Rhodopsin: Methods and Protocols (Methods in Molecular Biology, 2501)

371 Pages·2022·9.783 MB·English

by  Valentin Gordeliy (editor)

Methods in
Molecular Biology 2501
Valentin Gordeliy
Editor
Rhodopsin
Methods and Protocols
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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Rhodopsin
Methods and Protocols
Edited by
Valentin Gordeliy
Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
Editor
ValentinGordeliy
InstitutdeBiologieStructurale(IBS)
Universite´GrenobleAlpes,CEA,CNRS
Grenoble,France
ISSN1064-3745 ISSN1940-6029 (electronic)
MethodsinMolecularBiology
ISBN978-1-0716-2328-2 ISBN978-1-0716-2329-9 (eBook)
https://doi.org/10.1007/978-1-0716-2329-9
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Preface
Sincethediscoveryofthefirstmicrobialrhodopsin—alight-drivenprotonpumpbacterio-
rhodopsin(BR),asevenalphahelicalmembraneproteincomprisingtheretinal,in1971,BR
was a major driver of groundbreaking developments in membrane protein research. BR
studies stimulated important methodological developments in the fields like electron
microscopy and membrane protein crystallization. However, before 1999 there were only
several and only archaeal known rhodopsins, functioning as proton, chloride pumps, and
also sensory rhodopsins. At the end of the twentieth century not many of us, if any at all,
wouldimagineaneweraoftherhodopsinworldanditscontributionstotheapplicationsin
neuroscience.Notmanyenthusiastswereeager tocontinueworkingwiththeseproteins.
Butnatureplaystricksonus.Anewmicrobialrhodopsinerastartedin1999–2000when
thefirstbacterialrhodopsin,aprotonpump,wasdiscovered.Lateritappearedthatthereare
unexpectedly many rhodopsins and they are present in all the domains of life and even in
viruses. It turned out (which is amazing) that they execute such a diversity of functions
being“nearlythesame.”However,inthelate1990snobodycouldpredictgroundbreaking
discoveries of other rhodopsin functions and among them, probably the most significant
one,thediscoveryofchannelrhodopsins(ChRs).Forlifescience,itisthediscoveryofthe
proteinswhicharedifferentfromanyknownchannels.Forneuroscience,itwasthebiggest
luck.ChRsareprobablyamongtwomostimportant proteinsinapplicationsandopeneda
newfield—optogenetics.Amajorcoreofoptogeneticsismicrobialrhodopsins.
Among over 10,000 currently identified potential rhodopsin genes only a few of the
relatedproteinsarecharacterized.Thisdramaticallylimitsourknowledgeoftheirmolecular
functions and mechanisms and biotechnological applications. Another limitation is that
high-resolutionstructuresandmolecularmechanismsoftherecentlydiscoveredrhodopsins
(proteorhodopsin, sodium pump, inward proton pump) are yet unknown or, in the best
case,onlystructuresofthegroundstatesareavailable.Thisisalsothecaseofnativechannel
rhodopsinswhicharethefirstandstillmajor toolofoptogenetics.
The amazing scientific and technological potential of rhodopsins is still to be realized.
With the fast expansion of the field and the available numerous publications, a growing
number of the scientists involved in the corresponding studies require comprehensive and
practicalknowledgeconcentratedinoneplacewhichwillhelptorealizethischallenge.
Thechaptersofthebookprovideup-to-dateinformationontheadvancesmadeinthe
field of rhodopsins. The first three chapters introduce the reader to new discoveries and
developments which led to an amazing progress in the field of rhodopsins. The following
chapterswillintroducethereaderintothedetailsoftheadvancedmethodsusedinthefield
under discussion. They also provide detailed protocols which, as the authors believe, are
requested by a wide extensively growing auditorium of the researchers working with
rhodopsins and in the related scientific fields. For the convenience of the readers from
different scientific fields the chapters are grouped in accordance with the description of
the methods. Two chapters are devoted to the methods which are used to search for
rhodopsins with potentially new functions and properties. The following six chapters
providedetailedinformationonthemethodsusedtocharacterizethefunctionandstructure
withafocusonthosenecessaryforthestudiesofrhodopsinsatmolecularlevel.Mostofthe
new genes were discovered using metagenomics and in many cases the host is unknown
v
vi Preface
or/andcannotbeculturedinthelaboratory.Thisfactposesanadditionalproblemintheir
studies. Therefore, the methods described in these chapters play a major role in the
functional characterization of new rhodopsins. Taking into account a huge number of
new (not yet studied) rhodopsins, high-throughput methods are required for the studies.
Therefore, some of the chapters describe such methods. New cutting-edge technologies,
likenanovolumehighthroughputinmesocrystallization,time-resolvedserialcrystallogra-
phy at X-ray free electron lasers, and fourth generation X-ray synchrotron sources, arealso
presented in these chapters. Optogenetics is a diamond produced by rhodopsin studies. It
revolutionized neuroscience promising new approaches to the treatment of severe diseases
and has a potential for a further big application as a tool to control the physiology of
different cells. Therefore, the closing chapters of the book describe major advances in the
developmentofthistechnologyanditsmajorapplications.
Last but not least, there is little doubt about the huge potential and further great
progress in the rhodopsin field and also biotechnological applications of these proteins.
Newspecificapplicationsmayrequiremodificationsofthemethodsandprotocolsdescribed
in this volume. To face this challenge each of the chapters has an introduction aiming to
provide a laconic but clear and deep understanding of the principles of the methods. This
shouldhelpthereader tomodifythemethodsandprotocolsefficiently.
IthankalltheauthorsofthisvolumeofMethodsinMolecularBiologyfortheiragreement
to share their outstanding experience with others and spend considerable time to provide
thereader withgeneralandpracticalknowledgeinsoeffectiveandconcentratedaform.
Grenoble,France ValentinGordeliy
Contents
Preface ..................................................................... v
Contributors................................................................. ix
1 MicrobialRhodopsins ................................................... 1
ValentinGordeliy,KirillKovalev,ErnstBamberg,
FranciscoRodriguez-Valera,EgorZinovev,DmitriiZabelskii,
AlexeyAlekseev,RiccardoRosselli,IvanGushchin,andIvanOkhrimenko
2 MolecularBiologyofMicrobialRhodopsins................................ 53
MartinEngelhard
3 Rhodopsin-BasedOptogenetics:BasicsandApplications..................... 71
AlexeyAlekseev,ValentinGordeliy,andErnstBamberg
4 SearchingMetagenomesforNewRhodopsins.............................. 101
FranciscoRodriguez-Valera,AlinaPushkarev,RiccardoRosselli,
andOdedBe´j`a
5 E.coliExpressionandPurificationofMicrobialandViralRhodopsins......... 109
TarasBalandin,DmytroVolkov,AlexeyAlekseev,KirillKovalev,
DmitryBratanov,andValentinGordeliy
6 CrystallizationofMicrobialRhodopsins ................................... 125
KirillKovalev,RomanAstashkin,ValentinGordeliy,
andVadimCherezov
7 CrystallographicStudiesofRhodopsins:StructureandDynamics............. 147
MarieLuiseGru¨nbein,GabrielaNassKovacs,MarcoKloos,
AlexanderGorel,R.BruceDoak,RobertL.Shoeman,
ThomasR.M.Barends,andIlmeSchlichting
8 Time-ResolvedUV-VISSpectroscopyofMicrobialRhodopsins .............. 169
DmytroSoloviov,ValentinBorshchevskiy,andIgorChizhov
9 Solid-StateNMRSpectroscopyonMicrobialRhodopsins.................... 181
ClaraNassrinKriebel,JohannaBecker-Baldus,
andClemensGlaubitz
10 FTIRandRamanSpectroscopyofRhodopsins ............................. 207
HidekiKandoriandYasuhisaMizutani
11 Single-CellResolutionOptogeneticsViaExpression
ofSoma-TargetedRhodopsins............................................ 229
ChangyangLinghu,I-WenChen,DimitriiTanese,
ValeriaZampini,andOrA.Shemesh
12 ElectrophysiologicalCharacterizationofMicrobialRhodopsin
TransportProperties:ElectrometricandΔpHMeasurements
UsingPlanarLipidBilayer,CollodionFilm,andFluorescent
ProbeApproaches ...................................................... 259
TatyanaI.Rokitskaya,NinaL.Maliar,SergeyA.Siletsky,
ValentinGordeliy,andYuriN.Antonenko
vii
viii Contents
13 ElectrophysiologicalCharacterizationofMicrobialRhodopsins
byPatch-ClampExperiments............................................. 277
ThomasMager
14 MolecularOptimizationofRhodopsin-BasedTools
forNeuroscienceApplications............................................ 289
LiefE.Fenno,RivkaLevy,andOferYizhar
15 OptogeneticStudiesofMitochondria ..................................... 311
KaiChen,PatrickErnst,XiaoguangMargaretLiu,
andLufangZhou
16 InVivoandInVitroCharacterizationofCyclaseandPhosphodiesterase
Rhodopsins ............................................................ 325
YuehuiTian,ShiqiangGao,andGeorgNagel
17 OptogeneticControlofHumanStemCell-DerivedNeurons ................ 339
RouhollahHabibey,JohannesStriebel,KritikaSharma,
andVolkerBusskamp
Index ...................................................................... 361
Contributors
ALEXEYALEKSEEV • ResearchCenter forMolecularMechanismsofAgingandAge-Related
Diseases,MoscowInstituteofPhysicsandTechnology(NationalResearchUniversity),
Dolgoprudny,Russia
YURIN.ANTONENKO • DepartmentofBioenergetics,BelozerskyInstituteofPhysico-Chemical
Biology,LomonosovMoscowStateUniversity,Moscow,Russia
ROMANASTASHKIN • InstitutdeBiologieStructurale(IBS),Universite´GrenobleAlpes,CEA,
CNRS,Grenoble,France
TARAS BALANDIN • InstituteofBiologicalInformationProcessing(IBI-7:Structural
Biochemistry),ForschungszentrumJu¨lichGmbH,Ju¨lich,Germany;JuStruct:Ju¨lichCenter
forStructuralBiology,ForschungszentrumJu¨lichGmbH,Ju¨lich,Germany
ERNST BAMBERG • MaxPlanckInstituteofBiophysics,FrankfurtamMain,Germany
THOMASR.M.BARENDS • MaxPlanckInstituteforMedicalResearch,Heidelberg,Germany
JOHANNABECKER-BALDUS • InstituteofBiophysicalChemistry,GoetheUniversityFrankfurt,
FrankfurtamMain,Germany;CentreforBiomolecularMagneticResonance,Goethe
UniversityFrankfurt,FrankfurtamMain,Germany
ODEDBE´JA` • FacultyofBiology,Technion-IsraelInstituteofTechnology,Haifa,Israel
VALENTIN BORSHCHEVSKIY • ResearchCenter forMolecularMechanismsofAgingandAge-
RelatedDiseases,MoscowInstituteofPhysicsandTechnology(NationalResearch
University),Dolgoprudny,Russia;JointInstituteforNuclearResearch,Dubna,Russia
DMITRYBRATANOV • InstituteofBiologicalInformationProcessing(IBI-7:Structural
Biochemistry),ForschungszentrumJu¨lichGmbH,Ju¨lich,Germany;JuStruct:Ju¨lichCenter
forStructuralBiology,ForschungszentrumJu¨lichGmbH,Ju¨lich,Germany
VOLKERBUSSKAMP • DepartmentofOphthalmology,Universita€ts-AugenklinikBonn,
UniversityofBonn,Bonn,Germany
I-WENCHEN • SorbonneUniversite´,INSERM,CNRS,InstitutdelaVision,Paris,France
KAICHEN • DepartmentofBiomedicalEngineering,UniversityofAlabamaat
Birmingham,Birmingham,AL,USA;DivisionofCardiovascularDisease,Departmentof
Medicine,UniversityofAlabamaatBirmingham,Birmingham,AL,USA
VADIMCHEREZOV • BridgeInstitute,DepartmentofChemistry,UniversityofSouthern
California,LosAngeles,CA,USA
IGORCHIZHOV • InstituteforBiophysicalChemistry,HannoverMedicalSchool,Hannover,
Germany
R.BRUCEDOAK • MaxPlanckInstituteforMedicalResearch,Heidelberg,Germany
MARTINENGELHARD • DepartmentStructuralBiochemistry,MaxPlanckInstituteof
MolecularPhysiology,Dortmund,Germany
PATRICKERNST • DepartmentofBiomedicalEngineering,UniversityofAlabamaat
Birmingham,Birmingham,AL,USA;DivisionofCardiovascularDisease,Departmentof
Medicine,UniversityofAlabamaatBirmingham,Birmingham,AL,USA
LIEF E.FENNO • DepartmentsofPsychiatryandNeuroscience,UniversityofTexasAustin
DellMedicalSchool,Austin,TX,USA
SHIQIANGGAO • DepartmentofNeurophysiology,InstituteofPhysiology,Biocenter,
UniversityofWuerzburg,Wuerzburg,Germany
ix