The volume details techniques, methods, and conceptual developments to further the study of protein aggregation with emphasis on the pleiomorphic proteins implicated in etiology of neurodegeneration. Chapters guide readers through in vitro and in vivo studies of fibrillization and liquid-liquid phase separation processes, and offer a comprehensive account of the state-of-art of structural studies of protein aggregation. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents,…mehr
The volume details techniques, methods, and conceptual developments to further the study of protein aggregation with emphasis on the pleiomorphic proteins implicated in etiology of neurodegeneration. Chapters guide readers through in vitro and in vivo studies of fibrillization and liquid-liquid phase separation processes, and offer a comprehensive account of the state-of-art of structural studies of protein aggregation. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and reagents, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols. Authoritative and cutting-edge, Protein Aggregation: Methods and Protocols aims to be useful and practical guide to new researchers and experts looking to expand their knowledge.
Early aggregation of Amyloid-beta (1-42) studied by Fluorescence Correlation Spectroscopy.- Preparation and investigation of crucial oligomers in the early stages of Abeta40 and Abeta42 aggregation.- Preparation and fractionation of heterogeneous Abeta42 oligomers with different aggregation properties.- An efficient method of expression and purification of amyloid beta (Abeta1-42) peptide from E.coli.- Solid-state NMR structure of amyloid-beta fibrils.- Time-resolved in situ AFM measurement of growth rates of Abeta40 fibrils.- Monitoring kinetics of pH-dependent aggregation and disaggregation of the Pmel17 repeat domain.- Analysis of Tau:nucleoporin interactions by Surface Plasmon Resonance Spectroscopy.- Microfluidic chamber technology to study missorting and spreading of Tau protein in Alzheimer disease.- Using FRET-based biosensor cells to study the seeding activity of tau and -synuclein.- Functional applications of stable tau oligomers in cell biology and electrophysiology studies.- An additive-free model for tau self-assembly.- Cross-linking mass spectrometry analysis of metastable compact structures in intrinsically disordered proteins.- A validated method to prepare stable tau oligomers.- Light microscopy and dynamic light scattering to study liquid-liquid phase separation of Tau proteins in vitro.- Study of tau liquid-liquid phase separation in vitro.- Liquid-Liquid Phase Separation to study the association of proteins in solution.- Mapping phase diagram of tau-RNA LLPS under live cell coculturing conditions.- The role of buffers in wild-type HEWL amyloid fibril formation mechanism - a methodological approach.- Reproducible formation of insulin superstructures: amyloid-like fibrils, spherulites and particulates.- CD and solid-state NMR studies of low-order oligomers of transthyretin.- Identifying biological and biophysical features of different maturation states of -synuclein amyloid fibrils.- Preparation of -synuclein fibril, ribbon and fibril-91 amyloid polymorphs for structural studies.- Propagation of distinct alpha-synuclein strains within human reconstructed neuronal network and associated neuronal dysfunctions.- Single-particle analysis of the interaction between molecules and protein aggregated species by Dual-Color Time-Resolved Fluorescence Spectroscopy.- FRAP & FRET investigation of -synuclein fibrillization via liquid-liquid phase separation in vitro and in HeLa cells.- Spectrally-resolved FRET microscopy of -synuclein phase-separated liquid droplets.- Combined H-N cross polarization and carbonyl detection NMR spectroscopy allows to record high-resolution, high-sensitivity spectra of alpha-synuclein in bacterial cells.- Identification of distinct soluble states during fibril formation using multilinear analysis of NMR diffusiondata.- Structural analysis of SOD1 fibrils with mass spectrometry, limited proteolysis and atomic force microscopy (AFM).- Biophysical studies of LLPS and aggregation of TDP-43 LCD.- A spectrophotometric turbidity assay to study Liquid-Liquid Phase Separation of UBQLN2 in vitro.- An optimized SG detection method: Investigation of UBQLN2 effect on RNA-FUS interaction and SG formation.- Neuronal puncta/aggregate formation by wild-type and mutant UBQLN2.- In vivo analysis of a biomolecular condensate in the nervous system of C. elegans.- FLIM-FRET investigation of heterogeneous huntingtin aggregation in HeLa cells.- In vitro characterization of protein:nucleic acid liquid-liquid phase separation by microscopy methods and nanoparticle tracking analysis.- Cross-seeding assay in the investigation of the amyloid core of prion fibrils.- Mapping the domain structure and aggregation propensity of proteins using a Gateway plasmid vector system.
Early aggregation of Amyloid-beta (1-42) studied by Fluorescence Correlation Spectroscopy.- Preparation and investigation of crucial oligomers in the early stages of Abeta40 and Abeta42 aggregation.- Preparation and fractionation of heterogeneous Abeta42 oligomers with different aggregation properties.- An efficient method of expression and purification of amyloid beta (Abeta1-42) peptide from E.coli.- Solid-state NMR structure of amyloid-beta fibrils.- Time-resolved in situ AFM measurement of growth rates of Abeta40 fibrils.- Monitoring kinetics of pH-dependent aggregation and disaggregation of the Pmel17 repeat domain.- Analysis of Tau:nucleoporin interactions by Surface Plasmon Resonance Spectroscopy.- Microfluidic chamber technology to study missorting and spreading of Tau protein in Alzheimer disease.- Using FRET-based biosensor cells to study the seeding activity of tau and -synuclein.- Functional applications of stable tau oligomers in cell biology and electrophysiology studies.- An additive-free model for tau self-assembly.- Cross-linking mass spectrometry analysis of metastable compact structures in intrinsically disordered proteins.- A validated method to prepare stable tau oligomers.- Light microscopy and dynamic light scattering to study liquid-liquid phase separation of Tau proteins in vitro.- Study of tau liquid-liquid phase separation in vitro.- Liquid-Liquid Phase Separation to study the association of proteins in solution.- Mapping phase diagram of tau-RNA LLPS under live cell coculturing conditions.- The role of buffers in wild-type HEWL amyloid fibril formation mechanism - a methodological approach.- Reproducible formation of insulin superstructures: amyloid-like fibrils, spherulites and particulates.- CD and solid-state NMR studies of low-order oligomers of transthyretin.- Identifying biological and biophysical features of different maturation states of -synuclein amyloid fibrils.- Preparation of -synuclein fibril, ribbon and fibril-91 amyloid polymorphs for structural studies.- Propagation of distinct alpha-synuclein strains within human reconstructed neuronal network and associated neuronal dysfunctions.- Single-particle analysis of the interaction between molecules and protein aggregated species by Dual-Color Time-Resolved Fluorescence Spectroscopy.- FRAP & FRET investigation of -synuclein fibrillization via liquid-liquid phase separation in vitro and in HeLa cells.- Spectrally-resolved FRET microscopy of -synuclein phase-separated liquid droplets.- Combined H-N cross polarization and carbonyl detection NMR spectroscopy allows to record high-resolution, high-sensitivity spectra of alpha-synuclein in bacterial cells.- Identification of distinct soluble states during fibril formation using multilinear analysis of NMR diffusiondata.- Structural analysis of SOD1 fibrils with mass spectrometry, limited proteolysis and atomic force microscopy (AFM).- Biophysical studies of LLPS and aggregation of TDP-43 LCD.- A spectrophotometric turbidity assay to study Liquid-Liquid Phase Separation of UBQLN2 in vitro.- An optimized SG detection method: Investigation of UBQLN2 effect on RNA-FUS interaction and SG formation.- Neuronal puncta/aggregate formation by wild-type and mutant UBQLN2.- In vivo analysis of a biomolecular condensate in the nervous system of C. elegans.- FLIM-FRET investigation of heterogeneous huntingtin aggregation in HeLa cells.- In vitro characterization of protein:nucleic acid liquid-liquid phase separation by microscopy methods and nanoparticle tracking analysis.- Cross-seeding assay in the investigation of the amyloid core of prion fibrils.- Mapping the domain structure and aggregation propensity of proteins using a Gateway plasmid vector system.
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