Early stage protein misfolding and amyloid aggregation
Early Stage Protein Misfolding and Amyloid Aggregation, Volume 329, the latest in the International Review of Cell and Molecular Biology series presents comprehensive reviews and current advances in cell and molecular biology, including articles that address the structure and control of gene express...
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| Main Author | |
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| Format | eBook Book |
| Language | English |
| Published |
Cambridge, MA
Academic Press
2017
Elsevier Science & Technology |
| Edition | 1 |
| Series | International Review of Cell and Molecular Biology |
| Subjects | |
| Online Access | Get full text |
| ISBN | 9780128122525 0128122528 9780128122518 012812251X |
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| Abstract | Early Stage Protein Misfolding and Amyloid Aggregation, Volume 329, the latest in the International Review of Cell and Molecular Biology series presents comprehensive reviews and current advances in cell and molecular biology, including articles that address the structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. The series has a worldwide readership and maintains a high standard by publishing invited articles on important and timely topics as authored by prominent cell and molecular biologists.Provides comprehensive reviews and current advancesPresents a wide range of perspectives on specific subjects Includes valuable reference material for advanced undergraduates, graduate students, and professional scientists |
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| AbstractList | Early Stage Protein Misfolding and Amyloid Aggregation, Volume 329, the latest in the International Review of Cell and Molecular Biology series presents comprehensive reviews and current advances in cell and molecular biology, including articles that address the structure and control of gene expression, nucleocytoplasmic interactions, control of cell development and differentiation, and cell transformation and growth. The series has a worldwide readership and maintains a high standard by publishing invited articles on important and timely topics as authored by prominent cell and molecular biologists.Provides comprehensive reviews and current advancesPresents a wide range of perspectives on specific subjects Includes valuable reference material for advanced undergraduates, graduate students, and professional scientists |
| Author | Sandal, Massimo |
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| Notes | Includes bibliographical references and index |
| OCLC | 970041639 |
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| PageCount | 322 |
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| PublicationPlace | Cambridge, MA |
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| Publisher | Academic Press Elsevier Science & Technology |
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| Snippet | Early Stage Protein Misfolding and Amyloid Aggregation, Volume 329, the latest in the International Review of Cell and Molecular Biology series presents... |
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| SubjectTerms | Amyloid Prions Protein folding SCIENCE / Life Sciences / Biochemistry bisacsh |
| TableOfContents | 2.5. Other Computational and Bioinformatics Approaches -- 3. Perspectives -- References -- Chapter Three: Structural Characteristics of α-Synuclein Oligomers -- 1. Introduction -- 2. Amyloid Formation -- 2.1. Mechanisms of Formation of Amyloid Aggregates -- 2.2. Generic Features of the Structure of Amyloid Fibrils -- 2.3. Generic Features of the Structure of Amyloid Oligomers -- 2.4. Role in Disease -- 3. α-Synuclein -- 3.1. Association With PD and Other Neurodegenerative Disorders -- 3.2. Structural Characteristics of the Fibrillar State -- 3.3. Conversion From the Monomeric to the Fibrillar State -- 4. Oligomeric States of αS -- 4.1. Types of Oligomers Identified During In Vitro Fibril Formation -- 4.2. Stable In Vitro-Isolated Oligomers -- 4.2.1. Stabilized Through Protein Lyophilization -- 4.2.2. Stabilized by Chemical Compounds -- 4.2.2.1. Polyphenolic Compounds -- 4.2.2.2. Drug Molecules -- 4.2.2.3. Metal Ions -- 4.2.2.4. Dopamine -- 4.2.3. Stabilized Through Chemical Modifications in the Protein -- 4.2.3.1. Oxidation and Nitration -- 4.2.3.2. Formation of Protein Adducts -- 4.3. Oligomers Generated Upon Fibril Disaggregation -- 4.4. Oligomers Generated Upon Binding to Lipid Membranes -- 4.5. Features of αS Oligomers Identified In Vivo -- 4.5.1. Detection by Antibodies -- 4.5.2. Detection by Fluorescence Assays -- 4.5.3. Purification of Cell Lysates -- 5. Relationships Between Different Types of Amyloid Species -- 5.1. Relationships Between Different Oligomeric Species -- 5.2. Relationships Between Oligomeric and Fibrillar Aggregates -- 5.3. Multiplicity of Misfolding Pathways -- References -- Chapter Four: Effects of Intrinsic and Extrinsic Factors on Aggregation of Physiologically Important Intrinsically Disord ... -- 1. Aggregation of Intrinsically Disordered Proteins -- 2. Factors Influencing Aggregation of IDPs -- 2.1. Intrinsic Factors 3.8. Other Fungal and Invertebrate Prions -- 4. What Makes a Prion: Features That Define Prions -- 4.1. Defining Features of Prions -- 4.2. Structural Features of Animal Prions -- 4.3. Structural Characterization of Yeast Prions -- 4.4. Making Predictions: Using Biochemical Knowledge of Known Prions to Identify Other Prions and Understand the Prion St ... -- 4.4.1. Prion-Prion Interactions Help Reveal New Prions -- 4.4.2. Q/N or Other Amino Acid Composition as a Tool for Prion Identification -- 4.4.3. Other Bioinformatics and Proteomics Methods for Prion Identification -- 4.5. Strains -- 5. The Enlarging Prion Concept in Disease and Beyond -- 5.1. Introduction -- 5.2. Developing a Definition of a General Category of Prion-Like Conformational States -- 5.3. Prion-Like Proteins, Quasi-Prions, and Prionoids -- 5.4. The Intersection of Animals and Yeast: Studies of Yeast Prions Have Lead to Understanding of Human Amyloid Diseases -- 5.5. What Ties Together Prion-Like Phenomena -- 6. Concluding Remarks -- References -- Chapter Seven: The Structure of Mammalian Prions and Their Aggregates -- 1. Introduction -- 1.1. Infectious Mammalian Prions -- 1.2. Protease Resistance, Insolubility, and Aggregation -- 2. Amorphous Aggregates and Oligomers -- 2.1. Infectious Oligomers -- 2.2. Amorphous Aggregates -- 3. Two-Dimensional Crystals -- 3.1. Inducing Order in Two Dimensions -- 3.2. β-Helical Models -- 4. Amyloid Fibrils -- 4.1. The Helical Periodicity of Amyloid and Its Utility -- 4.1.1. X-Ray Fiber Diffraction -- 4.1.2. Electron Cryomicroscopy and Image Processing -- 4.2. The Structure of the Infectious Conformer -- 5. Outlook on the Future Structural Biology of Prions -- 6. Concluding Remarks -- Acknowledgments -- References -- Index -- Back Cover Front Cover -- Early Stage Protein Misfolding and Amyloid Aggregation -- Copyright -- Contents -- Contributors -- Chapter One: From the Evolution of Protein Sequences Able to Resist Self-Assembly to the Prediction of Aggregation Propensity -- 1. Introduction -- 2. Evolution of Protein Sequences: Need to be Functional vs Risk of Aggregation -- 2.1. Determinants of Order/Disorder as Strategies to Avoid Aggregation -- 2.2. Rate-Limiting Steps of Aggregation -- 2.2.1. Formation of Aggregation-Prone Conformations -- 2.2.2. Pathways to Amyloid Formation -- 3. Evolutionary Strategies to Inhibit Aggregation at the Primary Sequence Level -- 3.1. Patterns -- 3.2. Charges -- 3.3. β-Breakers -- 3.4. Gatekeepers -- 4. Evolutionary Strategies to Inhibit Aggregation at the Structural Level -- 4.1. Case Study: Native-Like Aggregation in the Acylphosphatase Structural Family -- 5. Evolutionary Strategies to Inhibit Aggregation at the Cellular Level -- 6. Development of the Algorithms Able to Identify Amyloid Hot Spots and Amyloid Propensity -- 6.1. Empirical Methods -- 6.2. Structure-Based Methods -- 6.3. Structure-Predicting Methods -- 6.4. Statistical Methods -- 6.5. Amyloid Datasets -- 7. Conclusions and Future Perspectives -- References -- Chapter Two: Protein Aggregation and Molecular Crowding: Perspectives From Multiscale Simulations -- 1. Introduction -- 1.1. Soluble Structured and Unstructured Proteins -- 1.2. Protein Aggregation -- 1.3. Protein Aggregation in a Crowded Environment -- 2. Computational Techniques -- 2.1. Enhanced Sampling Algorithms -- 2.1.1. Umbrella Sampling -- 2.1.2. Metadynamics -- 2.1.3. Replica-Exchange Methods -- 2.2. CG Simulations -- 2.2.1. CG Modeling of Water Molecules -- 2.2.2. Backmapping Algorithms -- 2.3. Electrostatic Analysis -- 2.4. (Macro)molecular Crowding: Application Cases 2.1.1. Mutations -- 2.1.2. Protein Expression Levels -- 2.1.3. Truncation -- 2.1.4. Posttranslational Modifications -- 2.1.4.1. PTMs of Aβ Peptides -- 2.1.4.2. PTMs of Tau Protein -- 2.1.4.3. PTMs of α-Synuclein -- 2.1.4.4. PTMs of PolyQ Proteins -- 2.2. External Factors -- 2.2.1. Binding of Metal Ions -- 2.2.2. Interaction With Small Molecules -- 2.2.2.1. Noncovalent Binding -- 2.2.2.2. Covalent Modification -- 2.2.3. Macromolecular Crowding -- 2.2.4. Lipid Membranes -- 2.2.5. Chaperones -- 3. Conclusions -- Acknowledgments -- References -- Chapter Five: The Nucleation of Protein Aggregates - From Crystals to Amyloid Fibrils -- 1. Protein Condensation -- 2. Nucleation - The Emergence of A New Phase -- 3. Heterogeneous Nucleation at Interfaces -- 4. Secondary Nucleation As a Special Case of Heterogeneous Nucleation -- 5. Experimental Methods to Study Nucleation of Condensed Protein Phases -- 6. Amyloid Oligomers And (Critical) Amyloid Nuclei -- 7. Outlook -- 8. Conclusions -- Acknowledgments -- References -- Chapter Six: What Makes a Prion: Infectious Proteins From Animals to Yeast -- 1. Introduction -- 2. Pathogens and the Emergence of the Prion Hypothesis -- 2.1. The Causative Agents of Infectious Disease -- 2.2. Cellular Causes of Infectious Diseases -- 2.3. Noncellular Causes of Disease in Animals -- 2.4. Unusual Disease Traits in Animals -- 2.5. Non-Mendelian Inheritance of Characters in the Baker´s Yeast -- 2.6. The Prion Hypothesis -- 3. Evidence Found: Identification of Animal, Yeast, and Other Prions -- 3.1. Scrapie in Sheep and Goats -- 3.2. Bovine Spongiform Encephalopathy -- 3.3. Kuru, CJD, Other Prion Diseases in Humans -- 3.4. Prion Diseases in Other Mammals -- 3.5. Prions in Other Eukaryotes -- 3.6. Evidence in Support of the Prion Hypothesis in Mammalian Disease -- 3.7. Reed Wickner´s Keen Observations in Yeast |
| Title | Early stage protein misfolding and amyloid aggregation |
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