Building a cell from its component parts PDF
Preview Building a cell from its component parts
Methods in Cell Biology Building a Cell from its Component Parts Volume 128 Series Editors Leslie Wilson DepartmentofMolecular,CellularandDevelopmentalBiology UniversityofCalifornia SantaBarbara,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(cid:129)BOSTON(cid:129)HEIDELBERG(cid:129)LONDON NEWYORK(cid:129)OXFORD(cid:129)PARIS(cid:129)SANDIEGO SANFRANCISCO(cid:129)SINGAPORE(cid:129)SYDNEY(cid:129)TOKYO AcademicPressisanimprintofElsevier AcademicPressisanimprintofElsevier 225WymanStreet,Waltham,MA02451,USA 525BStreet,Suite1800,SanDiego,CA92101-4495,USA 125,LondonWall,EC2Y5AS,UK TheBoulevard,LangfordLane,Kidlington,OxfordOX51GB,UK Firstedition2015 Copyright©2015ElsevierInc.AllRightsReserved. Nopartofthispublicationmaybereproducedortransmittedinanyformorbyanymeans, electronicormechanical,includingphotocopying,recording,oranyinformationstorage andretrievalsystem,withoutpermissioninwritingfromthepublisher.Detailsonhowto seekpermission,furtherinformationaboutthePublisher’spermissionspoliciesandour arrangementswithorganizationssuchastheCopyrightClearanceCenterandthe CopyrightLicensingAgency,canbefoundatourwebsite:www.elsevier.com/permissions. Thisbookandtheindividualcontributionscontainedinitareprotectedundercopyrightby thePublisher(otherthanasmaybenotedherein). Notices Knowledgeandbestpracticeinthisfieldareconstantlychanging.Asnewresearchand experiencebroadenourunderstanding,changesinresearchmethods,professional practices,ormedicaltreatmentmaybecomenecessary. Practitionersandresearchersmustalwaysrelyontheirownexperienceandknowledgein evaluatingandusinganyinformation,methods,compounds,orexperimentsdescribed herein.Inusingsuchinformationormethodstheyshouldbemindfuloftheirownsafety andthesafetyofothers,includingpartiesforwhomtheyhaveaprofessionalresponsibility. Tothefullestextentofthelaw,neitherthePublishernortheauthors,contributors,or editors,assumeanyliabilityforanyinjuryand/ordamagetopersonsorpropertyasa matterofproductsliability,negligenceorotherwise,orfromanyuseoroperationofany methods,products,instructions,orideascontainedinthematerialherein. ISBN:978-0-12-802450-8 ISSN:0091-679X ForinformationonallAcademicPresspublications visitourwebsiteathttp://store.elsevier.com Contributors Jose´ Alvarado FOMInstituteAMOLF,Amsterdam,TheNetherlands;MassachusettsInstituteof Technology,Cambridge, MA, USA R. Ayadi Natuur- en SterrenkundeandLaserLab, Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands Swathi Ayloo Department ofPhysiology andthe Pennsylvania MuscleInstitute,Perelman SchoolofMedicineatthe University ofPennsylvania,Philadelphia, PA, USA; Department ofBiology GraduateGroup,SchoolofArts and Sciences atthe University ofPennsylvania, 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.ParisDiderot, SorbonneParisCite´,Paris, France GuilhermePereiraCorreia Wellcome Trust/Cancer Research UKGurdon Instituteand Department of Biochemistry,University of Cambridge, Cambridge, UK Michael Diehl Department ofChemistry,Rice University,Houston, TX,USA; Department of Bioengineering,RiceUniversity, Houston, TX, USA MarileenDogterom DepartmentofBionanoscience,KavliInstituteofNanoscience,DelftUniversityof Technology,Delft, The Netherlands ChristineM. Field Department ofSystems Biology,Harvard Medical School, Boston, MA, USA; MarineBiologicalLaboratory,WoodsHole, MA, USA Daniel A. Fletcher Department ofBioengineering &Biophysics Program, University ofCalifornia, Berkeley,CA, USA; PhysicalBiosciences, Lawrence BerkeleyNational Laboratory, Berkeley, CA,USA xi xii Contributors Adam Frost Department ofBiochemistry,University ofUtah,SchoolofMedicine, Salt Lake City,UT, USA; Department ofBiochemistry and Biophysics, University of California,SanFrancisco, SanFrancisco, CA, USA JenniferL. Gallop WellcomeTrust/Cancer Research UKGurdonInstitute and Department of Biochemistry, University ofCambridge, Cambridge, UK AaronC. Groen Department ofSystems Biology, HarvardMedicalSchool,Boston, MA, USA; Marine BiologicalLaboratory, WoodsHole, MA, USA KennethK.Y.Ho Department ofMechanicalEngineering, University of Michigan,Ann Arbor,MI, USA Matthew A.Holden Department ofChemistry,University of Massachusetts, Amherst,MA, USA Erika L.F.Holzbaur Department ofPhysiology and the PennsylvaniaMuscle Institute,Perelman School ofMedicine atthe University ofPennsylvania,Philadelphia, PA,USA Raghav Kalia Department ofBiochemistry,University ofUtah,SchoolofMedicine, Salt Lake City,UT, USA; Department ofBiochemistry and Biophysics, University of California,SanFrancisco, SanFrancisco, CA, USA Kinneret Keren Department ofPhysics, Technion-Israel Instituteof Technology, Haifa, Israel; RussellBerrieNanotechnologyInstitute,Technion-IsraelInstituteofTechnology, Haifa,Israel;NetworkBiologyResearchLaboratories,Technion-IsraelInstituteof Technology, Haifa, Israel VolkerKiessling Center for Membrane Biology and Department ofMolecular Physiologyand BiologicalPhysics, University ofVirginia, Charlottesville, VA, USA Gijsje H. Koenderink FOM InstituteAMOLF,Amsterdam, The Netherlands Eric A.Kumar Department ofChemistry,Rice University,Houston, TX, USA; Department of Bioengineering, Rice University,Houston, TX,USA Dimitry Lamers FOM InstituteAMOLF,Amsterdam, The Netherlands Contributors xiii Joe¨lLemie`re Institut Curie, Centre de Recherche, Paris, France;CNRS, UMR168, Paris, France; UPMC Univ Paris 06, UMR 168, Paris, France; Univ.ParisDiderot, SorbonneParisCite´,Paris, France; Current address: Department ofMolecular BiophysicsandBiochemistry,NanobiologyInstitute,YaleUniversity,NewHaven, CT,USA Binyong Liang Center for Membrane Biology and Department ofMolecular Physiology and BiologicalPhysics, University ofVirginia,Charlottesville, VA, USA Allen P. Liu Department ofMechanical Engineering,University ofMichigan, Ann Arbor,MI, USA;DepartmentofBiomedicalEngineering,UniversityofMichigan,AnnArbor, MI, USA; Cellular and Molecular Biology Program, University ofMichigan, Ann Arbor, MI,USA; Biophysics Program, University ofMichigan,Ann Arbor, MI, USA AndriesLof FOM InstituteAMOLF,Amsterdam,The Netherlands Martin Loose Department ofSystems Biology,Harvard Medical School, Boston, MA, USA; Institute ofScience and TechnologyAustria,Klosterneuburg,Austria MayaMalik-Garbi Department ofPhysics, Technion-Israel Institute ofTechnology,Haifa,Israel TimothyJ. Mitchison Department ofSystems Biology,Harvard Medical School, Boston, MA, USA; MarineBiologicalLaboratory,WoodsHole, MA, USA KiyoshiMizuuchi LaboratoryofMolecularBiology,NationalInstituteofDiabetes,andDigestiveand Kidney Diseases, NationalInstitutesof Health, Bethesda,MD, USA VictoriaL. Murray Department ofMechanical Engineering,University ofMichigan, Ann Arbor,MI, USA Phuong A. Nguyen Department ofSystems Biology,Harvard Medical School, Boston, MA, USA; MarineBiologicalLaboratory,WoodsHole, MA, USA Anand Radhakrishnan Department ofChemistry,Rice University,Houston, TX,USA; Department of Bioengineering,RiceUniversity, Houston, TX, USA xiv Contributors David L. Richmond MaxPlanckInstituteofMolecularCellBiologyandGenetics,Dresden,Germany W.H. Roos Natuur-en Sterrenkunde and LaserLab,Vrije Universiteit, De Boelelaan, Amsterdam, The Netherlands JenniferL. Ross MolecularandCellular Biology GraduateProgram, Department ofPhysics, University ofMassachusetts Amherst,Amherst, MA, USA Sophie Roth DepartmentofBionanoscience,KavliInstituteofNanoscience,DelftUniversityof Technology, Delft, The Netherlands Daniel S.Saxton WellcomeTrust/Cancer Research UKGurdonInstitute and Department of Biochemistry, University ofCambridge, Cambridge, UK EvaM. Schmid Department ofBioengineering&Biophysics Program, University ofCalifornia, Berkeley,CA,USA Petra Schwille Department ofCellular and MolecularBiophysics, Max Planck Institute for Biochemistry, Martinsried,Germany EnasAbuShah Department ofPhysics, Technion-Israel Instituteof Technology, Haifa, Israel; RussellBerrieNanotechnologyInstitute,Technion-IsraelInstituteofTechnology, Haifa, Israel Kasimira T.Stanhope MolecularandCellular Biology GraduateProgram, Department ofPhysics, University ofMassachusetts Amherst,Amherst, MA, USA Thomas Surrey London ResearchInstitute,CancerResearchUK, London,UK Ce´cile Sykes Institut Curie,Centre de Recherche, Paris, France; CNRS,UMR168, Paris, France; UPMC UnivParis06, UMR 168,Paris, France; Univ.Paris Diderot, Sorbonne ParisCite´, Paris, France Nu´ria Taberner DepartmentofBionanoscience,KavliInstituteofNanoscience,DelftUniversityof Technology, Delft, The Netherlands Contributors xv Nathaniel Talledge Department ofBiochemistry,University ofUtah, SchoolofMedicine, Salt Lake City, UT,USA; Department ofBiochemistry and Biophysics,University of California, San Francisco, San Francisco, CA,USA Lukas K.Tamm Center for Membrane Biology and Department ofMolecular Physiology and BiologicalPhysics, University ofVirginia,Charlottesville, VA, USA James A.Taylor LaboratoryofMolecularBiology,NationalInstituteofDiabetes,andDigestiveand Kidney Diseases, NationalInstitutesof Health, Bethesda,MD, USA David Tsao Department ofChemistry,Rice University,Houston, TX,USA; Department of Bioengineering,RiceUniversity, Houston, TX, USA Anthony G.Vecchiarelli LaboratoryofMolecularBiology,NationalInstituteofDiabetes,andDigestiveand Kidney Diseases, NationalInstitutesof Health, Bethesda,MD, USA Astrid Walrant Wellcome Trust/Cancer Research UKGurdon Instituteand Department of Biochemistry,University of Cambridge, Cambridge, UK Hans Zeijlemaker FOM InstituteAMOLF,Amsterdam,The Netherlands Katja Zieske Department ofCellular and Molecular Biophysics,Max Planck Institutefor Biochemistry,Martinsried, Germany 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, thereductionistapproachofbuildingupcomplexityappealstomanywithphysical scienceandengineeringbackgrounds.Suchexperimentsareappealingbecausethe complexityofthecellularorganismcanbebuiltupsystematicallyaddinginonenew elementatatimeanddialinguptheconcentrationsofeachcomponentinasystem- atic way.Thehopeisthatsuch bottom-up approacheswillgarnernewquantitative insights at many levels. At the lowest level, we seek to elucidate single molecule activitiestobeabletohavequantitativenumbersforanalyticalmodelsandsimula- tions. As new components are added to one another, their activities can combine synergistically to create novel emergent behaviors. Since biology is inherently out ofequilibrium,thereisenergybeinginjectedthatcanenhancesuchsynergiesmak- ing evensimple-seeming systems appear complexand inherently interesting. Such emergence of complex behavior from interactions of simple components is likely tohavebeencriticalfortheoriginsoflife.Further,reductionistscientistsareseeking todeterminetheminimaldiversityofcomponentstocreatecell-likestructuresand activities.Especiallyineukaryoticsystems,thenumberofcomponentscontrolling cellfunctionappearsunnecessarilylargeandthemethodsforcellularcontrolappear baroque.Bydeterminingtheminimalvarietyofproteinsofeachfunctiontoperform 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 bioengi- neeringbased on cell-likenanodevices. Another interesting issue of the cell is thevariety 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 ulti- mately combine the two into cell-like patterns andorganizations. Wehavegroupedtogethercontributedchaptersthathavesimilarfocuses,starting with wholly in vitro reconstitutions of cytoskeleton. These contributions include methods for combining different motors and cytoskeletal components in defined waystoproducemorecomplexbehaviors,aswellasmethodstocombinecytoskel- etal assemblieswith fabricated devicessuch aschambers orpillararrays. Nextwemovetothemembranesystemsreconstitutedinvitro.Contributionsin thisareaincludechaptersonreconstitutingmembranefissionandfusion,aswellas reconstitutingimportantbiologicalprocessesthatnormallytakeplaceonmembrane surfaces, such as cell division andpolarity. Finally, we finish with systems that attempt to recreate cells as encapsulated systemsofchemicalsthatcanacttogetherasamachinetoperformfunctions.These chapters describe methods for encapsulating protein machines within vesicles or xvii
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