Encyclopedia of Biological Chemistry, Second Edition

3015 Pages·2013·155.65 MB·English

by  William J. Lennarz

William J. Lennarz
M. Daniel Lane
Encyclopedia of
Biologic
ry
I
I I
^1
E
NCYCLOPEDIA OF
BIOLOGICAL CHEMISTRY
SECOND EDITION
E
NCYCLOPEDIA OF
BIOLOGICAL CHEMISTRY
EDITORS-IN-CHIEF
WILLIAM J. LENNARZ
Stony Brook University,
Stony Brook, NY, USA
M. DANIEL LANE
Johns Hopkins University School of Medicine,
Baltimore, MD, USA
VOLUME 1 VOLUME 2 VOLUME 3 VOLUME 4
A–Dis DNA–L M–Q R–Z
AMSTERDAM BOSTON HEIDELBERG LONDON NE YORK OXFORD
PARIS SAN DIEGO SAN FRANCISCO SINGAPORE SYDNEY TOKYO
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Firstedition2004
Secondedition2013
Copyright#2013Elsevier,Inc.Allrightsreserved.
ThefollowingarticlesareUSGovernmentworksinthepublicdomainandarenotsubjecttocopyright:
AdipocyteFatMobilization:TheRegulatoryRolesofPerilipin1,AdiposeTriglycerideLipase,andHormone-SensitiveLipase
ArfFamily
CalciumSignaling:Calmodulin-DependentPhosphatase
CyclicAMPReceptorsofDictyostelium
CyclicNucleotidePhosphodiesterases
Cytokines
DNAMismatchRepairinDiseaseandAging
DNAPolymeraseb,Eukaryotic
Endocytosis
EukaryoticChemotaxis
GsFamilyofHeterotrimericGProteins
InositolPhosphateKinasesandPhosphatases
PhospholipaseC
PrionsofYeastandFungi:ProteinsActingasGenes
Riboswitches
StructureandRegulationofPyruvateDehydrogenases
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EDITORS-IN-CHIEF
M.DanielLane,Ph.D.isDistinguishedServiceProfessorofBiologicalChemistryattheJohnsHopkinsMedicalSchool.HereceivedB.S.and
M.S.degreesfromIowaStateUniversity,aPh.D.degreefromtheUniversityofIllinoisandanhonoraryDoctorofHumaneLettersdegree,
from Iowa State University. He did a Senior Postdoctoral Fellowship with Professor Feodor Lynen at the Max-Planck Institute Fu¨r
ZellchemieinMunich.FollowingfacultypositionsatVirginiaTechandNewYorkUniversitySchoolofMedicine,hejoined(in1970)
thefacultyattheJohnsHopkinsMedicalSchoolwhereheservedasDeLamarProfessorandDirectoroftheDepartmentofBiological
Chemistryfrom1978to1997.HewaselectedtomembershipintheNationalAcademyofSciencesandtheAmericanAcademyofArtsand
Sciences(1987)andasaFellowoftheAmericanSocietyofNutritionalSciences(1996).HereceivedtheMeadJohnsonAwardfromthe
AmericanSocietyfor Nutritional SciencesandtheWilliamC.RoseAwardfromtheAmericanSocietyfor Biochemistry andMolecular
BiologyandservedasPresidentoftheAmericanSocietyofBiochemistryandMolecularBiology.Heservedonnumerouseditorialboards
includingtheJournalofBiologicalChemistryandtheAnnualReviewsofBiochemistry.WithWilliamLennarzheco-editedthefirstedition
(2004)oftheEncyclopediaofBiologicalChemistry.CurrentlyheisAssociateEditorforBiochemicalandBiophysicalResearchCommu-
nications.HisearlyworkfocusedonenzymaticCO fixationreactions,notablythemechanismsbywhichtheB-vitamin,biotin,functions
2
incarboxylases.Hisresearchonacetyl-CoAcarboxylase,keyregulatoryenzymeoffattyacidsynthesis,ledhimtohispresentinterestsinthe
basicmechanismsoflipogenesis,adipogenesisandthehypothalamiccontrolofenergybalance.
WilliamJ.LennarzreceivedhisB.S.inChemistryfromPennsylvaniaStateUniversityandaPh.D.inOrganicChemistryfromtheUniversity
of Illinois. Subsequently he carried out postdoctoral work at Harvard with Konrad Bloch on fatty acid biosynthesis. In 1962 he was
appointedAssistantProfessoratJohnsHopkinsintheDepartmentofPhysiologicalChemistry.AfterpromotiontoAssociateProfessorin
1967,andfullProfessorin1971,heremainedatHopkinsuntil1983.Atthattime,hewasappointedRobertA.WelchProfessorandChairof
theDepartmentofBiochemistryandMolecularBiologyattheUniversityofTexasCancerCenter,M.D.AndersonHospital.In1989he
becameaLeadingProfessorandChairoftheDepartmentofBiochemistryandCellBiologyatSUNYatStonyBrook.In1990hefounded
andbecameDirectoroftheInstituteforCellandDevelopmentalBiologyatStonyBrook.
Dr.Lennarzhasservedonmanynationalandinternationalcommittees.HehasservedasPresidentoftheBiochemistryChairman’s
Organization,PresidentoftheAmericanSocietyforBiochemistryandMolecularBiology,andPresidentoftheSocietyforGlycobiology.
HewasamemberoftheExecutiveCommitteeoftheInternationalUnionofBiochemistryandMolecularBiologyforalmostadecade.
HehaspresentedspeciallecturesattheUniversityofNotreDame,theNIH,theUniversityofWestVirginia,JohnsHopkinsUniversity,
FloridaStateUniversity,theUniversityofCaliforniaatSanDiego,theUniversityofArkansas,IndianaUniversity,andtheMedicalCollegeof
Virginia.
HeisamemberoftheNationalAcademyofSciences.Thefocusofhisearlyworkwasonlipidsandbacterialcellsurfaces.Morerecent
effortshavebeeninthestructure,biosynthesis,andfunctionofcellsurfaceglycoproteins.Thebiosynthesisstudieswereinitiallycarriedout
in liver and oviduct, but these efforts now are focused in yeast. The functional studies have concentrated on the role of cell surface
glycoproteinsinfertilizationandearlydevelopmentintheseaurchinand,morerecently,thefrog.HeservedasDistinguishedProfessorand
Chairofhisdepartment.HenowisDistinguishedProfessorEmeritus.
v
EDITORIAL BOARD
WolfgangBaumeisterwasbornonNovember22,1946inWesselingnearCologne.StudyofbiologyMu¨nster
andBonnUniversity,doctorateDu¨sseldorfUniversity(1973),HabilitationinbiophysicsDu¨sseldorfUniversity
(1978), Heisenberg Scholarship Cambridge/England, head of a group (C3 level) at the Max Planck Institute
forBiochemistry(1981),AdjunctProfessorDu¨sseldorfUniversity(1982),AdjunctProfessorChemistryDept.
TUMunich(1987),DirectorandScientificMemberattheMaxPlanckInstituteofBiochemistry(since1988),
Honorary Professor, Physics Dept., TU Munich (2000). He was made a fellow with the German Academy of
SciencesLeopoldinain2001andwaselectedasaForeignAssociatewiththeUSNationalAcademyofSciences
in2010.
WolfgangBaumeisterhasbeenhonoredwithnumerousawardsforhisresearchincludingtheOttoWarburg
Medal of the German Society for Biochemistry and Molecular Biology (1998), the prize of the Geneva-based
Louis-Jeantet Foundation for Medicine (2003), the Ernst Schering Prize (2006), the Schleiden Medal of the
German Academy of Sciences Leopoldina (2005), and the Harvey Prize in Science and Technology of
theTechnion,Haifa(2005).
Ernesto Carafoli was born in 1932, in Italy. He gained his M.D. in 1957 at the University of Modena, Italy;
“Abilitation”(LiberaDocenza)inGeneralPathology(1965)andinBiochemistry(1968);FogartyInternational
Post-doctoralFellowintheDept.ofPhysiologicalChemistryoftheJohnsHopkinsUniversity,Baltimore,MD,
USA (1963–1965); Visiting Lecturer in the same department 1968–1969; Assistant Professor, then Associate
Professor of General Pathology in the University of Modena School of Medicine, (1959 to 1972); Professor
of General Pathology, University of Padova School of Medicine (Italy) (1973); Professor of Biochemistry,
SwissFederalInstituteofTechnology(ETH)(Zurich,Switzerland),(1973to1998);ChairmanoftheDept.of
Biochemistry of the Swiss Federal Institute of Technology (ETH) in 1978 and 1987 to 1991; Professor of
Biochemistry, University of Padova, School of Medicine, Italy (since 1990). From 1971 to 1991 Visiting
Professor for various periods in several Italian Universities, at the University of Nairobi (Kenya), at the
Universidad Nacional Autonoma of Mexico, Mexico City (Mexico), at the Universidad Central de Venezuela,
Caracas (Venezuela), and at Case Western Reserve University, Cleveland (OH, USA). He has been Fogarty
Scholar in Residence at the NIH from 1985 to 1988. Co-founder of the Venetian Institute of Molecular
Medicine (Padova, Italy), of which he was the first Scientific Director (2000 to 2005). He has received
numerous awards and honors including five Doctor Honoris Causa degrees. He is Member of several Acade-
mies,includingtheJohnsHopkinsSocietyofScholars,andhehasbeenmade“GrandeUfficiale”oftheOrder
ofMeritoftheRepublicofItaly,2006.
Dr. Carafoli has been a member of a number of professional Societies, including the Swiss Biochemical
Society, the Biochemical Society, the American Society for Cell Biology, the American Society of Biological
Chemistry and Molecular Biology (Honorary Member), the Society of General Physiology, the Biophysical
Society,theItalianSocietyofBiochemistry.HehasbeenamemberoftheEditorialBoardofnumerousjournals
intheareaofBiochemistry,Biophysics,andCellBiology.Hehasbeenco-organizerofabout50International
CongressesandSymposia,andofabout25AdvancedCourses,(heldinadozencountriesonbehalfofFEBS,
ICRO/UNESCO, the Gulbenkian Foundation, and WHO). He has delivered lectures (including a number of
PlenaryandKeynotelectures)atabout350InternationalCongresses,Symposia,Colloquia.Hehaswrittenover
500 articles in refereed journals on topics of muscle biochemistry, membrane biochemistry, mitochondrial
bioenergetics,membranetransportofions(calciumspeciallybypumps)regulationofcalciummetabolism,and
over100bookchaptersand70invitedreviewarticles.Hehaseditedabout20booksontopicsrelatedtohiswork.
vii
viii EditorialBoard
Pierre A. Coulombe is the E.V. McCollum Professor and Chair of the Department of Biochemistry and
Molecular Biology at the Bloomberg School of Public Health at Johns Hopkins University in Baltimore,
Maryland. He holds several joint appointments in the School of Medicine and the same institution.
Dr. Coulombe obtained a Ph.D. degree from Universite´ de Montre´al in Canada and underwent postdoctoral
training at the University of Chicago. At that time, he and Dr. Elaine Fuchs discovered that mutations in
keratins elicit epithelial fragility in transgenic mice and in individuals suffering from inherited blistering
diseases. He continues to explore the properties and function of keratin genes and proteins in the setting of
tissuerepairandcancer.
NancyL.CraigisanInvestigatorwiththeHowardHughesMedicalInstitute,aswellasaProfessorofMolecular
Biology and Genetics at the Johns Hopkins University School of Medicine,where her work is focused on the
molecular mechanisms by which transposable elements move and how they can be exploited for genome
engineering. After receiving a bachelor’s degree in biology and chemistry from Bryn Mawr College, she did
graduateworkoncellularresponsestoDNAdamageinE.coliwithJeffreyRobertsatCornellUniversity,leading
toherPh.D.degreeinbiochemistry.AsapostdoctoralfellowattheNationalInstitutesofHealth,shestudiedthe
mechanismofsite-specificrecombinationofbacteriophagelambdawithHowardNash.BeforejoiningHHMI,
she was Associate Professor of Microbiology and Immunology and of Biochemistry and Biophysics at the
University of California, San Francisco, where she began her research on Tn7 transposition. Dr. Craig is a
Member of the National Academy of Sciences and the American Academy of Arts and Sciences. She is
also a Fellow of the American Association for the Advancement of Science and the American Academy of
Microbiology.
Joel Moss, M.D., Ph.D. is Deputy Chief of the Cardiovascular and Pulmonary Branch, National Heart, Lung,
andBloodInstituteattheNationalInstitutesofHealth,Bethesda,Maryland,USA.HegraduatedfromBrandeis
University in 1967, Summa Cum Laude with Honors in Chemistry. In 1972, he received M.D. and Ph.D.
degreesfromNewYorkUniversitySchoolofMedicine,withhisdissertationintheDepartmentofBiochemistry
under the mentorshipofDr. M.Daniel Lane.Followingan internshipand residency inmedicine at the John
HopkinsHospital,hecompletedapost-doctoralfellowshipwithDr.MarthaVaughanandpulmonaryfellow-
ship with Dr. Ronald Crystal in the National Heart, Lung, and Blood Institute (NHLBI) at the National
InstitutesofHealth.Dr.Mosshascoauthoredover600scientificpapersonbasicandclinicalresearch,edited
or co-authored several books, and is a co-inventor of biotechnology patents. Dr. Moss was a member of the
NHLBIInstitutionalReviewBoard1988to2006,anditsChair1995to2006.Inthisregard,hehascoauthored
a textbook with Dr. Evan DeRenzo entitled: “Writing Clinical Research Protocols: Ethical Considerations”.
Dr.Moss hasreceivedmultipleawards, includingthePassanoFoundationYoung InvestigatorAward(1981),
theAFCRYoungInvestigatorAward(1981),andtheLAMFoundationAward(1999,2010).HeisaFellowof
theAmericanCollegeofChestPhysicians.Dr.MossisamemberofPhiBetaKappa,AlphaOmegaAlpha,the
American Society for Biochemistry and Molecular Biology, Association of American Physicians, American
Thoracic Society, and the American Society for Clinical Investigation (ASCI), of which he has served as a
CouncilorandVicePresident.
Inhisclinicalresearch,Dr.Mosshasfocusedondestructivelungdiseases(e.g.,lymphangioleiomyomatosis,
cystic fibrosis), with primary emphasis on the roles of infection/inflammation and susceptibility/ modifier
genesondiseaseprogressionandseverity.HisLAMresearchcentersontheabnormalsmoothmuscle-likecells
(LAMcells)thatproliferateinthelungs,lymphatics,andkidneys,andareresponsible forcysticlungdestruc-
tion and abnormalities in the lymphatic system. Subjects of his basic research include guanine nucleotide-
bindingregulatoryproteinsandpost-translationalmodificationofproteinsbyADP-ribosylation.
Carole Parent obtained her B.Pharm. and M.Sc. degrees from the University of Montre´al in Canada and her
Ph.D. in Pharmacy from the University of Illinois at Chicago. She then pursued postdoctoral studies in the
laboratory of Dr. Peter Devreotes at Johns Hopkins. In 2000, she joined the Laboratory of Cellular and
Molecular Biology at the Center for Cancer Research (NCI, NIH) where she is now Senior Investigator and
DeputyChief.Usingthreecomplementarymodelsystems,herresearchinterestsarecenteredonunderstanding
how cells detect and respond to external chemotactic signals and, in particular, how the relay of chemotactic
signalsfromcell-to-cellimpactssingleandgroupcellmigration.
CONTRIBUTORS
AAbe EAntony
UniversityofMichigan,AnnArbor,MI,USA WashingtonUniversitySchoolofMedicine,St.Louis,
MO,USA
PA¨delroth
StockholmUniversity,Stockholm,Sweden EArnold
RutgersUniversity,Piscataway,NJ,USA
AAdessi
UniversityofFlorence,Florence,Italy E-MAro
UniversityofTurku,Turku,Finland
PAgre
MAscoli
JohnsHopkinsBloombergSchoolofPublicHealth,
TheUniversityofIowaCarverCollegeofMedicine,Iowa
Baltimore,MD,USA
City,IA,USA
SAkira
JAAskari
WorldPremierInternationalImmunologyFrontier
UniversityofManchester,Manchester,UK
ResearchCenter,Osaka,Japan;OsakaUniversity,Osaka,
Japan JAtkinson
BrockUniversity,St.Catharines,ON,Canada
EAlani
CornellUniversity,Ithaca,NY,USA DSAuld
HarvardMedicalSchool,Boston,MA,USA
SAl-Attar
WageningenUniversity,Wageningen,TheNetherlands ABacolla
TheUniversityofTexas,Smithville,TX,USA
RWAlexander
WakeForestUniversity,Winston-Salem,NC,USA HBading
UniversityofHeidelberg,Heidelberg,Germany
WAli
SFBairstow
StonyBrookUniversity,StonyBrook,NY,USA
BaxterHealthcareCorporation,RoundLake,IL,USA
AAliverti
TOBaldwin
Universita`degliStudidiMilano,Milan,Italy
UniversityofArizona,Tucson,AZ,USA
ISAmbudkar
SWBallinger
NationalInstituteofDentalandCraniofacialResearch,
UniversityofAlabamaatBirmingham,Birmingham,
Bethesda,MD,USA
AL,USA
AAmcheslavsky
DPBallou
UniversityofCalifornia,Irvine,CA,USA
UniversityofMichigan,AnnArbor,MI,USA
RAAnderson JRBamburg
UniversityofWisconsin,Madison,WI,USA ColoradoStateUniversity,FortCollins,CO,USA
M-LAndre´ola VBandarian
UMR5234CNRS,Universite´VictorSegalen UniversityofMichigan,AnnArbor,MI,USA;University
Bordeaux2,Bordeaux,France ofArizona,Tucson,AZ,USA
ix
x Contributors
DBaniulis KMBernot
LithuanianResearchCentreforAgricultureandForestry, JohnsHopkinsUniversity,BloombergSchoolofPublic
Kaunas,Lithuania Health,Baltimore,MD,USA
OBannach MJBerridge
Heinrich-Heine-Universita¨tDu¨sseldorf,Du¨sseldorf, TheBabrahamInstitute,Cambridge,UK
Germany
JMBerrisford
MedicalResearchCouncilMitochondrialBiologyUnit,
JBarber
Cambridge,UK
ImperialCollege,London,UK
DMBers
KBarbieri
UniversityofCaliforniaatDavis,Davis,CA,USA
UniversityofMinnesota,Minneapolis,MN,USA
ABertoli
BBarker
UniversityofPadua,Padua,Italy
ThomasJeffersonUniversity,Philadelphia,PA,USA
LBettendorff
EJBartlett UniversityofLie`ge,Lie`ge,Belgium
UniversityofSussex,Brighton,UK
UBeuers
CEBarton UniversityofAmsterdam,Amsterdam,TheNetherlands
VanderbiltUniversity,Nashville,TN,USA
PJBeuning
RBassel-Duby NortheasternUniversity,Boston,MA,USA
UniversityofTexasSouthwesternMedicalCenter,Dallas,
ASBhagwat
TX,USA
WayneStateUniversity,Detroit,MI,USA
HBaum
SBheemanaik
King’sCollegeLondon,London,UK
IndianInstituteofScience,Bangalore,India
JWBaynes ABianchi
UniversityofSouthCarolina,Columbia,SC,USA UniversityofSussex,Brighton,UK
WABeard MBiel
NationalInstituteofEnvironmentalHealthSciences, Ludwig-Maximilians-Universita¨t,Munich,Germany
NationalInstitutesofHealth,ResearchTrianglePark,
ABindoli
NC,USA
UniversityofPadua,Padua,Italy
DHBechhofer
JABirchler
MountSinaiSchoolofMedicine,NewYork,NY,USA
UniversityofMissouri,Columbia,MO,USA
SJBenkovic HBirkedal-Hansen
ThePennsylvaniaStateUniversity,UniversityPark,PA, NationalInstitutesofHealth,Bethesda,MD,USA
USA
SMBlackman
RAOBennett JohnsHopkinsUniversitySchoolofMedicine,Baltimore,
StonyBrookUniversitySchoolofMedicine,StonyBrook, MD,USA
NY,USA
SCBlanchard
JLBenovic WeillCornellMedicalCollege,NewYork,NY,USA
ThomasJeffersonUniversity,Philadelphia,PA,USA
REBlankenship
PBernardi WashingtonUniversityinSt.Louis,St.Louis,MO,USA
UniversityofPadua,Padua,Italy
LBBloom
UniversityofFlorida,Gainesville,FL,USA
RBernasconi
InstituteforResearchinBiomedicine,Bellinzona, ABo¨ck
Switzerland UniversityofMunich,Munich,Germany
RBernhardt KLBogan
SaarlandUniversity,Saarbru¨cken,Germany TheUniversityofIowa,IowaCity,IA,USA
Contributors xi
RBorghese RBBrown
UniversityofBologna,Bologna,Italy UniversityofNebraskaMedicalCenter,Omaha,NE,
USA
SBorukhov
UniversityofMedicineandDentistryofNewJersey, MJBrownstein
SchoolofOsteopathicMedicine,Stratford,NJ,USA AzevanPharmaceuticals,Bethlehem,PA,USA
JDBoughterJr. DABryant
UniversityofTennesseeHealthScienceCenter,Memphis, ThePennsylvaniaStateUniversity,UniversityPark,PA,
TN,USA USA
FBouillaud PBrzezinski
CentreNationaldelaRechercheScientifiqueand StockholmUniversity,Stockholm,Sweden
Universite´ParisDescartes,Paris,France
MWBunce
ABoussac TheChildren’sHospitalofPhiladelphia,Philadelphia,
CentreNationaldelaRechercheScientifique,Gif-sur- PA,USA
Yvette,France
RMBurch
ABoveris Naurex,Inc.,Morris,CT,USA
UniversityofBuenosAires,BuenosAires,Argentina
PMJBurgers
NGBowery WashingtonUniversitySchoolofMedicine,St.Louis,
UniversityofBirminghamMedicalSchool,Birmingham, MO,USA
UK
SJWBusby
ABracher TheUniversityofBirmingham,Birmingham,UK
MaxPlanckInstituteofBiochemistry,Martinsried,
MButala
Germany
UniversityofLjubljana,Ljubljana,Slovenia
RABradshaw
DJButtle
UniversityofCalifornia,Irvine,CA,USA
UniversityofSheffield,Sheffield,UK
LBrandi
DBBylund
UniversityofCamerino,Camerino,Italy
UniversityofNebraskaMedicalCenter,Omaha,NE,
UBrandt USA
GoetheUniversity,FrankfurtamMain,Germany
ECadenas
CBrenner UniversityofSouthernCalifornia,LosAngeles,CA,USA
TheUniversityofIowa,IowaCity,IA,USA
MDCahalan
MDBreyer UniversityofCalifornia,Irvine,CA,USA
VanderbiltUniversity,Nashville,TN,USA
RCammack
RMBreyer King’sCollegeLondon,London,UK
VanderbiltUniversity,Nashville,TN,USA
MCampeol
MBrini UniversityofPaduaandVenetianInstituteofMolecular
UniversityofPadua,Padua,Italy Medicine,Padua,Italy
HLBrockman JCapecci
UniversityofMinnesota,Austin,MN,USA TuftsUniversitySchoolofMedicine,Boston,MA,USA
SJJBrouns ECarafoli
WageningenUniversity,Wageningen,TheNetherlands UniversityofPadua,Padua,Italy
DABrown JJCaramelo
StateUniversityofNewYork,StonyBrook,NY,USA Fundacio´nInstitutoLeloir,BuenosAires,Argentina
EMBrown GCarignani
HarvardMedicalSchool,Boston,MA,USA UniversityofPadua,Padua,Italy