Protein Engineering

443 Pages·2004·7.071 MB·English

by  Dan E. Robertson and Joseph P. Noel (Eds.)

METHODS IN ENZYMOLOGY
EDITORS-IN-CHIEF
John N. Abelson Melvin I. Simon
DIVISIONOFBIOLOGY
CALIFORNIAINSTITUTEOFTECHNOLOGY
PASADENA,CALIFORNIA
FOUNDINGEDITORS
Sidney P. Colowick and Nathan O. Kaplan
Contributors to Volume 388
Articlenumbersareinparenthesesandfollowingthenamesofcontributors.
Affiliationslistedarecurrent.
OmarB.Alexander(12),Departmentof JoelR.Cherry(15),NovozymesBiotech,
Biochemistry, Emory University School Inc.,Davis,California95616
of Medicine, Rollins Research Center,
Atlanta,Georgia3022 DavidW.Colby(27),DepartmentofChe-
mical Engineering andBiologicalEngi-
Frances H. Arnold (4), Division of neeringDivision,MassachusettsInstitute
Chemistry and Chemical Engineering, of Technology, Cambridge, Massachu-
California Institute of Technology, setts02139
Pasadena,California91125
Atze T. Das (28), Department of Hu-
Werner Basenmatter (9), Laboratory of
man Retrovirology, Academic Medi-
Organic Chemistry, Swiss Federal Insti-
cal Center, 1105-AZ Amsterdam, The
tute of Technology, Zurich CH-8093,
Netherlands
Switzerland
MarkusBaumann(18),InstituteofChem- JonathanS.Dordick(13),Chemicaland
BiologicalEngineeringDepartment,Re-
istry and Biochemistry, Department of
nsselaerPolytechnicInstitute,Troy,New
TechnicalChemistryandBiotechnology,
York12180
Greifswald University, Greifswald D-
17487,Germany Mark J. Dycaico (11), Diversa Corpora-
Stephen J. Benkovic (6), Department of tion,SanDiego,California92121
Chemistry, Pennsylvania State Univer-
JeffreyEndelman(4),DivisionofChem-
sity,UniversityPark,Pennsylvania16802
istryandChemicalEngineering,Califor-
BenBerkhout(28),DepartmentofHuman nia Institute of Technology, Pasadena,
Retrovirology,AcademicMedicalCenter, California91125
1105-AZAmsterdam,TheNetherlands
Fred Fenel (14), Carbozyme Ltd., 02015
Robert R. Birge (26), Departments of Espoo,Finland
ChemistryandMolecularandCellBiol-
ogy, University of Connecticut, Storrs, Dirk Franke (20), Department of Chem-
Connecticut06269 istry,TheScrippsResearchInstitute,La
Jolla,California92037
Uwe T. Bornscheuer (18), Institute of
Chemistry and Biochemistry, Depart- Melissa L. Geddie (12), Department of
ment of Technical Chemistry and Bio- Biochemistry, Emory University School
technology, Greifswald University, of Medicine, Rollins Research Center,
GreifswaldD-17487,Germany Atlanta,Georgia3022
JosephChappell(8),DepartmentofAgr- Christilyn P. Graff (27), Department of
onomy:PlantPhysiology,Biochemistry, Chemical Engineering and Biological
and Molecular Biology Program, Col- EngineeringDivision,MassachusettsIn-
lege of Agriculture, University of Ken- stituteofTechnology,Cambridge,Massa-
tucky,Lexington,Kentucky40502 chusetts02139
ix
x contributors to volume 388
Kevin A. Gray (1), Diversa Corporation Peter Kast (9), Laboratory of Organic
SanDiego,California92121 Chemistry, Swiss Federal Institute of
Technology, Zurich CH-8093, Switzer-
Bryan T. Greenhagen (8), College of
land
Agriculture, University of Kentucky,
Lexington,Kentucky40502 Brenda A. Kellogg (27), Department of
Chemical Engineering and Biological
Shigeaki Harayama (2), Biotechnology
EngineeringDivision,MassachusettsIn-
DevelopmentCenter,NationalInstituteof
stitute of Technology, Cambridge, Mas-
Technology and Evaluation, Kisarazu-
sachusetts02139
shi,Chiba292-0818,Japan
Chaitan Khosla (23), Departments of
ErikHenke(18),InstituteofChemistryand
Chemical Engineering, Chemistry, and
Biochemistry, Department of Technical
Biochemistry,StanfordUniversity,Stan-
Chemistry and Biotechnology, Greifs-
ford,California94305
wald University, Greifswald D-17487,
Germany Miho Kikuchi (2), Marine Biotechnology
Institute,KamaishiWate026-0001,Japan
JasonR.Hillebrecht(26),Departmentsof
ChemistryandMolecularandCellBiol- Masanobu Kitagawa (7), Department of
ogy, University of Connecticut, Storrs, Biosciences and Informatics, Faculty of
Connecticut06269 Science and Technology, Keio Univer-
sity,Yokohama223-8522,Japan
Donald Hilvert (9), Laboratory of
Organic Chemistry, Swiss Federal Insti- KanehisaKojoh(7),DepartmentofBios-
tute of Technology, Zurich CH-8093, ciences and Informatics, Faculty of
Switzerland ScienceandTechnology,KeioUniversity,
Yokohama223-8522,Japan
Suk-Bong Hong (22), Wyeth Research,
Cambridge,Massachusetts60064 MonikaKonarzycka-Bessler(18),Insti-
tuteofChemistryandBiochemistry,De-
AlexanderR.Horswill(6),Department
partment of Technical Chemistry and
of Chemistry, Pennsylvania State Uni-
Biotechnology, Greifswald University,
versity, University Park, Pennsylvania
GreifswaldD-17487,Germany
16802
Jeremy F. Koscielecki (26), Department
Che-Chang Hsu (20), Department of
ofChemistry,UniversityofConnecticut,
Chemistry, The Scripps Research Insti-
Storrs,Connecticut06269
tute,LaJolla,California92037
KeithA.Kretz(1),DiversaCorporation
JanneJa¨nis(14),DepartmentofChemis-
SanDiego,California92121
try, University of Joensuu, 80101 Joen-
suu,Finland Pawan Kumar (23), Department of Che-
mical Engineering, Stanford University,
OsamuKagami(2),MarineBiotechnology
Stanford,California94305
Institute,KamaishiWate026-0001,Japan
MikeLafferty(11),DiversaCorporation,
Satoshi Kaneko (3), National Food
SanDiego,California92121
Research Institute, Biological Function
Division, Molecular Function Labora- MichaelH.Lamsa(15),NovozymesBio-
tory,Tsukuba,Ibaraki305-8642,Japan tech,Inc.,Davis,California95616
contributors to volume388 xi
Pyung C. Lee (25), Department of Bio- Hee-SungPark(17),DepartmentofBiolo-
chemistry, University of Minnesota, St. gical Studies, Korea Advanced Institute
Paul,Minnesota55126 ofScienceandTechnology,Yusung-Gu,
Taejon305-701,Korea
Matti Leisola (14), Laboratory of Bio-
processEngineering,HelsinkiUniversity David E. Paschon (10), Department of
ofTechnology,02015-HUT,Finland Chemical and Biomolecular Engi-
neering, Johns Hopkins University,
Uwe Linne (24), Biochemie/Fachbereich Baltimore,Maryland21218
Chemie, Philipps-Universita˜t Marburg,
Frank M. Raushel (22), Department of
HansMeerweinStrasse,35032Marburg,
Chemistry,TexasA&MUniversity,Col-
Germany
legeStation,Texas77843
PaulE.O’Maille(8),StructuralBiology Manfred T. Reetz (21), Max-Planck-
Laboratory,TheSalkInstituteforBiolo-
Institutfu¨rKohlenforschung,45470Mu¨l-
gicalStudies,LaJolla,California92037
heimAnDerRuhr,Germany
Mohamed A. Marahiel (24), Biochemie/ Toby H. Richardson (1), Diversa Cor-
Fachbereich Chemie, Philipps-Universi- porationSanDiego,California92121
ta˜t Marburg, Hans-Meerwein Strasse,
35032Marburg,Germany DanE.Robertson(1),DiversaCorpora-
tionSanDiego,California92121
Ichiro Matsumura (12), Department of
Lori A. Rowe (12), Department of Bio-
Biochemistry, Emory University School
chemistry, Emory University School of
of Medicine, Rollins Research Center,
Medicine, Rollins Research Center,
Atlanta,Georgia3022
Atlanta,Georgia3022
Benjamin N. Mijts (25), Department of
Marlen Schmidt (18), Institute of Chem-
Biochemistry, University of Minnesota,
istry and Biochemistry, Department of
St.Paul,Minnesota55126
TechnicalChemistryandBiotechnology,
Todd A. Naumann (6), Department of Greifswald University, Greifswald D-
Chemistry, Pennsylvania State Univer- 17487,Germany
sity,UniversityPark,Pennsylvania16802 Rolf D. Schmid (19), Institute ofTechni-
JosephP.Noel(8),StructuralBiologyLa- calBiochemistry,UniversityofStuttgart,
boratory,TheSalkInstituteforBiologi- D-70569Stuttgart,Germany
calStudies,LaJolla,California92037 Claudia Schmidt-Dannert (25), Depart-
Ki-HoonOh(17),R&DCenterofBiopro- ment of Biochemistry, University of
ducts, Institute of Science and Technol- Minnesota,St.Paul,Minnesota55126
ogy, C.J. Corporation, Ichon 467-810, Jay M. Short (1), Diversa Corporation
Korea
SanDiego,California92121
MichikoOnimaru(7),DepartmentofBios- Jonathan J. Silberg (4), Division of
ciences and Informatics, Faculty of Chemistry and Chemical Engineering,
ScienceandTechnology,KeioUniversity, CaliforniaInstituteofTechnology,Pasa-
Yokohama223-8522,Japan dena,California91125
MarcOstermeier(10),LaboratoryofOr- Grazyna E. Sroga (13), Chemical and
ganic Chemistry, Swiss Federal Insti- BiologicalEngineeringDepartment,Re-
tute of Technology, Zurich CH-8093, nsselaerPolytechnicInstitute,Troy,New
Switzerland York12180
xii contributors to volume 388
Boris Steipe (16), University of Toronto, Vlada B. Urlacher (19), Institute of
Program in Proteomics and Bioinfor- Technical Biochemistry, University of
matics Departments of Biochemistry Stuttgart,D-70569Stuttgart,Germany
and Molecular and Medical Genetics,
Koen Verhoef (28), Department of Hu-
TorontoM5S1A1,Ontario,Canada
man Retrovirology, Academic Medical
HakSung-Kim(17),DepartmentofBiolo- Center,1105-AZAmsterdam,TheNeth-
gical Studies, Korea Advanced Institute erlands
ofScienceandTechnology,Yusung-Gu,
KevinJ.Wise(26),DepartmentsofChem-
Taejon305-701,Korea
istry and Molecular and Cell Biology,
JeffreyS.Swers(27),DepartmentofChe- University of Connecticut, Storrs, Con-
mical Engineering andBiologicalEngi- necticut06269
neeringDivision,MassachusettsInstitute
K. Dane Wittrup (27), Department of
of Technology, Cambridge, Massachu-
Chemical Engineering and Biological
setts02139
EngineeringDivision,Massachusetts In-
Noriko Tabata (7), Department of Bios- stituteofTechnology,Cambridge,Massa-
ciences and Informatics, Faculty of chusetts02139
Science and Technology, Keio Univer-
Chi-Huey Wong (20), Department of
sity,Yokohama223-8522,Japan
Chemistry, The Scripps Research Insti-
Xuqiu Tan (1), Diversa Corporation San tute,LaJolla,Californai92037
Diego,California92121
Hiroshi Yanagawa (7), Department of
Yi Tang (23), Department of Chemical Biosciences and Informatics, Faculty of
Engineering, Stanford University, Stan- Science and Technology, Keio Univer-
ford,California94305* sity,Yokohama223-8522,Japan
Ming-DawTsai(8),JohnstonLaboratory, Yik A. Yeung (27), Department of Che-
DepartmentsofChemistryandBiochem- micalEngineeringandBiological Engi-
istry, Ohio State University, Columbus, neeringDivision,MassachusettsInstitute
Ohio43210 of Technology, Cambridge, Massachu-
setts02139
ToruTsuji(7),DepartmentofBiosciences
andInformatics,FacultyofScienceand HuiminZhao(5),DepartmentofChemical
Technology,KeioUniversity,Yokohama andBiologicalEngineering,Universityof
223-8522,Japan IllinoisatUrbana,Urbana,Illinois61801
Ossi Turunen (14), Laboratory of Bio-
processEngineering,HelsinkiUniversity
ofTechnology,02015-HUT,Finland
*Currentaddress:DepartmentofChemicalEngineering,UniversityofCalifornia,LosAngeles,
California90095.
Preface
Basedupona few principlefolding paradigms, proteins haveevolvedto carry
out a vast number of highly tuned, interactive functions within the metabolic
web.Theprocessofnaturalselection,usingalimitedsetofaminoacids,afew
basic mechanisms for mutation and recombination, and the functional output
oftheresultantthreedimensionalarchitecture,isabletoparseanearlyinfinite
varietyofaminoacidsequencesandlengthstooptimizephenotypicparameters
and protein functions in the context of the cell, the organism, and sometimes
theorganism’senvironmentalniche.Theresultsofthisselectionprocessarea
testamentto theplasticity of protein foldsand the underlyingchemistry asso-
ciated with a particular three dimensional arrangement of amino acids, which
togethervalidatetheefficiencyofNature’sevolutionaryprocessperfectedover
severalbillionyears.
Within the last decade, a confluence of new technologies in molecular bio-
logy, biochemistry, and automation engineering has revolutionized our ability
to understand, harness, and ultimately accelerate the evolutionary process.
Usingcomprehensivemutagenesis,largelibrariesofgenesequencesandtheir
associatedvariantscanberapidlycreatedand,withintelligent,targetedassays,
screened for the acquisition and optimization of any intensive or extensive
phenotypic variable. Substrate and enantiomeric selectivity, catalytic activity,
relief from inhibition, temperature, or oxidant stability, operating optima as
wellasefficiencyofgeneexpressioninnativeandheterologoushosts,areafew
oftheparametersthathavebeenoptimizedinalaboratorysetting.Nearlyall
general protein classes have been targeted for engineering and found to be
amenable to the rapid acquisition of adaptive changes necessary for new
applications. Those of us who may have thought that Nature had already
reached seeming perfection in the form of optimized gene products were
surprised by the seemingly unlimited potential for phenotypic enhancement
and ex situ application of proteins. These new technologies have engendered
theexplorationofmanynewmedical,agricultural,andindustrialopportunities.
Wehavedividedthisvolumeintofivesectionstobesthighlightparticularly
inventiveandeffectivelaboratoryevolutiontechniques,somehighthroughput
and ultra high throughput screening technologies, and some results of the
application of these technology developments in the fields of industrial
catalysis, pathway engineering, protein therapeutics, and device design. We
hope to present a balanced picture of the current state of the art as it exists
in2004.
xiii
xiv PREFACE
Wethankallofthecontributingauthorsforsharingtheirknowledgewiththe
scientificcommunity.Thisfieldisinitsinfancyanditisbytheapplicationand
extensionofeffortslikethesethatnewknowledgeandnewtechnologieswillbe
builtuponthisalreadyfirmlyrootedfoundation.
Dan E. Robertson
Joseph P. Noel
METHODS IN ENZYMOLOGY
VolumeI.PreparationandAssayofEnzymes
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeII.PreparationandAssayofEnzymes
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeIII.PreparationandAssayofSubstrates
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeIV.SpecialTechniquesfortheEnzymologist
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeV.PreparationandAssayofEnzymes
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeVI.PreparationandAssayofEnzymes(Continued)
PreparationandAssayofSubstrates
SpecialTechniques
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeVII.CumulativeSubjectIndex
EditedbySidneyP.ColowickandNathanO.Kaplan
VolumeVIII.ComplexCarbohydrates
EditedbyElizabethF.NeufeldandVictorGinsburg
VolumeIX.CarbohydrateMetabolism
EditedbyWillisA.Wood
VolumeX.OxidationandPhosphorylation
EditedbyRonaldW.EstabrookandMaynardE.Pullman
VolumeXI.EnzymeStructure
EditedbyC.H.W.Hirs
VolumeXII.NucleicAcids(PartsAandB)
EditedbyLawrenceGrossmanandKivieMoldave
VolumeXIII.CitricAcidCycle
EditedbyJ.M.Lowenstein
VolumeXIV.Lipids
EditedbyJ.M.Lowenstein
VolumeXV.SteroidsandTerpenoids
EditedbyRaymondB.Clayton
xv
xvi methods in enzymology
VolumeXVI.FastReactions
EditedbyKennethKustin
VolumeXVII.MetabolismofAminoAcidsandAmines(PartsAandB)
EditedbyHerbertTaborandCeliaWhiteTabor
VolumeXVIII.VitaminsandCoenzymes(PartsA,B,andC)
EditedbyDonaldB.McCormickandLemuelD.Wright
VolumeXIX.ProteolyticEnzymes
EditedbyGertrudeE.PerlmannandLaszloLorand
VolumeXX.NucleicAcidsandProteinSynthesis(PartC)
EditedbyKivieMoldaveandLawrenceGrossman
VolumeXXI.NucleicAcids(PartD)
EditedbyLawrenceGrossmanandKivieMoldave
VolumeXXII.EnzymePurificationandRelatedTechniques
EditedbyWilliamB.Jakoby
VolumeXXIII.Photosynthesis(PartA)
EditedbyAnthonySanPietro
VolumeXXIV.PhotosynthesisandNitrogenFixation(PartB)
EditedbyAnthonySanPietro
VolumeXXV.EnzymeStructure(PartB)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXXVI.EnzymeStructure(PartC)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXXVII.EnzymeStructure(PartD)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXXVIII.ComplexCarbohydrates(PartB)
EditedbyVictorGinsburg
VolumeXXIX.NucleicAcidsandProteinSynthesis(PartE)
EditedbyLawrenceGrossmanandKivieMoldave
VolumeXXX.NucleicAcidsandProteinSynthesis(PartF)
EditedbyKivieMoldaveandLawrenceGrossman
VolumeXXXI.Biomembranes(PartA)
EditedbySidneyFleischerandLesterPacker
VolumeXXXII.Biomembranes(PartB)
EditedbySidneyFleischerandLesterPacker
VolumeXXXIII.CumulativeSubjectIndexVolumesI-XXX
EditedbyMarthaG.DennisandEdwardA.Dennis
VolumeXXXIV.AffinityTechniques(EnzymePurification:PartB)
EditedbyWilliamB.JakobyandMeirWilchek
methodsin enzymology xvii
VolumeXXXV.Lipids(PartB)
EditedbyJohnM.Lowenstein
VolumeXXXVI.HormoneAction(PartA:SteroidHormones)
EditedbyBertW.O’MalleyandJoelG.Hardman
VolumeXXXVII.HormoneAction(PartB:PeptideHormones)
EditedbyBertW.O’MalleyandJoelG.Hardman
VolumeXXXVIII.HormoneAction(PartC:CyclicNucleotides)
EditedbyJoelG.HardmanandBertW.O’Malley
VolumeXXXIX.HormoneAction(PartD:IsolatedCells,Tissues,
andOrganSystems)
EditedbyJoelG.HardmanandBertW.O’Malley
VolumeXL.HormoneAction(PartE:NuclearStructureandFunction)
EditedbyBertW.O’MalleyandJoelG.Hardman
VolumeXLI.CarbohydrateMetabolism(PartB)
EditedbyW.A.Wood
VolumeXLII.CarbohydrateMetabolism(PartC)
EditedbyW.A.Wood
VolumeXLIII.Antibiotics
EditedbyJohnH.Hash
VolumeXLIV.ImmobilizedEnzymes
EditedbyKlausMosbach
VolumeXLV.ProteolyticEnzymes(PartB)
EditedbyLaszloLorand
VolumeXLVI.AffinityLabeling
EditedbyWilliamB.JakobyandMeirWilchek
VolumeXLVII.EnzymeStructure(PartE)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXLVIII.EnzymeStructure(PartF)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeXLIX.EnzymeStructure(PartG)
EditedbyC.H.W.HirsandSergeN.Timasheff
VolumeL.ComplexCarbohydrates(PartC)
EditedbyVictorGinsburg
VolumeLI.PurineandPyrimidineNucleotideMetabolism
EditedbyPatriciaA.HoffeeandMaryEllenJones
VolumeLII.Biomembranes(PartC:BiologicalOxidations)
EditedbySidneyFleischerandLesterPacker
VolumeLIII.Biomembranes(PartD:BiologicalOxidations)
EditedbySidneyFleischerandLesterPacker