Building a cell from its component parts

388 Pages·2015·24.246 MB·English

by  Marshall, Wallace F., Ross, Jennifer

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
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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