Analytical ultracentrifugation:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Amsterdam [u.a.]
Elesevier, Acad. Press
2015
|
| Ausgabe: | 1. ed. |
| Schriftenreihe: | Methods in enzymology
562 |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XX, 567 S., [14] Bl. Ill., graph. Darst. |
| ISBN: | 9780128029084 |
Internformat
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| 245 | 1 | 0 | |a Analytical ultracentrifugation |c ed. by James L. Cole |
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| 300 | |a XX, 567 S., [14] Bl. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
| _version_ | 1804175231740280832 |
|---|---|
| adam_text | CONTENTS
Contributors xiii
Preface xix
1. Next-Generation AUC Adds a Spectral Dimension: Development
of Multiwavelength Detectors for the Analytical Ultracentrifuge 1
Joseph Z. Pearson, Frank Krause, Dirk Haffke, Borries Demeler,
Kristian Schilling, and Helmut Cölfen
1. Introduction 2
2. Development of MWL Absorbance Detectors 4
3. Hardware and Control System of Second-Generation MWL Detectors 6
4. MWL Data From AUC 11
5. Data Visualization and Experimental Results 12
6. Discussion 20
7. Summary and General Discussion of the Impacts of MWL AUC Data
in the Field of Biopolymers 24
Acknowledgments 25
Supplemental Information 25
References 25
2. Next-Generation AUC: Analysis of Multiwavelength Analytical
Ultracentrifugation Data 27
Gary E. Gorbet, Joseph Z. Pearson, Aysha K. Demeler, Helmut Cölfen,
and Borries Demeler
1. Introduction 28
2. Computational Treatment of Multiwavelength Data 29
3. Applications 40
4. Discussion 42
5. Conclusion 45
Acknowledgments 46
References 46
3. Sedimentation Velocity: A Classical Perspective 49
John J. Correia and Walter F. Stafford
1. Early History 50
2. Irreversible Thermodynamics 52
v
vi Contents
3. Sedimentation Velocity 53
4. Balanced Forces in Diffusion 54
5. Balanced Forces in Sedimentation 56
6. Derivation of the Lamm Equation 58
7. Heterogeneous Paucidisperse Systems 58
8. Nonidea! Systems 60
9. Interacting Systems 63
10. Solutions of the Lamm Equation 65
11. Equipment and Optical Systems 67
12. Sedimentation Velocity Experimental Design 69
Acknowledgments 74
References 74
4. Hydrodynamic Modeling and Its Application in AUC 81
Mattia Rocco and Olwyn Byron
1. Introduction 82
2. AUC and Hydrodynamics 83
3. The Hydration issue 86
4. Segmental Flexibility and Intrinsically Disordered Structures 88
5. Available Programs for Rigid Body HM 89
6. Comparing the Performance of Various Methods 96
7. A Step-by-Step Guide to Performing Correct HM Using Atomic Coordinates 98
8. Selected Literature Examples 100
9. Concluding Remarks 103
References 103
5. Calculations and Publication-Quality Illustrations for Analytical
Ultracentrifugation Data 109
Chad A. Bräutigam
1. Introduction 110
2. General Features of GUSSI 111
3. Utility Functions of GUSSi 116
4. Summary 130
Acknowledgments 130
References 130 6 * *
6. Sedimentation Equilibrium Analysis of CIpB Self-Association
in Diluted and Crowded Solutions 135
Carlos Alfonso, Urko del Castillo, lanire Martin, Arturo Muga,
and Germán Rivas
1. introduction 136
Contents
vii
2. Experimental Approaches and Analysis 139
3. Summary of Experimental Results 148
4. CIpB Association Equilibrium and Disaggregase Activity 156
5. Concluding Remarks 157
Acknowledgments 158
References 158
7* Analysis of Linked Equilibria 161
JiaBei Lin and Aaron L. Lucius
1. Introduction 161
2. Determination of ԼՈ/0 for an Assembling System 168
3. Global Fitting of Sedimentation Velocity Data as a Function of Protein
Concentration Kinetic Considerations 169
4. Global Analysis Using the 1-2-4-6 Model with Rapid Dissociating Oligomers 175
5. Global Analysis Using the 1-2-4-6 Model with Slow Dissociation of
Oligomers 180
6. Global Analysis with Rate Constants in the Detectable Range 181
7. Conclusions 183
References 185
8. Elucidating Complicated Assembling Systems in Biology Using
Size-and-Shape Analysis of Sedimentation Velocity Data 187
Catherine T. Chaton and Andrew B. Herr
1. Techniques for Studying Macromolecular Mixtures 188
2. An Overview of the Standard Sedimentation Coefficient Distribution
Approach 190
3. Two-Dimensional Size-and-Shape Analysis 194
4. Case Study: Cyclic GMP-AMP Synthase Oligomerization 196
5. Case Study: IRF-3 Phosphorylation by TBK-1 199
6. Conclusions 201
Acknowledgments 202
References 202 9
9. Quaternary Structure Analyses of an Essential
Oligomeric Enzyme 205
Tatiana P. Soares da Costa, Janni B. Christensen, Sebastien Desbois,
Shane E. Gordon, Ruchi Gupta, Campbell J. Hogan, Tao G. Nelson,
Matthew T. Downton, Chamodi K. Gardhi, Belinda M. Abbott, John Wagner,
Santosh Panjikar, and Matthew A. Perugini
1. Introduction 206
2. Catalytic Function of DHDPS 207
Contents
viii
3. Structure of DHDPS 208
4. Conclusions 220
References 222
10. Characterization of intrinsically Disordered Proteins by
Analytical Ultracentrifugation 225
David J. Scott and Donald J. Winzor
1. Introduction 226
2. Ultracentrifugal Procedures 226
3. Extent of Structural Information Obtained 233
4. Concluding Remarks 237
References 238
11. Sedimentation Velocity Analysis of the Size Distribution of
Amyloid Oligomers and Fibrils 241
Yee-Foong Mok, Geoffrey J. Howlett, and Michael D.W. Griffin
1. Introduction 242
2. Preparative Ultracentrifugation 243
3. Analytical Ultracentrifugation 246
4. Heterogeneous Systems 251
5. Summary 254
Acknowledgments 254
References 254
12. AUC and Small-Angle Scattering for Membrane Proteins 257
Aline Le Roy, Kai Wang, Beatrice Schaack, Peter Schuck, Cécile Breyton,
and Christine Ebei
1. Introduction 258
2. Membrane Proteins in AUC 260
3. Membrane Proteins in SAXS and SANS 274
Acknowledgments 283
References 283 13 * *
13. Hydrodynamic Models of G-Quadrup!ex Structures 287
Jonathan B. Chaires, William L. Dean, Huy T. Le, and John O. Trent
1. Introduction 288
2. Correlating Molecular Structure with Experimental Solution Hydrodynamic
Measurements—General Comments 290
3. HYDROPRO Software 291
4. Getting Structure Files and Building Models 291
Contents
ix
5. Software for Model Building 291
6. Protocol for Running HYDROPRO on Quadruplex Nucleic Add
Structure Files 292
7. Extending the Static Hydrodynamic Bead Model By Analyzing Molecular
Dynamics Trajectories 294
8. Accelerated Molecular Dynamics Can Explore More Conformational Space 295
9. Examining Higher Order Quadruplexes from the Human Telomere
Sequence 297
10. Experimental Determination by Analytical Ultracentrifugation 298
11. The Partial Specific Volume Problem 300
12. Correlation of Calculated and Measured Hydrodynamic Properties 301
References 302
14. Analytical Ultracentrifugation as a Tool to Study Nonspecific
Protein-DNA Interactions 305
Teng-Chieh Yang, Carlos Enrique Catalano, and Nasib Karl Maluf
1. Introduction 306
2. Nonspecific Interaction Model 307
3. Case Studies 314
4. Summary 328
Acknowledgments 328
References 329
15. Characterization of Homogeneous, Cooperative Protein-DNA
Clusters by Sedimentation Equilibrium Analytical
Ultracentrifugation and Atomic Force Microscopy 331
Ingrid Tessmer and Michael G. Fried
1. Introduction 332
2. Measurement of DNA Binding 334
3. AFM Tests of the HBC Model 338
Acknowledgments 345
References 345 16 * *
16. Sedimentation Velocity Analysis of Large Oligomeric Chromatin
Complexes Using Interference Detection 349
Ryan A. Rogge and Jeffrey C. Hansen
1. Introduction 350
2. Theory 350
3. Equipments 352
4. Setting Up the Interferometer Laser: Laser Delay and Duration 352
X
Contents
5. Radial Calibration of Interference Detector 353
6. Final Considerations for Interference Sedimentation Velocity Run 353
7. Experimental 354
8. Data Analysis 357
9. Discussion 358
References 360
17. Dissecting Steroid Receptor Function by Analytical
Ultracentrifugation 363
David L Bain, Rolando W. De Angeiis, Keith D. Connaghan, Qin Yang,
Gregory D. Degala, and James R. Lambert
1. Introduction 364
2. AUC Analysis of Steroid Receptor Self-Assembly 366
3. Integrating AUC Results into Understanding Receptor-Promoter Interactions 374
4. Implications for Receptor-Mediated Transcriptional Regulation 383
5. Conclusions and Future Directions 386
Acknowledgments 386
References 387
18. Ultracentrifuge Methods for the Analysis of Polysaccharides,
Glycoconjugates, and Lignins 391
Stephen E. Harding, Gary G. Adams, Fahad Almutairi, Qushmua Alzahrani,
Tayyibe Erten, M. Samil Kök, and Richard B. Gillis
1. Introduction 392
2. Polysaccharides 394
3. Glycoconjugates 396
4. Lignins 396
5. Relevant Recent Advances in AUC and Related Procedures 397
6. Examples of Applications to Specific Carbohydrate Systems 411
7. Analytical Ultracentrifuge Analysis of Interactions Involving Carbohydrate
Polymers 412
8. Conclusions 427
References 428 19
19. Analytical Ultracentrifugation and Its Role in Development
and Research of Therapeutical Proteins 441
Jun Liu, Sandeep Yadav, James Andya, Barthélemy Demeule,
and Steven J. Shire
1. The Development of Analytical Ultracentrifugation and Its Role in
Biology and Biotechnology 442
Contents
XI
2. Analysis of Aggregates by AUC 444
3. Early Studies of the Use of AUC in Determining Molecular Weight and Size
Distribution of Protein Drugs 447
4. AUC and Formulation Development 455
5. Using AUC to Characterize Immune Complexes 456
6. Assessment of Dosing of Anti-lgE by AUC Competitive Binding Experiments 459
7. Using the Competitive Binding AUC Method to Critically Evaluate SPR
Measurements 463
8. Investigation of Protein-Protein Interactions and Impact on Viscosity 466
9. Summary and Conclusions 471
References 472
20. Guidance to Achieve Accurate Aggregate Quantitation in
Biopharmaceuticals by SV-AUC 477
Kelly K. Arthur, Brent S. Kendrick, and John P. Gabrielson
1. Introduction 478
2. Applications of SV-AUC 479
3. Optimizing SV-AUC Method Parameters and Applying Real-Time Controls 483
4. Method Lifecycle Maintenance: Monitoring and Controlling SV-AUC
Method Performance Over Time 487
5. Conclusions 499
References 499
21. Protein Assembly in Serum and the Differences from
Assembly in Buffer 501
John J. Hill and Thomas M. Laue
1. Introduction 502
2. Materials and Methods 504
3. Results 509
4. Conclusions 523
Acknowledgments 525
References 525
Author Index 529
Subject Index 553
|
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| discipline | Chemie / Pharmazie Biologie |
| edition | 1. ed. |
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| id | DE-604.BV042927167 |
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| indexdate | 2024-07-10T07:13:00Z |
| institution | BVB |
| isbn | 9780128029084 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-028354336 |
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| physical | XX, 567 S., [14] Bl. Ill., graph. Darst. |
| publishDate | 2015 |
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Analytical ultracentrifugation ed. by James L. Cole 1. ed. Amsterdam [u.a.] Elesevier, Acad. Press 2015 XX, 567 S., [14] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 562 Biopolymere (DE-588)4006893-6 gnd rswk-swf Ultrazentrifugieren (DE-588)4186746-4 gnd rswk-swf Nachweis (DE-588)4115334-0 gnd rswk-swf Labortechnik (DE-588)4123602-6 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Ultrazentrifugieren (DE-588)4186746-4 s Labortechnik (DE-588)4123602-6 s DE-604 Biopolymere (DE-588)4006893-6 s Nachweis (DE-588)4115334-0 s 1\p DE-604 Cole, James L. Sonstige oth Methods in enzymology 562 (DE-604)BV000000938 562 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028354336&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p cgwrk 20201028 DE-101 https://d-nb.info/provenance/plan#cgwrk |
| spellingShingle | Analytical ultracentrifugation Methods in enzymology Biopolymere (DE-588)4006893-6 gnd Ultrazentrifugieren (DE-588)4186746-4 gnd Nachweis (DE-588)4115334-0 gnd Labortechnik (DE-588)4123602-6 gnd |
| subject_GND | (DE-588)4006893-6 (DE-588)4186746-4 (DE-588)4115334-0 (DE-588)4123602-6 (DE-588)4143413-4 |
| title | Analytical ultracentrifugation |
| title_auth | Analytical ultracentrifugation |
| title_exact_search | Analytical ultracentrifugation |
| title_full | Analytical ultracentrifugation ed. by James L. Cole |
| title_fullStr | Analytical ultracentrifugation ed. by James L. Cole |
| title_full_unstemmed | Analytical ultracentrifugation ed. by James L. Cole |
| title_short | Analytical ultracentrifugation |
| title_sort | analytical ultracentrifugation |
| topic | Biopolymere (DE-588)4006893-6 gnd Ultrazentrifugieren (DE-588)4186746-4 gnd Nachweis (DE-588)4115334-0 gnd Labortechnik (DE-588)4123602-6 gnd |
| topic_facet | Biopolymere Ultrazentrifugieren Nachweis Labortechnik Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028354336&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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