Advanced Spectroscopic Methods to Study Biomolecular Structure and Dynamics

560 Pages·2022·22.427 MB·English

by  Prakash Saudagar, Timir Tripathi

ADVANCED SPECTROSCOPIC
METHODS TO STUDY
BIOMOLECULAR STRUCTURE
AND DYNAMICS
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ADVANCED SPECTROSCOPIC
METHODS TO STUDY
BIOMOLECULAR STRUCTURE
AND DYNAMICS
Edited by
PRAKASH SAUDAGAR
AssistantProfessor, Department of Biotechnology,
NationalInstituteofTechnologyWarangal,Warangal,India
TIMIR TRIPATHI
Senior Assistant Professor, Molecular and Structural
Biophysics Laboratory, Department of Biochemistry,
North-Eastern Hill University, Shillong, India
RegionalDirector,RegionalDirector’sOffice,IndiraGandhi
NationalOpen University (IGNOU),Regional Center
Kohima,Kohima,India
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Contents
Contributors xiii
Editorsbiography xix
Foreword xxi
Preface xxiii
1. Fundamentals of spectroscopy for biomolecular structure
and dynamics 1
NiharikaNag,SantanuSasidharan,PrakashSaudagar,andTimirTripathi
1. Introductiontospectroscopy 1
2. Generaldesignofaspectrometerinstrumentation 14
3. Variousspectroscopicmethods 15
4. Conclusions 30
References 30
2. Fluorescence-based techniques to assess biomolecular
structure anddynamics 37
JakubSławskiandJoannaGrzyb
1. Introduction 37
2. Environmentaleffectsusedinfluorescence
structuralstudies 41
3. Fo€rsterresonanceenergytransfer 48
4. Fluorescencequenching 50
5. Fluorescenceanisotropy 55
6. Diffusion-basedestimationofbiomolecularsizeandshape 57
7. Biomoleculesinsitu 64
8. Conclusions 69
References 69
3. Structural analysis of biomacromolecules using circular
dichroismspectroscopy 77
XueZhao,YuxuanWang,andDiZhao
1. Introduction 77
2. ApplicationsofCDinproteinstudies 78
3. ApplicationsofCDinstudyingpolysaccharides 84
vii
viii Contents
4. ApplicationsofCDinnucleicacidmeasurements 91
5. Conclusionsandoutlook 93
References 96
4. Nuclear magneticresonance spectroscopy for protein
structure, folding,and dynamics 105
SouryaBhattacharya,SebantiGupta,andSaugataHazra
1. Introduction 105
2. NMRspectroscopyapproachestostudyproteinfolding
anddynamics 107
3. Conclusionandfutureprospects 121
References 122
5. Advanced NMR spectroscopy methodsto study protein
structure and dynamics 125
AshishA.KawaleandBjo€rnM.Burmann
1. Introduction 125
2. TraditionalNMRspectroscopyapproachesforsmall-medium-sized
proteins 127
3. Proteinbackbonedynamics 130
4. NMRspectroscopyforlargeproteins 136
5. Methodsforprobingproteindynamicsoflargeproteins 138
6. Methodsforsimultaneousstudyofthestructureanddynamics
ofproteins 144
7. Conclusions 145
Acknowledgments 146
References 146
6. Applications of infraredspectroscopy to study proteins 153
RiyaSahu,BaneshSooram,SantanuSasidharan,NiharikaNag,
TimirTripathi,andPrakashSaudagar
1. Introduction 153
2. Infraredspectrum 154
3. Infraredspectrumforthestructuralcharacterization
ofproteins 155
4. Infraredspectrophotometers 156
5. TypesofIRmeasurements 158
6. IRabsorptionanddetectionofaminoacidsidechains 159
7. IRabsorptionanddetectionoftheproteinbackbone 159
8. IRspectroscopyforstudyingproteins 161
Contents ix
9. StudyingproteinswithIRspectroscopy:Casestudies 163
10. Conclusionandfutureperspectives 164
References 164
7. Ramanspectroscopy to study biomolecules, theirstructure,
and dynamics 173
MuSu,JiajieMei,ShangPan,JunjieXu,TingtingGu,QiaoLi,
XiaorongFan,andZhenLi
1. Introduction 173
2. ApplicationsofRamanspectroscopy 178
3. Conclusions 196
Acknowledgments 198
References 198
8. Spectroscopic investigation of biomolecular dynamics
using light scattering methods 211
EvaRoseM.Balog
1. Introduction 211
2. Basicsoflightscattering 214
3. Applicationsoflightscatteringmethods 216
4. Conclusionandfutureperspectives 221
References 221
9. Protein footprinting bymass spectrometry: H/D exchange,
specificaminoacidlabeling,andfastphotochemicaloxidation
of proteins 227
RaviKant,AustinB.Moyle,PrashantN.Jethva,andMichaelL.Gross
1. Introduction 227
2. Hydrogen-deuteriumexchangemassspectrometry 228
3. Specificaminoacidlabeling 240
4. FPOPforproteinstructuralstudies 251
5. Conclusions 261
Acknowledgments 262
References 262
10. Small-angle scattering techniques for biomolecular structure
anddynamics 271
AndreaMathildeMebert,MaríaEmiliaVillanueva,GabrielIbrahinTovar,
JonásJos(cid:2)ePerezBravo,andGuillermoJavierCopello
1. Introductiontosmall-anglescatteringexperiments 271