Methods in Cell Biology Building a Cell from its Component Parts Volume 128 Series Editors Leslie Wilson Department of Molecular, Cellular and Developmental Biology University of California Santa Barbara, California Phong Tran University of Pennsylvania Philadelphia, USA & Institut Curie, Paris, France Methods in Cell Biology Building a Cell from its Component Parts Volume 128 Edited by Jennifer Ross Department of Physics, University of Massachusetts Amherst, USA Wallace F Marshall Department of Biochemistry & Biophysics, University of California San Fransisco at Mission Bay, USA AMSTERDAM • BOSTON • HEIDELBERG • LONDON NEW YORK • OXFORD • PARIS • SAN DIEGO SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier Academic Press is an imprint of Elsevier 225 Wyman Street, Waltham, MA 02451, USA 525 B Street, Suite 1800, San Diego, CA 92101-4495, USA 125, London Wall, EC2Y 5AS, UK The Boulevard, Langford Lane, Kidlington, Oxford OX5 1GB, UK First edition 2015 Copyright © 2015 Elsevier Inc All Rights Reserved No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher Details on how to seek permission, further information about the Publisher’s permissions policies and our arrangements with organizations such as the Copyright Clearance Center and the Copyright Licensing Agency, can be found at our website: www.elsevier.com/permissions This book and the individual contributions contained in it are protected under copyright by the Publisher (other than as may be noted herein) Notices Knowledge and best practice in this field are constantly changing As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary Practitioners and researchers must always rely on their own experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein In using such information or methods they should be mindful of their own safety and the safety of others, including parties for whom they have a professional responsibility To the fullest extent of the law, neither the Publisher nor the authors, contributors, or editors, assume any liability for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions, or ideas contained in the material herein ISBN: 978-0-12-802450-8 ISSN: 0091-679X For information on all Academic Press publications visit our website at http://store.elsevier.com Contributors Jose´ Alvarado FOM Institute AMOLF, Amsterdam, The Netherlands; Massachusetts Institute of Technology, Cambridge, MA, USA R Ayadi Natuur- en Sterrenkunde and LaserLab, Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands Swathi Ayloo Department of Physiology and the Pennsylvania Muscle Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Department of Biology Graduate Group, School of Arts and Sciences at the University of Pennsylvania, Philadelphia, PA, USA Hella Baumann London Research Institute, Cancer Research UK, London, UK Kevin Carvalho Institut Curie, Centre de Recherche, Paris, France; CNRS, UMR168, Paris, France; UPMC Univ Paris 06, UMR 168, Paris, France; Univ Paris Diderot, Sorbonne Paris Cite´, Paris, France Guilherme Pereira Correia Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK Michael Diehl Department of Chemistry, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA Marileen Dogterom Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands Christine M Field Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Marine Biological Laboratory, Woods Hole, MA, USA Daniel A Fletcher Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA; Physical Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA xi xii Contributors Adam Frost Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, UT, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA Jennifer L Gallop Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK Aaron C Groen Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Marine Biological Laboratory, Woods Hole, MA, USA Kenneth K.Y Ho Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA Matthew A Holden Department of Chemistry, University of Massachusetts, Amherst, MA, USA Erika L.F Holzbaur Department of Physiology and the Pennsylvania Muscle Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA Raghav Kalia Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, UT, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA Kinneret Keren Department of Physics, Technion-Israel Institute of Technology, Haifa, Israel; Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel; Network Biology Research Laboratories, Technion-Israel Institute of Technology, Haifa, Israel Volker Kiessling Center for Membrane Biology and Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA Gijsje H Koenderink FOM Institute AMOLF, Amsterdam, The Netherlands Eric A Kumar Department of Chemistry, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA Dimitry Lamers FOM Institute AMOLF, Amsterdam, The Netherlands Contributors Joeăl Lemie`re Institut Curie, Centre de Recherche, Paris, France; CNRS, UMR168, Paris, France; UPMC Univ Paris 06, UMR 168, Paris, France; Univ Paris Diderot, Sorbonne Paris Cite´, Paris, France; Current address: Department of Molecular Biophysics and Biochemistry, Nanobiology Institute, Yale University, New Haven, CT, USA Binyong Liang Center for Membrane Biology and Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA Allen P Liu Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA; Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA; Biophysics Program, University of Michigan, Ann Arbor, MI, USA Andries Lof FOM Institute AMOLF, Amsterdam, The Netherlands Martin Loose Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Institute of Science and Technology Austria, Klosterneuburg, Austria Maya Malik-Garbi Department of Physics, Technion-Israel Institute of Technology, Haifa, Israel Timothy J Mitchison Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Marine Biological Laboratory, Woods Hole, MA, USA Kiyoshi Mizuuchi Laboratory of Molecular Biology, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA Victoria L Murray Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA Phuong A Nguyen Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Marine Biological Laboratory, Woods Hole, MA, USA Anand Radhakrishnan Department of Chemistry, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA xiii xiv Contributors David L Richmond Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany W.H Roos Natuur- en Sterrenkunde and LaserLab, Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands Jennifer L Ross Molecular and Cellular Biology Graduate Program, Department of Physics, University of Massachusetts Amherst, Amherst, MA, USA Sophie Roth Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands Daniel S Saxton Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK Eva M Schmid Department of Bioengineering & Biophysics Program, University of California, Berkeley, CA, USA Petra Schwille Department of Cellular and Molecular Biophysics, Max Planck Institute for Biochemistry, Martinsried, Germany Enas Abu Shah Department of Physics, Technion-Israel Institute of Technology, Haifa, Israel; Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa, Israel Kasimira T Stanhope Molecular and Cellular Biology Graduate Program, Department of Physics, University of Massachusetts Amherst, Amherst, MA, USA Thomas Surrey London Research Institute, Cancer Research UK, London, UK Ce´cile Sykes Institut Curie, Centre de Recherche, Paris, France; CNRS, UMR168, Paris, France; UPMC Univ Paris 06, UMR 168, Paris, France; Univ Paris Diderot, Sorbonne Paris Cite´, Paris, France Nu´ria Taberner Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands Contributors Nathaniel Talledge Department of Biochemistry, University of Utah, School of Medicine, Salt Lake City, UT, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA Lukas K Tamm Center for Membrane Biology and Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA James A Taylor Laboratory of Molecular Biology, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA David Tsao Department of Chemistry, Rice University, Houston, TX, USA; Department of Bioengineering, Rice University, Houston, TX, USA Anthony G Vecchiarelli Laboratory of Molecular Biology, National Institute of Diabetes, and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA Astrid Walrant Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK Hans Zeijlemaker FOM Institute AMOLF, Amsterdam, The Netherlands Katja Zieske Department of Cellular and Molecular Biophysics, Max Planck Institute for Biochemistry, Martinsried, Germany xv Preface The cell interior is another world that we are only beginning to explore Although there are a number of approaches for examining the inner workings of the cell, the reductionist approach of building up complexity appeals to many with physical science and engineering backgrounds Such experiments are appealing because the complexity of the cellular organism can be built up systematically adding in one new element at a time and dialing up the concentrations of each component in a systematic way The hope is that such bottom-up approaches will garner new quantitative insights at many levels At the lowest level, we seek to elucidate single molecule activities to be able to have quantitative numbers for analytical models and simulations As new components are added to one another, their activities can combine synergistically to create novel emergent behaviors Since biology is inherently out of equilibrium, there is energy being injected that can enhance such synergies making even simple-seeming systems appear complex and inherently interesting Such emergence of complex behavior from interactions of simple components is likely to have been critical for the origins of life Further, reductionist scientists are seeking to determine the minimal diversity of components to create cell-like structures and activities Especially in eukaryotic systems, the number of components controlling cell function appears unnecessarily large and the methods for cellular control appear baroque By determining the minimal variety of proteins of each function to perform a specific task, scientists are beginning to create a molecular toolkit of activities This avenue of research also has implications for a new area of cellular bioengineering based on cell-like nanodevices Another interesting issue of the cell is the variety and diversity of systems one can choose to work on Of course, reductionists are seeking to give fundamental and universal insight to these processes, so they typically focus on aspects of the cell that appear fundamental As such, many of the authors contributing to this volume have chosen to focus on the cytoskeleton and membrane systems to ultimately combine the two into cell-like patterns and organizations We have grouped together contributed chapters that have similar focuses, starting with wholly in vitro reconstitutions of cytoskeleton These contributions include methods for combining different motors and cytoskeletal components in defined ways to produce more complex behaviors, as well as methods to combine cytoskeletal assemblies with fabricated devices such as chambers or pillar arrays Next we move to the membrane systems reconstituted in vitro Contributions in this area include chapters on reconstituting membrane fission and fusion, as well as reconstituting important biological processes that normally take place on membrane surfaces, such as cell division and polarity Finally, we finish with systems that attempt to recreate cells as encapsulated systems of chemicals that can act together as a machine to perform functions These chapters describe methods for encapsulating protein machines within vesicles or xvii ... Tubulin from bovine brain (TL238 Cytoskeleton, Inc., USA); 100 mM Fluorescent HiLyte 488 tubulin from porcine brain (TL488M Cytoskeleton, Inc.); 50 mM rhodamine tubulin from porcine brain (TL590M... experience and knowledge in evaluating and using any information, methods, compounds, or experiments described herein In using such information or methods they should be mindful of their own safety... Huisman, S M., & Brunner, D (2011) Cell polarity in fission yeast: a matter of confining, positioning, and switching growth zones Seminars in Cell & Developmental Biology, 22, 799e805