cholesterol metabolism, Expression and Characterization of Phospholipase Cb and Ce enzymes, Assembling Retromer-coated membrane tubules for in vitro structure-function studies, Quantitative analysis of S-acylation, Inhibition of palmitoyltransferases, Exploiting protein lipidation to create peptide-based biomaterials, and much more.Additional sections discuss Optogenetic control of lipid-modifying enzyme activity using LOV domain insertions, Chemoproteomics approaches for inhibition of diacylglycerol kinases, Inhibition of sterol transfer protein function, Preparation of K-Ras4B containing synthetic modifications via expressed protein ligation, Regulation of lipin enzymes on membranes, Use of novel synthetic analogues to decipher the interactions of phosphatidic acids species, Analyzing lipid-nuclear receptor interactions, and much more.Provides readers with the latest advances in the biochemistry of lipids and biological membranesFocus on cutting-edge protocols by leaders in the disciplines of lipid and membrane chemistry, biochemistry, biophysics, and biologyCovers approaches for probing membrane dynamics and interorganelle lipid transport

Lipids and Membranes: Dynamics and Interorganelle Lipid Transport, Volume 728 covers lipids, a chemically diverse set of biological molecules subject to rapid metabolism and transport. This dynamic behavior has motivated the development of methods across multiple disciplines for their detection and manipulation. Split into three parts, the book's chapters include topics such as Assay of phospholipid scrambling, Tracking lipid transport with bifunctional lipids, Tracking interorganelle lipid transport using genetically encoded mass tags, Molecular Dynamics Simulation of Lipid and Ligand Binding in ORD Domains, Imaging lipid droplet-organelle membrane contact sites using fluorogenic complementation, Studying interactions of amphipathic helices with lipid droplets, and more.Additional chapters cover Metabolic labeling of to trace changes in sphingolipid metabolism, Imaging intracellular lipid heterogeneity with fluorogen-activated coincidence sensing, Tagging lipoproteins in mycobacteria, Probes for studying sphingolipid dynamics, Measuring Flipper-TR Lifetime with Multiple Analysis Strategies, Reconstitution approaches to understanding cellular lipid dynamics, Prediction and characterization of the bacterial lipid handling machinery, From Molecular Dynamics to Cryo-EM: Imaging Liposomes in Silico, and much more.Provides readers with the latest advances in the biochemistry of lipids and biological membranesFocuses on cutting-edge protocols by leaders in the disciplines of lipid and membrane chemistry, biochemistry, biophysics, and biologyCovers methods for tracking lipid metabolism, posttranslational modification of proteins with lipids (lipidation), and non-covalent lipid-protein interactions

Protein termini represent a major route to protein regulation. From the moment the very first amino acid of a polypeptide chain exits the ribosome there is potential for steering from the cellular environment. This volume of Methods in Enzymology Modifications and Targeting of Protein Termini focuses on Protein N-termini and C-termini and their modifications which include acetylation, arginylation, myristoylation and oxidation. Also, the impact of terminal modifications is covered, in particular the impact on protein turnover and the ubiquitin E3 ligases which specifically recognize protein N-termini (N-degrons) and C-termini (C-degrons). In addition to the detailed methods and laboratory protocols, the chapters include informative overviews and reviews of the different subfields.Provides the authority and expertise of leading contributors from an international board of authorsIncludes the latest information on modifications and targeting of proteins via their N- and C-terminal ends

Histone Deacetylases in Neurodegenerative Disease, Part A, Volume 733 in the Methods in Enzymology series, highlights new advances, with this volume presenting chapters on topics such as HDAC Inhibitor-Induced Endoplasmic Reticulum (ER) Stress, Specific activation of p300/CBP Lysine acetyltransferases induces adult neurogenesis and synaptic plasticity, Chromatin immunoprecipitation assay for analyzing histone H3-mediated regulation of copper homeostasis, Histone Deacetylase 6 modulates Tau structure and function, Histone Acetylation in Parkinson Disease, DNA methylation and histone modification in hypoxic conditions, The extracellular Histone Deacetylase 6 modulates the actin networks in neuronal cells, Epigenetic modulators as therapeutics for neurodegenerative disorder/Alzheimer's disease, and much more.Additional chapters explore Sirtunins in mitochondrial physiology and energy homeostasis, Sirtunins in metabolic homeostasis, Conformational flexibility of histone variant CENP-ACse4 is regulated by histone H4: A mechanism to stabilize soluble Cse4, Analysis of copper toxicity by western blotting of secretory proteins translocated via Sec61 channel, Histone deacetylase as a potential therapeutic target for memory disorders, Histone deacetylases in Neurodegeneration, Role of Deubiquitinases in Regulating Tau Acetylation and Autophagic Clearance in Alzheimer’s Disease, Histone deacetylases in Neurodegeneration and neuronal plasticity, and more.Provides the latest information on Enzymology researchOffers outstanding and original reviews on a range of research topics surrounding Histone Deacetylases in Neurodegenerative Disease, Part AServes as an indispensable reference for researchers and students alike

Overall, this volume serves as a comprehensive methodological resource that integrates RNA-binding proteins, RNA metabolism, phase separation, and neurodegenerative disease mechanisms. As Volume 743 of the Methods in Enzymology series, RNA-Binding Proteins highlights recent advances in the field through chapters covering topics such as RNA-Binding Proteins: Structure, Function, and RNA Interactions; RNA Granules, Phase Separation, and Biomolecular Condensates; RNA Regulation in Cellular Physiology; RNA-Binding Proteins in Neurobiology and Neurodegeneration; RNA Processing, Editing, Splicing, and Decay; Non-Coding RNAs, Small RNAs, and RNA Therapeutics; and Experimental and Computational Methods for RNA-Protein Interaction Analysis. Collectively, these contributions provide valuable methodological and conceptual insights, making the volume highly relevant to researchers in molecular biology, neuroscience, RNA biology, and translational medicine.Covers both fundamental RNA biology (RNA editing, RNA-protein interactions, RNA decay, splicing and disease-oriented applications)Integrates structural, biophysical, computational, and cellular approachesFeatures high-impact reviews exploring the latest discoveries and methodologies in RNA-binding protein research

Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters. Each chapter is written by an international board of authors.Provides the latest information on Enzymology researchOffers outstanding and original reviews on a range of Enzymology research topicsServes as an indispensable reference for researchers and students alike

A central theme of this volume is the dynamic relationship between RNA structure, RNA-binding proteins, and cellular organization. The chapters integrate experimental, computational, biochemical, biophysical, imaging, and systems-level approaches to investigate how RNA-protein interactions regulate RNA processing, translation, localization, stability, phase separation, and cellular stress responses. As Volume 746 of the Methods in Enzymology series, the volume emphasizes the integration of methodological innovation with biological applications, providing researchers with practical approaches to dissect how RNA-protein interactions govern RNA fate and function, biomolecular condensate formation, and stress granule assembly.Overall, this collection highlights the transition of RNA biology from a primarily sequence-centered discipline toward a more dynamic view in which RNA structure, molecular interactions, phase separation, cellular organization, and signaling are intimately connected. It will therefore be a valuable resource for researchers and students seeking both practical methodologies and mechanistic insights into the rapidly expanding field of RNA biology.RNA Recognition and RNA-Binding Protein FunctionRNA G-Quadruplexes and Protein CondensationRNA, Biomolecular Condensates, and TranslationViral RNA-Protein InteractionsRNA-Protein Interactions and Molecular NetworksRNA, Epigenetic Regulation, and TumorigenesisRNA Modifications, Non-Coding RNAs, and Post-Transcriptional RegulationFeatures high-impact reviews exploring the latest discoveries and methodologies in RNA-binding protein research

Histone Deacetylases in Neurodegenerative Disease, Part B, Volume 734 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on timely topics surrounding the Interaction of HDAC6 ZnF UBP with Tau affects its stability by NMR and Simulation studies, Protocols for In Vitro Analysis of Liquid-Liquid Phase Separation of Proteins, Histone deacetylases in NS, Histone Deacetylase 6 ZnF UBP domain enhances podosome formation in neuronal cells studied by high-resolution confocal microscopy, Methodological approach to Investigate Peroxiredoxin 1 Deacetylation by Histone Deacetylase 6, Critical structural features of HDAC11 inhibitors, and much more.Additional chapters in this release include Histone Deacetylases 1 and 2 Regulate Microglia Function during Development, Homeostasis, and Neurodegeneration, Elucidation of Site-Specific Ubiquitination on Chaperones in Response to Mutant Huntingtin, Protein acetylation dynamics (histone and non-histone) and role protein deacetylases in disease, Epigenetic Clues: Predicting Maternal Depression Through DNA Methylation, A short guide on in vivo transfection of flag-HDAC4 in dentate gyrus for study of adult neurogenesis in brain trauma, Decoding the Acetylation Journey from Neural Crest to Melanocyte, and more.Provides the latest information on Enzymology researchOffers outstanding and original reviews on a range of research topics surrounding Histone Deacetylases in Neurodegenerative Disease, Part BServes as an indispensable reference for researchers and students alike

Flavoproteins and Flavoenzymes, Volume 738 in the Methods in Enzymology series, highlights new advances in the field, with this new volume presenting interesting chapters on a variety of timely topics, including Kirisu2 and KiPaD: global analysis of rapid flavoprotein redox kinetics from stopped-flow multi, ilagros Mendina, A Generic First Approach to Dissecting Flavoenzyme Catalytic Cycles, Removing Covalent Constraints of Protein Loops and Lids by a Split-Gene Strategy, Designing Oxygen Reaction Sites in Flavoprotein Dehydrogenases, Converting Noncovalent Flavoproteins into Covalently Flavinylated Proteins, Complexities of Riboflavin Biosynthesis, Reactions of Riboflavin Catabolism, and much more.Additional sections cover Ferredoxin-dependent thioredoxin reductase, Thermophilic Methylenetetrahydrofolate Reductases, Ion-Pumping NADH:Quinone Oxidoreductase, Loading E. coli Dihydroorotate Dehydrogenase with Coenzyme Q, and Single-Component Halogenases.Provides the latest information on Flavoproteins and Flavoenzymes researchOffers outstanding and original reviews on a range of Flavoproteins and Flavoenzymes research topicsServes as an indispensable reference for researchers and students alike

Enzyme Microfluidics, Volume 737 in the Methods in Enzymology series, presents detailed methodological descriptions and protocols that cover a wide range of microfluidics-based approaches for mechanistic enzymology, high-throughput screening, and enzyme engineering campaigns. The volume includes both established methods as well as advances in the field. Sections in this new release cover four unique sections, including Chips and Reagents, Enzyme Characterization, Enzyme Engineering, and Moving Beyond Microfluidics (from micro to nanoscale). Specific chapters delve into Joint Methods for Fabricating Microfluidic Chips, A liquid handling robotic workflow for quantifying the activity of antibiotic resistance genes (ARGs) in cell-free protein synthesis, and much more.Additional chapters cover Preparation of uniform microcrystals by droplet microfluidics for time-resolved serial crystallography, Droplet microfluidic HDX for investigating highly dynamic proteins, An Accessible, Low-Cost Platform for High-Throughput Microfluidic Enzyme Kinetics, High-Throughput Data Processing, DA-MEK, Mass Spectrometry of Droplets, Digital Bioassay Using a Femtoliter Reactor Array Device, Confocal absorbance droplet sorting, Sequence-Function Data Analysis from Microfluidics Screening, and much more.Presents detailed protocols for a range of state-of-the-art microfluidic approaches for enzymology, helping make them accessible to non-specialist labsCovers recent advances in high-throughput enzyme activity detection including fluorescence, absorbance, mass spectrometry, and droplet physical propertiesProvides both basic protocols for establishing microfluidic workflows as well as cutting-edge technologies for accelerating characterization and discovery of enzymes

Thiamine Pyrophosphate (TPP)-Dependent Enzymes, Volume 736 in the Methods in Enzymology series covers this diverse group of ubiquitous enzymes with timely chapters on Methods for Studying ThDP-dependent Mycobacterial MenDs (SEPHCHC Synthases), Mammalian 2-hydroxyacyl-CoA lyases, discovery and assays, Anti-infective target 1-deoxy-d-xylulose-5-phosphate synthase (DXS) and drug design for enzyme inhibition, Expression, Purification, and Mechanistic Studies of DXP synthases from Deinococcus radiodurans, Plasmodium falciparum, and Plasmodium vivax, Comparison of the catalysis of ThPP-dependent enzymes AHAS, ALS, and DXS, and much more.Additional sections cover Plant and fungal acetohydroxyacid synthases (AHAS): Methods for heterologous expression, kinetic characterization, and structural analysis, Biochemical and Structural characterization of novel ‘split-gene’ archeal transketolases, 4-Hydroxybenzoylformate decarboxylase enzymes from Rhodococcus jostii RHA1 and Pseudomonas fluorescens Pf-5: characterization and involvement in bacterial lignin degradation, Engineering of phosphoketolase from Bifidobacterium adolescentis for increased activity on non-phosphorylated substrates and application in a cell-free reaction system for ATP regeneration, Repurposing TPP-dependent enzymes with anodic oxidation for the conversion of aldehydes to enantioenriched carboxylic acids, and much more.Provides detailed descriptions of innovative and original methodological approaches described by the world’s leading experts in thiamine pyrophosphate-dependent enzymesPresents a complete description of a panel of techniques associated with the subject addressedIncludes non-exhaustive examples that will allow the reader to understand this family of enzymes and the current methodological approaches implemented in this context