Encyclopedia of Biological Chemistry, Second Edition PDF
Preview Encyclopedia of Biological Chemistry, Second Edition
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 Academic Press is an imprint of Elsevier AcademicPressisanimprintofElsevier 32JamestownRoad,LondonNW17BY,UK 30CorporateDrive,Suite400,BurlingtonMA01803,USA 525BStreet,Suite1900,SanDiego,CA92101-4495,USA 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 Nopartofthispublicationmaybereproduced,storedinaretrievalsystemortransmittedinanyformorbyanymeanselectronic, mechanical,photocopying,recordingorotherwisewithoutthepriorwrittenpermissionofthepublisher. PermissionsmaybesoughtfromElsevier’sScience&TechnologyRightsdepartmentinOxford,UK:phone(þ44)(0)1865843830; fax(þ44)(0)1865853333;email:[email protected]. AlternativelyyoucansubmityourrequestonlinebyvisitingtheElsevierwebsiteathttp://elsevier.com/locate/permissionsandselecting ObtainingpermissiontouseElseviermaterial. Notice Noresponsibilityisassumedbythepublisherforanyinjuryand/ordamagetopersonsorpropertyasamatterofproductsliability, negligenceorotherwise,orfromanyuseoroperationofanymethods,products,instructionsorideascontainedinthematerialherein. BritishLibraryCataloguinginPublicationData AcataloguerecordforthisbookisavailablefromtheBritishLibrary LibraryofCongressCataloging-in-PublicationData AcatalogrecordforthisbookisavailablefromtheLibraryofCongress ISBN:978-0-12-378630-2 ForinformationonallElsevierpublications visitourwebsiteatstore.elsevier.com PrintedandboundintheUnitedStatesofAmerica 13 14 15 16 17 10 9 8 7 6 5 4 3 2 Editorial:JoCollett,CariOwen Production:JustinTaylor 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
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