Amyloid Proteins: Methods and Protocols PDF
Preview Amyloid Proteins: Methods and Protocols
M M B ™ ETHODS IN OLECULAR IOLOGY Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Amyloid Proteins Methods and Protocols Second Edition Edited by Einar M. Sigurdsson Departments of Physiology and Neuroscience, and Psychiatry, School of Medicine, New York University, New York, NY, USA Miguel Calero Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain María Gasset Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain Editors Einar M. Sigurdsson Miguel Calero Departments of Physiology and Centro Nacional de Microbiología Neuroscience, and Psychiatry Instituto de Salud Carlos III School of Medicine Majadahonda, Madrid, Spain New York University New York, NY, USA María Gasset Instituto de Química-Física Rocasolano CSIC, Madrid, Spain ISSN 1064-3745 e-ISSN 1940-6029 ISBN 978-1-61779-550-3 e-ISBN 978-1-61779-551-0 DOI 10.1007/978-1-61779-551-0 Springer New York Dordrecht Heidelberg London Library of Congress Control Number: 2012930138 © Springer Science+Business Media, LLC 2012 All rights reserved. This work may not be translated or copied in whole or in part without the written permission of the publisher (Humana Press, c/o Springer Science+Business Media, LLC, 233 Spring Street, New York, NY 10013, USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with any form of information storage and retrieval, electronic adaptation, computer software, or by similar or d issimilar methodology now known or hereafter developed is forbidden. The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject to proprietary rights. Cover illustration: The cover art depicts fibers assembled from full-length Tau and observed by Atomic Force Microscopy. Courtesy of Susanne Wegmann (D. Müller laboratory, ETHZ Basel, Switzerland). Printed on acid-free paper Humana Press is part of Springer Science+Business Media (www.springer.com) Preface Amyloid diseases are characterized by the deposition of insoluble fi brous amyloid proteins. The word “amyloid” indicates a starch-like compound, and though a misnomer, continues to be the accepted term for this group of protein conformational disorders. Approximately 30 different proteins can form amyloid and although there is usually no homology in their amino acid sequence, all share a β -pleated sheet as the polymer scaffold. Historically, these β -pleated deposits were detected by histological dyes, and the characteristic fi bril structure confi rmed with electron microscopy. As these amyloids were purifi ed and sequenced, vari- ous in vitro techniques were developed, often using synthetic peptides and/or highly puri- fi ed amyloids derived from diseased tissue. Development of animal models occurred concurrently and some of these diseases can now be passed on to animals by injecting them with amyloid-rich tissue fractions, or shown to spread between cells in vivo or in culture, suggesting a transmissible nature of these protein polymers. However, for most amyloi- doses, transgenic technology has been necessary for recapitulating the disease. Together, these in vitro and in vivo models have been used to understand the etiology and pathogen- esis of amyloid diseases as well as to screen for drugs to prevent the formation of and/or clear these aggregates. Several of these methods and protocols are detailed in this second edition of Amyloid Proteins: Methods and Protocols , using examples from various amyloids. Substantial changes have been made from the fi rst edition of this volume. Several classic methods/protocols that did not warrant updates are not included in the second edition. Importantly, numerous new chapters have been added that cover new techniques and/or topics not addressed in the fi rst edition. Such expansion was made possible with the help of two new editors, Drs. María Gasset and Miguel Calero, who graciously agreed to participate in this project. The volume is divided into three parts. Part I contains in vitro assays, starting with a few chapters that focus on the preparation of amyloid and its precursors. These are followed by chapters detailing specifi c analytical methods for studying these proteins. Part II describes cell culture models and assays for production of amyloid proteins, and Part III consists of protocols for amyloid extraction from tissue, its detection in vitro and in vivo, as well as nontransgenic methods for developing amyloid mouse models. Most of the chapters follow a similar format and are detailed protocols for performing a particular procedure. However, certain chapters focus more on the general principles and theoretical issues of a particular method. It is our hope that these chapters will be useful for both students and scientists new to the amyloid fi eld, as well as for seasoned investigators learning new techniques to further their research. We would like to thank the authors for their contribution and the series editor, Dr. John M. Walker, for the opportunity to edit this book. New York, NY, USA Einar M. Sigurdsson Madrid, Spain Miguel Calero Madrid, Spain María Gasset v Contents Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi PART I IN VITRO MODELS AND ASSAYS 1 Rapid Generation of Dityrosine Cross-linked Aβ Oligomers via Cu-Redox Cycling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Adam P. Gunn, Blaine R. Roberts, and Ashley I. Bush 2 Application of Photochemical Cross-linking to the Study of Oligomerization of Amyloidogenic Proteins . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Dahabada H.J. Lopes, Sharmistha Sinha, Clark Rosensweig, and Gal Bitan 3 Preparation of Stable Amyloid b-Protein Oligomers of Defined Assembly Order . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 Clark Rosensweig, Kenjiro Ono, Kazuma Murakami, Devin K. Lowenstein, Gal Bitan, and David B. Teplow 4 Purification and Fibrillation of Full-Length Recombinant PrP. . . . . . . . . . . . . . . . . 33 Natallia Makarava and Ilia V. Baskakov 5 Featuring Amyloids with Fourier Transform Infrared and Circular Dichroism Spectroscopies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53 Miguel Calero and María Gasset 6 Quasielastic Light Scattering Study of Amyloid b-Protein Fibrillogenesis. . . . . . . . . 69 Aleksey Lomakin and David B. Teplow 7 Conformations of Microtubule-Associated Protein Tau Mapped by Fluorescence Resonance Energy Transfer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85 Sadasivam Jeganathan, Subashchandrabose Chinnathambi, Eva-Maria Mandelkow, and Eckhard Mandelkow 8 Measuring the Kinetics of Amyloid Fibril Elongation Using Quartz Crystal Microbalances. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101 Alexander K. Buell, Christopher M. Dobson, and Mark E. Welland 9 X-Ray Fibre Diffraction Studies of Amyloid Fibrils . . . . . . . . . . . . . . . . . . . . . . . . . 121 Kyle L. Morris and Louise C. Serpell 10 Structural Characterization of Prefibrillar Intermediates and Amyloid Fibrils by Small-Angle X-Ray Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137 Annette Eva Langkilde and Bente Vestergaard 11 Atomic Force Fluorescence Microscopy in the Characterization of Amyloid Fibril Assembly and Oligomeric Intermediates . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157 Valeriy Ostapchenko, Maria Gasset, and Ilia V. Baskakov 12 Investigating Fibrillar Aggregates of Tau Protein by Atomic Force Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169 Susanne Wegmann, Daniel J. Muller, and Eckhard Mandelkow vii viii Contents 13 Structural Studies of Amyloids by Quenched Hydrogen–Deuterium Exchange by NMR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185 Marçal Vilar, Lei Wang, and Roland Riek 14 Cyclic Amplification of Prion Protein Misfolding . . . . . . . . . . . . . . . . . . . . . . . . . . 199 Marcelo A. Barria, Dennisse Gonzalez-Romero, and Claudio Soto 15 Search for Amyloid-Binding Proteins by Affinity Chromatography . . . . . . . . . . . . . 213 Miguel Calero, Agueda Rostagno, and Jorge Ghiso PART II CELL CULTURE MODELS AND ASSAYS 16 Establishing the Links Between Aβ Aggregation and Cytotoxicity In Vitro Using Biophysical Approaches. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227 Asad Jan and Hilal A. Lashuel 17 Preparation of Cultured Human Vascular Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . 245 Ingvar H. Olafsson, Dadi Th. Vilhjalmsson, and Finnbogi R. Thormodsson 18 Murine Cerebrovascular Cells as a Cell Culture Model for Cerebral Amyloid Angiopathy: Isolation of Smooth Muscle and Endothelial Cells from Mouse Brain. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261 Sebastien A. Gauthier, Susmita Sahoo, Sonia S. Jung, and Efrat Levy 19 In Vitro Assays Measuring Protection by Proteins such as Cystatin C of Primary Cortical Neuronal and Smooth Muscle Cells . . . . . . . . . . . . . . . . . . . . . 275 Sebastien A. Gauthier, Belen Tizon, Susmita Sahoo, and Efrat Levy 20 Study of Neurotoxic Intracellular Calcium Signalling Triggered by Amyloids . . . . . 289 Carlos Villalobos, Erica Caballero, Sara Sanz-Blasco, and Lucía Núñez 21 Bacterial Amyloids . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303 Yizhou Zhou, Luz P. Blanco, Daniel R. Smith, and Matthew R. Chapman 22 Study of Amyloids Using Yeast . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321 Reed B. Wickner, Dmitry Kryndushkin, Frank Shewmaker, Ryan McGlinchey, and Herman K. Edskes 23 Cell-to-Cell Transmission of α-Synuclein Aggregates . . . . . . . . . . . . . . . . . . . . . . . 347 Seung-Jae Lee, Paula Desplats, He-Jin Lee, Brian Spencer, and Eliezer Masliah PART III IN VIVO MODELS AND ASSAYS 24 Subcutaneous Adipose Tissue Biopsy for Amyloid Protein Studies. . . . . . . . . . . . . . 363 Per Westermark 25 Analysis of S100 Oligomers and Amyloids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373 Hugo M. Botelho, Günter Fritz, and Cláudio M. Gomes 26 S100A8/A9 Amyloidosis in the Ageing Prostate: Relating Ex Vivo and In Vitro Studies. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387 Anna L. Gharibyan, Dina Raveh, and Ludmilla A. Morozova-Roche 27 Isolation of Amyloid by Solubilization in Water. . . . . . . . . . . . . . . . . . . . . . . . . . . . 403 Dadi Th. Vilhjalmsson, Indiana E. Ingolfsdottir, and Finnbogi R. Thormodsson Contents ix 28 Histological Staining of Amyloid and Pre-amyloid Peptides and Proteins in Mouse Tissue . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411 Hameetha B. Rajamohamedsait and Einar M. Sigurdsson 29 A Pentameric Luminescent-Conjugated Oligothiophene for Optical Imaging of In Vitro-Formed Amyloid Fibrils and Protein Aggregates in Tissue Sections. . . . 425 K. Peter R. Nilsson, Mikael Lindgren, and Per Hammarström 30 In Vivo Magnetic Resonance Imaging of Amyloid-β Plaques in Mice . . . . . . . . . . . 435 Youssef Zaim Wadghiri, Dung Minh Hoang, Thomas Wisniewski, and Einar M. Sigurdsson 31 The Mouse Model for Scrapie: Inoculation, Clinical Scoring, and Histopathological Techniques . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453 Michele A. Di Bari, Romolo Nonno, and Umberto Agrimi 32 Biochemical Isolation of Insoluble Tau in Transgenic Mouse Models of Tauopathies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473 Carl Julien, Alexis Bretteville, and Emmanuel Planel 33 Tissue Processing Prior to Analysis of Alzheimer’s Disease Associated Proteins and Metabolites, Including Aβ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 493 Stephen D. Schmidt, Ralph A. Nixon, and Paul M. Mathews 34 Aβ Measurement by Enzyme-Linked Immunosorbent Assay. . . . . . . . . . . . . . . . . . 507 Stephen D. Schmidt, Matthew J. Mazzella, Ralph A. Nixon, and Paul M. Mathews 35 Cognitive and Sensorimotor Tasks for Assessing Functional Impairments in Mouse Models of Alzheimer’s Disease and Related Disorders . . . . . . . . . . . . . . . 529 Allal Boutajangout, Yong Sheng Li, David Quartermain, and Einar M. Sigurdsson Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 541
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