Structural Proteomics: High-Throughput Methods

350 Pages·2021·10.73 MB·English

by  Raymond J. Owens

Methods in
Molecular Biology 2305
Raymond J. Owens Editor
Structural
Proteomics
High-Throughput Methods
Third Edition
M M B
ETHODS IN OLECULAR IO LO GY
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JohnM.Walker
School of Lifeand MedicalSciences
University ofHertfordshire
Hatfield, Hertfordshire, UK
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Structural Proteomics
High-Throughput Methods
Third Edition
Edited by
Raymond J. Owens
The Rosalind Franklin Institute, Harwell Science Campus, Didcot, UK
Editor
RaymondJ.Owens
TheRosalindFranklinInstitute
HarwellScienceCampus
Didcot,UK
ISSN1064-3745 ISSN1940-6029 (electronic)
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Preface
2021 marksthe 50thAnniversary oftheProtein DataBank(PDB),the global initiativefor
the curation and dissemination of macromolecular structures to the international research
community. It is therefore appropriate that the opening chapter in this third edition of
StructuralProteomicsintheMethodsinMolecularBiologyseries,byVelankarandcolleagues
from the PDB, summarizes the current status of the PDB and its role in the future of
structural biology. The PDB contains over 160,000 protein structures, but this is still a
fractionofthetotalnumberofproteinsequencesavailablefromgenomicdata.Therefore,in
silico methods for predicting protein structure from sequence play an important part in
structural proteomics. In the following two chapters, Edmunds and McGuffin and
Madhusudhan et al. provide comprehensive and complementary user guides to the bioin-
formatics tools and resources for ab initio modeling of proteins and complexes, including
ligand-dockingalgorithms.
Structural proteomics has been one of the key drivers for the development of stream-
lined workflows for sample preparation. The production of high-quality samples for struc-
tural studies, particularly mammalian membrane proteins and protein complexes, remains
challenging.Newprotocolsfortacklingthesedifficult-to-expresstargetsinhighereukaryote
cells(insectandmammaliancells)aredescribedinthechaptersbyKrasnoselskaandvanden
Heuvel for the transient expression of membrane proteins in mammalian and insect cells,
respectively. Novel approaches to protein production include the genome engineering of
either the expression host or vector. Poterszman et al. describe a gene editing protocol to
introduce purification tags into endogenous proteins for purification of macromolecular
complexes. In the next two chapters, the crossover into synthetic biology is covered by
BergerandKubickandcolleagues.Protocolsformodifyingthegenomeofthebaculovirus,a
widelyusedexpressionvector,toproduceanovelsyntheticvirusarereportedbytheBerger
group. In the next chapter, Kubick et al. describe incorporating non-natural amino acids
usingmammaliancell-freeexpressiontoproducefluorescentlabelingofantibodies.
IsotopiclabelingofendogenousproteinsforNMRhasnowbeenextendedtomamma-
liancells,andBaldusetal.describetheproductionofisotopicallylabelledmicrotubulesand
analysis of their interaction with MT-associated protein by solid-state NMR. X-ray crystal-
lographyremainsakeytechniqueforstructuralanalysis;OrvilleandAllerpresentthestate-
of-the-art in the use of electron-free lasers for time-resolved crystallography. Since the
publication of the last edition of Methods in Molecular Biology focused on Structural
Proteomics,advancesindetectortechnologyandsoftwarealgorithmshavebroughtmicros-
copy(cryo-EM)totheforefrontofstructuralbiology.Therefore,fivechaptersinthisthird
edition are devoted to aspects of the use of electrons in structural biology. The so-called
resolution revolution now means that the structures of large proteins and complexes can
now be routinely determined at near-atomic resolution. Experimental and data analysis
workflowsaredescribedinthechaptersbyRenaultandSorzano,respectively.Theintroduc-
tion of phase contrast methods has contributed to increasing resolution, and a guide to
settingupandtroubleshootingtheVoltaphaseplateincryo-EMdatacollectionisdetailed
in the chapter by von Loeffelholz and Klaholz. In addition to single particle techniques,
modern methods in cryo-EM include cryoelectron tomography and Microcrystal Electron
Diffraction (MicroED). The combination of using focused ion beam milling to prepare
v
vi Preface
lamella thin enough for electrons to penetrate with cryo-EM imaging is providing protein
structural information within cells. The cryoelectron tomography workflow for sample
preparation and analysis is described in the chapter by Nova´cˇek et al. MicroED described
byDaneliusandGonenisthenewestcryo-EMtechniqueenablingtherapiddetermination
of peptide and organic molecule structures from microcrystalline powders. The technique
has important applications in the structural analysis of pharmaceutical compounds and
naturalproducts.
I am grateful to all the contributors to this book for sharing their experience and
expertise. I would also like to thank the Methods in Molecular Biology series editor, John
Walker, for his guidance inpreparing this volume and Springer for theopportunity to edit
thethirdedition.
Didcot,UK RaymondJ.Owens
Contents
Preface ..................................................................... v
Contributors................................................................. ix
PART I STRUCTURAL BIOINFORMATICS
1 TheProteinDataBankArchive........................................... 3
SameerVelankar,StephenK.Burley,GenjiKurisu,
JeffreyC.Hoch,andJohnL.Markley
2 ComputationalMethodsfor theElucidationofProteinStructure
andInteractions ........................................................ 23
NicholasS.EdmundsandLiamJ.McGuffin
3 MethodsforMolecularModellingofProteinComplexes .................... 53
TejashreeRajaramKanitkar,NeeladriSen,SanjanaNair,
NeeleshSoni,KaustubhAmritkar,YogendraRamtirtha,
andM.S.Madhusudhan
PART II PROTEIN PRODUCTION
4 High-LevelProductionofRecombinantEukaryoticProteins
fromMammalianCellsUsingLentivirus................................... 83
EsterBehielsandJonathanElegheert
5 TransientTransfectionandExpressionofEukaryoticMembrane
ProteinsinExpi293FCellsandTheirScreeningonaSmallScale:
ApplicationforStructuralStudies......................................... 105
GannaO.Krasnoselska,MaudDumoux,NadishaGamage,
HarishCheruvara,JamesBirch,AndrewQuigley,
andRaymondJ.Owens
6 ReproducibleandEasyProductionofMammalianProteins
byTransientGeneExpressioninHighFiveInsectCells ..................... 129
MarenSchubert,ManfredNimtz,FedericoBertoglio,
StefanSchmelz,PeerLukat,andJoopvandenHeuvel
7 SynBac:EnhancedBaculovirusGenomesbyIterativeRecombineering ........ 141
HannahCrocker,BarbaraGorda,MartinPelosse,
DeepakBalajiThimiriGovindaRaj,andImreBerger
8 GeneTaggingwiththeCRISPR-Cas9SystemtoFacilitate
MacromolecularComplexPurification..................................... 153
SylvainGeny,SimonPichard,ArnaudPoterszman,
andJean-PaulConcordet
vii
viii Contents
9 SynthesisofFluorescentlyLabeledAntibodiesUsingNon-Canonical
AminoAcidsinEukaryoticCell-FreeSystems .............................. 175
MarlittStech,Nathana¨elRakotoarinoro,TamaraTeichmann,
AnneZemella,LenaThoring,andStefanKubick
PART III STRUCTURE DETERMINATION
10 Solid-StateNMRSpectroscopyforStudyingMicrotubules
andMicrotubule-AssociatedProteins...................................... 193
YanzhangLuo,ShengqiXiang,AlessandraLuciniPaioni,
AgnesAdler,PeterJanHooikaas,A.S.Jijumon,CarstenJanke,
AnnaAkhmanova,andMarcBaldus
11 DynamicStructuralBiologyExperimentsatXFEL
orSynchrotronSources.................................................. 203
PierreAllerandAllenM.Orville
12 FromTubetoStructure:SPACryo-EMWorkflowUsingApoferritin
asanExample .......................................................... 229
ChristophA.Diebolder,RebeccaS.Dillard,andLudovicRenault
13 ImageProcessinginCryo-ElectronMicroscopyofSingleParticles:
ThePowerofCombiningMethods ....................................... 257
CarlosOscarS.Sorzano,AmayaJime´nez-Moreno,DavidMaluenda,
ErneyRamı´rez-Aportela,MartaMartı´nez,AnaCuervo,RobertMelero,
JoseJavierConesa,RubenSa´nchez-Garcı´a,DavidStrelak,JiriFilipovic,
EstrellaFerna´ndez-Gime´nez,FedericodeIsidro-G(cid:1)omez,DavidHerreros,
PabloConesa,LauradelCan˜o,YuniorFonseca,JorgeJime´nezdelaMorena,
JoseRamonMacı´as,PatriciaLosana,RobertoMarabini,
andJose-MariaCarazo
14 SetupandTroubleshootingofVoltaPhasePlateCryo-EM
DataCollection......................................................... 291
OttilievonLoeffelholzandBrunoP.Klaholz
15 Cryo-FocusedIonBeamLamellaPreparationProtocol
forinSituStructuralBiology............................................. 301
JanaMoravcova´,RadkaDopitova´,Matya´ˇsPinkas,andJirˇı´ Nova´cˇek
16 ProteinandSmallMoleculeStructureDetermination
bytheCryo-EMMethodMicroED....................................... 323
EmmaDaneliusandTamirGonen
Index ...................................................................... 343
Contributors
AGNESADLER • NMRSpectroscopy,BijvoetCenter forBiomolecularResearch,Utrecht
University,Utrecht,TheNetherlands
ANNAAKHMANOVA • CellBiology,NeurobiologyandBiophysics,DepartmentofBiology,
FacultyofScience,UtrechtUniversity,Utrecht,TheNetherlands
PIERREALLER • DiamondLightSourceLtd,Didcot,UK
KAUSTUBHAMRITKAR • IndianInstituteofScienceEducationandResearchPune,Pashan,
Pune,India
MARCBALDUS • NMRSpectroscopy,BijvoetCenter forBiomolecularResearch,Utrecht
University,Utrecht,TheNetherlands
ESTERBEHIELS • Univ.Bordeaux,CNRS,InterdisciplinaryInstituteforNeuroScience
(IINS),UMR5297CNRS/UB,Bordeaux,France
IMREBERGER • BristolSyntheticBiologyCentreBrisSynBio,BiomedicalSciences,Schoolof
Biochemistry,UniversityofBristol,Bristol,UK;SchoolofChemistry,MaxPlanckBristol
CentreforMinimalBiology,Bristol,UK
FREDERICOBERTOGLIO • DepartmentofBiotechnology,InstitutfuerBiochemie,
BiotechnologieundBioinformatik, TechnischeUniversitaetBraunschweig,
Braunschweig,Germany
JAMESBIRCH • DiamondLightSourceLtd,Didcot,UK
STEPHENK.BURLEY • ResearchCollaboratoryforStructuralBioinformaticsProteinData
Bank,CenterforIntegrativeProteomicsResearch,InstituteforQuantitativeBiomedicine,
Rutgers,TheStateUniversityofNewJersey,Piscataway,NJ,USA;Departmentof
ChemistryandChemicalBiology,Rutgers,TheStateUniversityofNewJersey,Piscataway,
NJ,USA;RutgersCancerInstituteofNewJersey,RobertWoodJohnsonMedicalSchool,
NewBrunswick,NJ,USA;SkaggsSchoolofPharmacyandPharmaceuticalSciencesand
SanDiegoSupercomputerCenter,UniversityofCalifornia,SanDiego,LaJolla,CA,USA
LAURA DELCAN˜O • NationalCentreforBiotechnology(CSIC),Madrid,Spain
JOSE-MARIACARAZO • NationalCentreforBiotechnology(CSIC),Madrid,Spain
HARISHCHERUVARA • DiamondLightSourceLtd,Didcot,UK
JEAN-PAULCONCORDET • LaboratoireStructureetInstabilite´desGe´nomes,InsermU1154,
CNRSUMR7196,MuseumNationald’HistoireNaturelle,Paris,France
JOSEJAVIER CONESA • NationalCentreforBiotechnology(CSIC),Madrid,Spain
PABLO CONESA • NationalCentreforBiotechnology(CSIC),Madrid,Spain
HANNAHCROCKER • BristolSyntheticBiologyCentreBrisSynBio,BiomedicalSciences,School
ofBiochemistry,UniversityofBristol,Bristol,UK
ANACUERVO • NationalCentreforBiotechnology(CSIC),Madrid,Spain
EMMADANELIUS • DepartmentofBiologicalChemistry,UniversityofCaliforniaLosAngeles,
LosAngeles,CA,USA;DepartmentofPhysiology,UniversityofCaliforniaLosAngeles,Los
Angeles,CA,USA;HowardHughesMedicalInstitute,UniversityofCaliforniaLos
Angeles,LosAngeles,CA,USA
CHRISTOPHA.DIEBOLDER • TheNetherlandsCentreforElectronNanoscopy(NeCEN),
LeidenUniversity,Leiden,TheNetherlands
REBECCA S.DILLARD • TheNetherlandsCentreforElectronNanoscopy(NeCEN),Leiden
University,Leiden,TheNetherlands
ix