Table Of ContentVOLUMESIXHUNDRED AND SEVENTYSEVEN
M
ETHODS IN
ENZYMOLOGY
Small Angle Scattering Part A: Methods
for Structural Investigation
METHODS IN ENZYMOLOGY
Editors-in-Chief
ANNA MARIE PYLE
Departments of Molecular, Cellular and Developmental
Biology and Department of Chemistry
Investigator, Howard Hughes Medical Institute
Yale University
DAVID W. CHRISTIANSON
Roy and Diana Vagelos Laboratories
Department of Chemistry
University of Pennsylvania
Philadelphia, PA
Founding Editors
SIDNEY P. COLOWICK and NATHAN O. KAPLAN
VOLUMESIXHUNDRED AND SEVENTYSEVEN
M
ETHODS IN
ENZYMOLOGY
Small Angle Scattering Part A: Methods
for Structural Investigation
Edited by
JOHN A. TAINER
Robert A. Welch Chair in Chemistry
Departments of Molecular & Cellular Oncology
and of Cancer Biology Director Structural Biology
University of Texas MD Anderson Cancer Center
Houston, TX
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Firstedition2022
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Contents
Contributors xi
Preface xv
1. Advanced sampleenvironmentsandsample requirements for
biologicalSAXS 1
Melissa A.Graewert andDmitri I.Svergun
1. Introduction 2
2. Correlationbetweenthephysicalprocessofthescatteringeventand
samplerequirements 4
3. Automatedsampleloadingrobotics 14
4. Couplingofonlinepurificationsystems 21
5. Specializedsampleenvironments 30
References 35
2. Contrastvariation SAXS: Sample preparation protocols,
experimental procedures, and data analysis 41
JosueSanEmeterio, SuzetteA. Pabit, andLois Pollack
1. Introduction 42
2. Background:SAXSandCV-SAXS 44
3. WhatinformationcanbeextractedfromCV-SAXSdata? 49
4. Experimentalconsiderations 53
5. Doingtheexperiment 62
6. Examplesofinformationextracted 65
7. Conclusionsandoutlook 77
Acknowledgments 77
References 78
3. Deuteration for biological SANS: Case studies,success and
challenges inchemistry andbiology 85
Anthony P.Duff,Marina Cagnes, TamimA. Darwish,
AnwenM. Krause-Heuer, MichaelMoir, CarlRecsei, AgataRekas,
RobertA. Russell,Karyn L.Wilde, and NageshwarR.Yepuri
1. Deuterationforsmallangleneutronscattering 87
2. ProteinSANS 92
3. Membranes:Sterolsandphysiologicallyrelevantlipids 100
v
vi Contents
4. Deuterationbychemicalsynthesis 100
5. Examplesofusesofdeuterationforneutronscattering 105
6. Deuterationfacilities 106
7. Deuterationfacilityuse:Costs,feasibility,andqualityoftheexperiment 107
8. ThenamingofIsotopologues:Aproblemforstructuralbiologists,industry,
anddatabases 109
9. Proposalsfortheregistrationofdeuteratedcompounds 120
10. Concludingremarks 120
References 121
4. Planning,executing and assessing the validityof SANS contrast
variation experiments 127
SusanKrueger
1. Introduction 128
2. Experimentplanning 132
3. Datacollectionandassessmentofvalidity 142
4. Furtherdataanalysisandmodelrefinement 147
5. Concludingremarks 151
Acknowledgments 151
Disclaimer 151
References 151
5. Technicalconsiderationsforsmall-angleneutronscatteringfrom
biologicalmacromoleculesinsolution:Crosssections,contrasts,
instrument setup and measurement 157
ZuzannaPietras, KathleenWood, Andrew E.Whitten, andCy M. Jeffries
1. Introduction 158
2. Nuclearcrosssections 159
Notes 171
3. Smallangleneutronscatteringinstruments 171
4. Themeasurementapproach 179
5. Summary 185
Acknowledgments 186
References 187
6. Size exclusionchromatography coupled small angle X-ray
scatteringwithtandemmultianglelightscatteringattheSIBYLS
beamline 191
DanielJ. Rosenberg, GregL.Hura, andMichal Hammel
1. Introduction 192
2. Endstationdesign 193
Contents vii
3. SamplepreparationforSEC-SAXS-MALS 198
4. Dataacquisition 202
5. Dataprocessing 207
6. Datavalidationandanalysis 210
7. Summaryandconclusion 214
Acknowledgments 215
References 215
7. SEC-SAXS:Experimentalset-upandsoftwaredevelopmentsbuild
upa powerful tool 221
JavierP(cid:1)erez, Aur(cid:1)elien Thureau, andPatrice Vachette
1. Introduction 222
2. Theinstrument 223
3. Dataprocessing 231
4. ComparativeanalysisofSEC-SAXSdatasetsusingthevariousavailable
programs 238
5. Conclusion 245
Acknowledgments 247
References 247
8. Stopped-flow-time-resolved SAXS for studiesofligand-driven
protein dimerization 251
HenningTidowand Inokentijs Josts
1. Introduction 252
2. Samplepreparation 254
3. Stopped-flowexperiment:Themeasurement 255
4. Dataanalysisandinterpretation 257
5. SingularvaluedecompositionandOLIGOMERanalysisoftime-resolved
SAXSdata 258
6. FittingakineticmodeltoextractrateconstantsfromSF-SAXSdata 260
7. Summaryandconclusions 260
Acknowledgments 260
References 260
9. Time-resolved small-angle neutronscattering (TR-SANS)for
structural biology of dynamic systems:Principles, recent
developments, andpracticalguidelines 263
AnneMarteland Frank Gabel
1. Introduction,principlesandlimitations 264
2. Examplesfromdiverseclassesofbiologicalsystems 271
viii Contents
3. ConsiderationsonsamplestateandpracticalguidelinesforthedesignofTR-
SANSexperiments 275
4. Conclusionsandfutureperspectives 281
Acknowledgment 283
References 283
10. Protein fibrillation from another small angle: Sample
preparation andSAXSdata collection 291
Bente Vestergaard and AnnetteEvaLangkilde
1. Introduction 292
2. Generalmethodandsafetynotes 297
3. Feasibility,designandoptimization 299
4. Themainexperiment:SAXSdatacollection 309
5. Summaryandconclusions 316
Acknowledgments 317
References 317
11. High-pressureSAXS, deep life, andextremebiophysics 323
Richard E. Gillilan
1. Introduction 324
2. Structuraleffectsofpressureonbiomolecularsystems 325
3. PressuredependenceofSAXS 332
4. Methods 340
5. Summaryandconclusions 348
Acknowledgments 350
References 350
12. Characterizationof biological materials with soft X-ray
scattering 357
Joshua T.Del Mundo,Sintu Rongpipi,Enrique D.Gomez, and
Esther W.Gomez
1. Introduction 358
2. Samplepreparationfordryordehydratedmaterials 363
3. Samplepreparationforliquidsandhydratedsolids 367
4. Storingandtransportingsamples 369
5. Mountingsamplesontoasamplebar 370
6. PerformingNEXAFSexperiments 372
7. PerformingRSoXSexperiments 374
8. OpportunitiesininstrumentationforresonantsoftX-rayscatteringof
biologicalsystems 379
Contents ix
9. Conclusionandoutlook 380
Acknowledgments 380
References 381
13. Scattering measurementson lipid membrane structures 385
Lin Yang
1. Introduction 385
2. Informationcontentsinthescatteringdata 387
3. Generalexperimentalplanningconsiderations 391
4. Biologicalmembranes 394
5. Modelmembranestructures 396
6. Concludingremarks 409
References 410
14. Studying integral membraneprotein bySANS using stealth
reconstitutionsystems 417
Inokentijs Josts, Dominique-Maurice Kehlenbeck,Julius Nitsche, and
Henning Tidow
1. Introduction 418
2. Contrastvariationinsmall-angleneutronscattering(SANS)byselective
deuterationoflipidsandproteinsforuseasstealthcarriersystems 420
3. Reconstitutionofintegralmembraneproteins(IMP)intostealthcarrier
systems/example:ReconstitutionofMsbAintostealthnanodiscs 423
4. SANSdataacquisitionandanalysisofIMP/stealthnanodiscsamples 428
5. Summaryandconclusions 429
Acknowledgments 429
References 430
15. Predicting solution scattering patternswith explicit-solvent
molecular simulations 433
LeonieChatzimagas and JochenS. Hub
1. Introduction 434
2. Implicit-solventmethods 437
3. Explicit-solventSASpredictionswiththeWAXSiSmethod 441
4. Theory 444
5. Workflow 446
6. Practicalconsiderations 450
7. Summary 452
Acknowledgments 453
References 453
