New Models of the Cell Nucleus: Crowding, Entropic Forces, Phase Separation, and Fractals

493 Pages·2014·31.196 MB·English

by  Ronald Hancock and Kwang W. Jeon (Eds.)

International Review of Cell
and Molecular Biology
SeriesEditors
GEOFFREY H. BOURNE 1949–1988
JAMES F. DANIELLI 1949–1984
KWANGW. JEON 1967–
MARTINFRIEDLANDER 1984–1992
JONATHAN JARVIK 1993–1995
Editorial AdvisoryBoard
PETER L. BEECH WALLACE F. MARSHALL
ROBERT A. BLOODGOOD BRUCE D. MCKEE
KEITH BURRIDGE MICHAELMELKONIAN
HIROO FUKUDA KEITH E. MOSTOV
RAY H. GAVIN ANDREAS OKSCHE
MAY GRIFFITH MADDYPARSONS
WILLIAM R. JEFFERY TERUO SHIMMEN
KEITH LATHAM ALEXEY TOMILIN
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CONTRIBUTORS
WilliamM.AumillerJr.
DepartmentofChemistry,PennsylvaniaStateUniversity,UniversityPark,Pennsylvania,
USA
Aure´lienBancaud
CNRSGDR3536,UniversityPierreetMarieCurie-Paris6,Paris;CNRS,LAAS,and
Universite´ deToulouse,LAAS,Toulouse,France
VictorM.Bolanos-Garcia
FacultyofHealthandLifeSciences,DepartmentofBiologicalandMedicalSciences,Oxford
BrookesUniversity,Oxford,UnitedKingdom
PascalCarrivain
CNRSGDR3536,andLPTMCUMR7600,CNRS,Universite´ PierreetMarieCurie-
Paris6,Paris,France
BradleyW.Davis
DepartmentofChemistry,PennsylvaniaStateUniversity,UniversityPark,Pennsylvania,
USA
AlanR.Denton
DepartmentofPhysics,NorthDakotaStateUniversity,Fargo,NorthDakota,USA
RonaldHancock
LavalUniversityCancerResearchCentre,CRCHUQ-Oncology,Que´bec,Canada,and
BiosystemsGroup,BiotechnologyCentre,SilesianUniversityofTechnology,Gliwice,
Poland
DieterW.Heermann
InstituteforTheoreticalPhysics;InterdisciplinaryCenterforScientificComputing(IWR),
Heidelberg,Germany;TheJacksonLaboratory,BarHarbor,Maine,USA,andShanghai
CenterforBioinformationTechnology(SCBIT),Shanghai,PRChina
Se´bastienHuet
CNRS,UMR6290,InstitutGe´ne´tiqueetDe´veloppementdeRennes;Universite´Rennes1,
Universite´ Europe´ennedeBretagne,Structurefe´de´rativederecherche,Biosit,Faculte´ de
Me´decine,Rennes,andCNRSGDR3536,UniversityPierreetMarieCurie-Paris6,Paris,
France
HansjoergJerabek
InstituteforTheoreticalPhysics,andInterdisciplinaryCenterforScientificComputing
(IWR),Heidelberg,Germany
ChristineD.Keating
DepartmentofChemistry,PennsylvaniaStateUniversity,UniversityPark,Pennsylvania,
USA
xi
xii Contributors
JunSooKim
DepartmentofChemistryandNanoScience,GlobalTop5ResearchProgram,Ewha
WomansUniversity,Seoul,RepublicofKorea
ChristopheLavelle
CNRSGDR3536,UniversityPierreetMarieCurie-Paris6;NationalMuseumofNatural
History;CNRSUMR7196,andINSERMU565,Paris,France
AndrewMugler
FOMInstituteAMOLF,Amsterdam,TheNetherlands
ThoruPederson
PrograminCellandDevelopmentalDynamics,DepartmentofBiochemistryandMolecular
Pharmacology,UniversityofMassachusettsMedicalSchool,Worcester,Massachusetts,USA
HubertRanchon
CNRSGDR3536,UniversityPierreetMarieCurie-Paris6,Paris;CNRS,LAAS,and
Universite´ deToulouse,LAAS,Toulouse,France
AngeloRosa
ScuolaInternazionaleSuperiorediStudiAvanzati,Trieste,Italy
TakahiroSakaue
DepartmentofPhysics,GraduateSchoolofSciences,KyushuUniversity,Fukuoka,Japan
NaokiSugimoto
FrontierInstituteforBiomolecularEngineeringResearch(FIBER)andFacultyofFrontiers
ofInnovativeResearchinScienceandTechnology(FIRST),KonanUniversity,Kobe,Japan
IgalSzleifer
DepartmentofBiomedicalEngineering;DepartmentofChemistry,andChemistryofLife
ProcessesInstitute,NorthwesternUniversity,Evanston,Illinois,USA
PieterReintenWolde
FOMInstituteAMOLF,Amsterdam,TheNetherlands
Jean-MarcVictor
CNRSGDR3536,andLPTMCUMR7600,CNRS,Universite´ PierreetMarieCurie-
Paris6,Paris,France
MatthiasWeiss
DepartmentofExperimentalPhysicsI,UniversityofBayreuth,Bayreuth,Germany
MihoYanagisawa
DepartmentofPhysics,GraduateSchoolofSciences,KyushuUniversity,Fukuoka,Japan
KenichiYoshikawa
FacultyofLifeandMedicalSciences,DoshishaUniversity,Kyotanabe,Kyoto,Japan
ChristopheZimmer
InstitutPasteur,Unite´ ImagerieetMode´lisation;CNRSURA2582,Paris,France
PREFACE
Interestinthecellnucleushasbeenheightenedinrecentyears,andtheprin-
ciples which determine structure and functions have become considerably
clearer during the nearly 30 years since the publication of a volume in this
serieswithasimilartheme(Berezney,R.,Jeon,K.W.(Eds.),1995.Nuclear
matrix—structural and functional organization. Int. Rev. Cytol. 162). It is
noteworthythatthisprogresshasbeenduelargelytoideasfromthefieldsof
biophysics,physicalchemistryandpolymer,colloid,andsoft-matterscience,
andalsotothedevelopmentof powerfulsimulationmethodsfor modeling
the conformations and interactions of macromolecules.
In presenting this volume, our hope is to encourage cell and molecular
biologiststobecomemorefamiliarwithandunderstandthesenewconcepts
and methods, and the crucial contributions which they are making to our
perception of the nucleus. They are likely to be essential factors in all the
systems in the nucleus and in their activities.
It is a great pleasure to thank the authors for their willing and friendly
cooperationandforfindingthetimetopreparetheircontributionsinspite
of their busy schedules. We also thank workers at Elsevier Academic Press
for having produced an excellent volume.
RONALD HANCOCK AND KWANG W. JEON
July 2013
xiii
CHAPTER ONE
The Nuclear Physique
Thoru Pederson1
PrograminCellandDevelopmentalDynamics,DepartmentofBiochemistryandMolecularPharmacology,
UniversityofMassachusettsMedicalSchool,Worcester,Massachusetts,USA
1Correspondingauthor:e-mailaddress:[email protected]
Contents
1. Introduction:ABriefHistoryofBiophysics 1
2. TheBiophysicalNucleus 5
2.1 Nuclearstructureatmesoscopicscale 5
2.2 Physicallawsgoverningnuclearfunction 7
2.3 Whatliesaheadandthemethodsthatmaybeinplay 10
Acknowledgments 11
References 11
Abstract
Thisvolumebringstogetheranumberofperspectives onhowcertainphysicalphe-
nomenacontributetothefunctionaldesignandoperationofthenucleus.Thiscollec-
tion could not be more timely, resonating with an increasing awareness of the
opportunitiesthatlieattheinterfaceofcellbiologyandthephysicalsciences.Forexam-
ple,thiswas amajorthemeinthe2012and2013annualmeetings oftheAmerican
SocietyforCellBiology,andonethattheSocietyaimstoemphasizeevenfurthergoing
forward.Inaddition,theemergingcanonicalrelevanceofthephysicalsciencestocell
biologyhasinrecentsummersmadeamostconspicuousappearanceinthecurriculum
(lecturesandintenselabs)ofthefamedPhysiologyCourseattheMarineBiologicalLab-
oratoryinWoodsHole.So,muchcreditisduetoRonaldHancockandKwangJeon,the
coeditorsofthisvolume,andalltheauthorsforcreatingaworkthatissoaucourant.
ItallstartedwiththeBigBang
Robertson(2007)
1. INTRODUCTION: A BRIEF HISTORY OF BIOPHYSICS
The English word “physics” deerives, as the plural, from the Greek
noun “physic” (Fίzik) and has historically been applied to both medicine
(thepracticeof“physik”)and,moredurably,naturalphenomena(excluding
InternationalReviewofCellandMolecularBiology,Volume307 #2014ElsevierInc. 1
ISSN1937-6448 Allrightsreserved.
http://dx.doi.org/10.1016/B978-0-12-800046-5.00001-1
2 ThoruPederson
life). The former term is no longer used in medicine except on occasion
whenoneseesthataprofessoratsomevenerablemedicalschoolholdsatitle
such as “The (insert an august name here, such as Vesalius or Paracelsus)
Professor of Physik.” No one can quite be sure when the prefix “bio” was
first attached to physics. The combined word does not appear in any of
Aristotle’s brilliant essays on either physics or natural history, for example,
though his treatise “Movement of Animals” (translated by Farquharson,
1984) makes for fascinating reading, particularly bearing in mind that he
wrote more than two millenia before the time of Newton.
In themid-eighteenthcentury, theItalian physician andphysicist Luigi
Galvani(1737–1798)discoveredthatthelegmuscleofarecentlysacrificed
frog could conduct static electricity from a piece of metal, resulting in a
twitch.Thisallowedhimtomaketheleapthatelectricityisrelatedtomuscle
activityinthelivinganimal.ThesubsequentdiscoverybytheGermanphy-
sicianandphysiologistEmilduBois-Reymound(1818–1896)ofwhatcame
tobeknownasthenerveactionpotentialpavedthewayforwhatcouldbe
called the “pre-biophysics era.” In due course, as the field of biochemistry
evolved,aparallellineofthinkingarosethat“mechanical”andindeedeven
“engineering” principles were as much at play in living systems as
chemistry—a doctrine promoted particularly by the German–American
biologist Jacques Loeb (1859–1924).
Bythe1920s,thearrivalofbiophysicswasathand,atleastinaformthat
took up that name. It was both an approach (particular equipment) and a
discipline(avisionofmechanism)andwasdriven,atleasttoaconsiderable
degreebyphysiologistscontinuingtobumpintophysicalunderpinningsof
biologicalprocesses.Buttherewasasecond,portentousdomainofbiophys-
ics in the wind.
Back in 1912, the German physicist, Max von Laue (1879–1960), had
discovered the diffraction of X-rays by crystalline materials, and subse-
quently he and others realized that this diffraction from the lattice would
allow the crystal’s structure to be deduced by calculating the pattern back
through reciprocal space. In due course, it occurred to several people that
such an approach might be applied to more complex molecules than crys-
tallineminerals.TheundisputedleaderofthismovementwastheIrishphys-
icistJohnDesmondBernal(1901–1971).Hewasaformidablegeniuswho,
evenasanundergraduateatCambridge,presentedoneofhisprofessorswith
a penetrating mathematical analysis of the 230 crystal space groups, an
achievement even more striking given that he had not done well on the
mathematics tripos, leading him to turn to the natural sciences curriculum
BiophysicalAspectsoftheNucleus 3
(Brown, 2005). Later, having become a leading crystallographer, arguably
the leading one, Bernal encouraged his former student Dorothy Crowfoot
Hodgkin(1910–1994)totakeupthelargertask(asboththesizeoftheunit
cell and magnitude of the achievement, if reached) of tackling biological
molecules. By the age of 35, Hodgkin had got the structure of penicillin
beforeithadbeendeterminedbychemicalmeans.Thiswasamonumental
achievement,andshefolloweditinduecoursebysolvingthestructuresof
vitamin B and insulin.
12
Inparallelwiththesetriumphs,therearrivedtheeraofX-raydiffraction
analysisofbothcrystallineproteinsand(wetordry)biologicalfibersasinthe
case of collagen, wool, and DNA, and these endeavors, in particular in the
X-ray crystallography field, increasingly took on the name “biophysics” in
manyvenues.Thus,forexample,thelaboratoryatKing’sCollege,London,
whereMauriceWilkinsand,later,RosalindFranklinundertookX-raydif-
fractionofDNAhadlongbeennamedtheBiophysicsUnitoftheMedical
ResearchCouncil.Thetermbiophysicshadbecome,bytheendofthewar,
part of the scientific lexicon. The crystallographic axis of biophysics soon
reached its first “post-Hodgkin” pinnacle in the DNA work of Wilkins
and Franklin at King’s, and of Watson and Crick at the University of
Cambridge Department of Physics’ Cavendish Laboratory, and, subse-
quently, in the structural solutions of myoglobin and hemoglobin by John
KendrewandMaxPerutz,respectively,attheMedicalResearchCouncil’s
Laboratory of Molecular Biology in Cambridge. Despite the name of this
latterinstitute,itsfoundingwasadirectresultofthebiophysicserathatBernal
and Hodgkin had pioneered, and which England so proudly led for more
than three decades.
Inthe1950s,anotherdimensionofbiophysicscomingtofruitionwasthe
study of cellstructure. Phase contrast microscopy,a majoradvance in light
microscopy, had been discovered in 1930 by the Dutch physicist Frits
Zernike(1888–1966),forwhichhereceivedthe1953NobelPrizeinPhys-
ics,unshared.Meanwhile,alsointheearly1930s,theGermanphysicistErnst
Ruska(1906–1988)haddevelopedtheprinciplesandprototypesoftheelec-
tron microscope, for which he received the 1988 Nobel Prize in Physics,
shared with Gerd Binning and Heinrich Rohrer for their invention of
thescanningtunnelingmicroscope.Bythetimephase-contrastandelectron
microscopyarrived,manycytologists,biochemists,andevenphyscicts(vide
infra)weretrying to define“protoplasm.”Rivals seemedready tobet their
first-born children on “gel” versus “sol” models of protoplasm. In his very
first work with live material, Francis Crick measured the recoil of
4 ThoruPederson
intracellularironparticleswhensubjectedtoamagneticfield,asaprobeof
therheologicaland,thus,cross-sectionaldensityofcytoplasm(Crick,1950;
Crick and Hughes, 1950). I recently reread the first paper (the second is
beyond my expertise in the physics required) and would recommend it
toallcellbiologistsasamodelofexperimentaleleganceforitstime,aswell
as a marvelous example of fine writing.
Exceptfortheobviousriskofconfusing(orannoying)readers,thischap-
ter might have been titled “Nuclear Physics” and this point reminds us, of
course, of another major development in biology that sprang from pure
physics, namely, the codiscovery of radioactivity by Marie Curie and
Henri Becquerel. The subsequent understanding of this phenomenon
(i.e., “nuclear physics,” literally) led to the use of unstable isotopes by the
Hungarian chemist George de Hevesy (1885–1966; Nobel Prize in
Chemistry,1943)andRudolfScho˝nheimer(1898–1941)astracerstopursue
the biosynthesis and flux of molecules in living systems. Later, the stable
isotopenitrogen-15wasthekeytotheMeselson–Stahlexperimentdemon-
stratingthesemiconservativereplicationofDNA,dubbed“themostbeau-
tifulexperimentinbiology”(Holmes,2001).Theentryofradioisotopesto
biologicalresearchwaspurebiophysics,althoughtheybecamesuchstandard
toolsthattheirusewasnotlabeledasbiophysicsperse.Sotoowastheallied
field of radiation biology.
Comingtothemodernera(1975–present),biophysicsmightbedefined
by what is publishedin theBiophysicalJournal (reminding meof aprofessor
who told the class that lipids are defined as substances that are soluble in a
lipid solvent). Huge advances have taken place in our ability to measure
things such as the diffusion-based transport of molecules in cells—thanks
mainlytotheadventoffluorescentdyesandproteins.Morerecently,injust
thelastdecade,advanceshavecrackedtheAbbe´ limit((cid:1)200nm)forspatial
resolution in diffraction-limited optical microscopy. And meanwhile, the
introductionof“optogenetics,”pioneeredbyGeroMiesenbo˝ckandrefined
byKarlDeisseroth,hasbroughtnewmeaningto“biophysics.”Thismethod
exploits the biophysical properties of opsins as sensors, combined with
reportingfluorescentproteins,toallowcellphysiologytobeobservedinreal
time.ThispastMay,Iattendedatalkinwhichthespeaker,AdamCohenof
Harvard University, showed videos of an action potential running down a
neuron and culminating in synaptic transmission. Never did I dream that
Iwouldseesuchathinginlivecells,asopposedtoonanoscilloscopescreen.
Driving home I pondered: Sic transit gloria biophysica.
BiophysicalAspectsoftheNucleus 5
2. THE BIOPHYSICAL NUCLEUS
Letusnowturntospecificallythenucleus,thesubjectofthisvolume.
Forthepurposesofthisintroductorychapter,threekeyquestionscanbeposed:
Whatisthestructureofthenucleusatthemesoscopicscale?Towhatextentdo
certain phenomena in the nucleus obey purely physical laws? What are the
emergingmethodsthatcantacklethephysicsofthenucleusgoingforward?
Beforewemoveon,Iwanttomentionaguidelinethatthebiophysicist
DanielBrantontaughtme.Atthe1982meetingoftheAmericanSocietyfor
CellBiology,Iwasinchargeoftheprogramandinvitedhimtochaironeof
the symposia. In his introductory remarks, he said he had instructed the
speakerstoemphasizeanyplacesintheirworkwheretheformationofcova-
lentbondshadnotbeenatplay.Ithoughtthiswasamostenablingdeviceat
thetime(andhisspeakersindeedobeyed).Itremainsavaluableconstructfor
us all, as we delve into any part of biology.
2.1. Nuclear structure at mesoscopic scale
Bythetimecytochemicalstudieshadrevealedtheverylargeproportionof
thenuclearvolumeoccupiedbyDNA,atleastinmostcells,itbecamelog-
icaltoassumethatthephysicalpropertiesofthenucleusderivemostlyfroma
veryhighconcentrationoftheseextraordinarilylongpolymers(Thediscov-
eryofuninemywasjustaroundthecornerbut,inanycase,noonedoubted
thattheDNAmoleculeswereverylong,whetherchromosome-sizeornot.).
Later, Thomasand ChristophCremerand colleagues insightfully deduced,
fromchromosomebreaksinducedininterphasecellsbyUVirradiation,that
eachchromosomeoccupiedadistinctportionofthenuclearvolume,rather
thanbeingintertwined(Cremeretal.,1982).Thisandsubsequentworkby
themandothersbroughttheconceptofchromosomesterritories(Pederson,
2003,2004)andalso,moresubtly,hintedthatwhilethechromosomeswere
not entangled, the amount of interchromosomal space in the nucleus was
relatively small. Nonetheless, it was natural for the curious to ponder
whethertheinterchromosomespaceitselfpossessedsomekindofstructure.
Meanwhile, in the 1960s, Ilya Zbarsky in Moscow was subjecting iso-
lated nuclei to escalating concentrations of NaCl and noted that, after the
histoneandmuchothernuclearproteinhadbeenextracted,aresidualstruc-
ture remained. In a refinement of his work, Berezney and Coffey used
DNase and salt extraction to obtain a residual fraction that contained only