Single molecule dynamics in life science:
Gespeichert in:
| Weitere Verfasser: | , |
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| Format: | Buch |
| Sprache: | English |
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Wiley-VCH
2009
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| Beschreibung: | XVIII, 328 S. Ill., graph. Darst. |
| ISBN: | 9783527312887 |
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| 245 | 1 | 0 | |a Single molecule dynamics in life science |c ed. by Toshio Yanagida and Yoshiharu Ishii |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2009 | |
| 300 | |a XVIII, 328 S. |b Ill., graph. Darst. | ||
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| 337 | |b n |2 rdamedia | ||
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| 650 | 4 | |a Models, Molecular | |
| 650 | 4 | |a Molecular Biology |x methods | |
| 650 | 4 | |a Molecular Structure | |
| 650 | 4 | |a Molecules | |
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| 700 | 1 | |a Ishii, Yoshiharu |4 edt | |
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Datensatz im Suchindex
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Advances in instrumentation over the last few years have established
single molecule measurements as a major method in many biological
laboratories. Exploiting the full power of such measurements is depend¬
ent on a good understanding of single molecule behavior and enzymol-
ogy·
In this first comprehensive resource on the topic, two of the world's
most distinguished single molecule scientists have put together a team
of pioneers in the field to show how to both set up and interpret a single
molecule experiment. Following an introduction to single molecule
measurements and enzymology, the authors consider molecular motors
and mechanical properties before moving on to the applications
themselves. Detailed discussions of studies on protein enzymes,
ribozymes and nucleic acids are also included.
This book is indispensable reading for a growing number of scien¬
tists.
Toshio Yanagida did his undergraduate and graduate studies in semi-conductor physics at Osaka
University, Japan. He then switched to biophysics in
1970
to pursue a career in basic science. He
is now professor of the Osaka University Graduate School of Frontier
Biosciences,
and leading
projects at WPI Immunology Frontier Research Center and life science division of'Yuragi"
project, Osaka University
inJapan.
His teams are leading the development of single-molecule
detection techniques to investigate the molecular motor of contracting muscle. Professor
Yanagida is a founding editor of the Journal "Small". For his scientific achievements, he has
received numerous awards, among them the Japan Academy Award and the Japanese Imperial
Award.
Yoshiharu Ishii studied physics and biophysics at the Universities of Tokyo and Nagoya, Japan.
From
7983
onwards he worked at the Boston
Biomedical
Research Institute, USA, returning to
Japan in
7992
to pursue his research career in applied biophysics. He organized research teams
"Biomotron", "Single Molecule Processes", and
"Sofi
Nano-machines" with Prof. Yanagida to
develop single molecule detection techniques. He is currently a research manager in Core
Research for Evolutional Science and Technology (CREST) in Japan Science and Technology
agency (JST)- Dr. Ishii is an editorial board member of the journal "Open Biochemistry".
Contents
Prefece XIII
List of Contributors XV
1 A Road Map to Single Molecule Dynamics 1
Yoshiharu Ishii
1-1 Visualization of Single Molecules 1
1.2 Single Molecule Position Tradring 1
1-3 Single Molecules in live Cells 2
1.4 Fluorescence Spectroscopy and Biomolecular Dynamics 3
1.5 Single Molecule Manipulation and Molecular Motors 4
1.6 Mechano-Chemical Coupling of Molecular Motors 5
1.7 DNA-Based Motors 5
1.8 Imaging with AFM and Force Measurements 6
References 6
2 Single Molecule Study for Elucidating the Mechanism Used by
Biosystems to Utilize Thermal Fluctuations 11
Toshio Yanagida
2.1 Introduction 11
2.1.1 Differences between Man-Made and Biological Molecular Machines 11
2.1.2 Single Molecule Imaging and Nano-Detection 13
2.2 Simultaneous Measurements of Individual ATP Hydrolysis Cydes
and Mechanical Events by a Myosin Motor 14
2.2.1 ATP Hydrolysis Cydes 14
2.2.2 Mechanical Events 16
2.2.3 Simultaneous Measurements 16
2.3 Resolving the Process of a Displacement by Scanning Probe
Nanometry 16
2.3.1 Observation and Manipulation of a Single Myosin Motor 18
2.3.2 Displacements 18
Single Mdleade Dynamics in liß Science. Edited by T. Yanagida and Y. Ishii
Copyright © 2009 W1LEY-VCH Verlag GmbH Co. KGaA, Weinhom
ISBN: 978-3-527-31288-7
VI Contents
2.3.3 Sub-steps within a Displacement 20
2.3.4 Natureof Sub-steps 22
2.3.5 Comparing the Actions of Individual Myosin Motors with those
of Musde 22
2.3.6 OtherTypesof Molecular Motors 24
2.4 Biased Brownian Step Model 27
2.4.1 Asymmetrie Potential 27
2.4.2 Comparison with Other Studies 29
2.4.3 Computer Simulation: from a Single Molecular Motor to Musde 31
2.5 Condusion for the Unique Medianism of Biological Molecular
Machines 33
References 35
3 Imaging and Molecular Motors 41
Yale E. Goldman
3.1 Introduction 41
3.2 Methods 42
3.2.1 Detection of Single Fluorophores 42
3.2.2 Sub-Diffraction Localization of Fluorescent Molecules 50
3.2.3 Darkfield Imaging with One Nanometer Accuracy (DIONA) 53
3.2.4 Single-molecule High Resolution Imaging with Photobleaching
(SHRImP) 53
3.2.5 Single Molecule Fluorescence Resonance Energy Transfer
(smFRET) 53
3.2.6 Orientation of Single Molecules 54
3.2.7 Polarized Total Internal Reflection Fluorescence Microscopy
(polTIRF) 55
3.2.8 Defocused Orientational and Positional Imaging (DOPI) 57
3.3 Molecular Motors 58
3.3.1 Myosin V 60
3.3.2 Myosin II 65
3.3.3 Myosin VI 66
3.3.4 Conventional Kinesin 68
3.3.5 Other Kinesins 69
3.3.6 Dyneins 71
3.3.7 Single Molecule Intracellular Imaging 73
3.4 Conclusions 75
References 76
4 Ion Channels 87
Tom Ide, Minako Hirano, and Yuko Takeuchi
4.1 Introduction 87
4.2 Artifidal Bilayers 88
4.2.1 Solid Supported Bilayers 88
4.2.2 Self-Standing Bilayers 89
Contents VII
4.3 Simultaneous Optical and Electrical Recording of the Single
BK-Channels 92
4.4 Detection of Channel Conformational Change 95
4.5 "Optical Patch-Clamping" 95
4.6 Conclusion 96
References 96
5 Signal Transduction across the Plasma Membrane 99
Masahiro Heda, Tatsuo Shibata, and Yasushi Sako
5.1 Introduction 99
5.2 Signal Transduction Mediated by Receptor Tyrosine Kinase 99
5.3 Assodation between EGF and EGFR and Formation of the Signaling
DimersofEGFR 100
5.4 Amplification and Propagation of EGFR Activation 104
5.5 Dynamics of the NGF/NGFR Complex 105
5.6 Stochastik Signal Processing and Transduction in living Cells 108
5.7 Chemotactic Signaling System of Eukaryotic Cells 109
5.8 Stochastic Nature of Chemotactic Signaling Molecules 109
5.9 Stochastic Model of Transmembrane Signaling by Chemoattractant
Receptors 111
5.10 Condusions 115
References 115
6 Dynamics of Membrane Receptors: Single-molecule Tracking
of Quantum Dot Liganded Epidermal Crowth Factor 117
Guy M. Hagen, Keith A. Lidke, Bernd Rieger, Diane S. Lidke,
Wouter Caarls, Donna J. Amdt-Jovin, and Thomas M.Jovin
6.1 Introduction 117
6.2 Single QD Imaging 118
6.3 Retrograde Transport of Activated EGFR Dimers 118
6.4 Single QD-EGF-EGFR Traddng 121
6.5 Programmable Array Microscopy 122
6.6 Conduding Remarks 125
Appendix 6.A: Materials and Methods 126
6.A.1 Reagents 126
6.A.2 Cell Lines 126
6.A.3 Cell Treatments 126
6.A.4 QD Conjugation to Epidermal Growth Factor 126
6.A.5 Wide-field Microscopy 126
6.A.6 PAM 127
6.A.7 Hyperspectral Imaging 127
Appendix 6.B: Software and Image Processing 128
6.B.1 Single Partide Tracking 128
6.B.2 Real Time Optically-sectioned Imaging with the PAM 128
References 129
7 Studying the Dynamics of Ligand-Receptor Complexes by
Single-Molecule Techniques 131
Christophe Daneion and Horst Vogel
7.1 Introduction 131
7.2 Labeling Methods for Cell Surface Receptors 132
7.2.1 General Considerations 132
7.2.2 Suppressor tRNA Technology 134
7.2.3 06-Alkylguanine-DNA Alkyltransferase (AGT) 134
7.2.4 Acyl-carrier Protein (ACP) 135
7.2.5 Nitrilotriacetate (NTA) 135
7.2.6 Reversible Sequential Labeling (ReSeq) 136
7.3 Functional Mobility of Receptors in Cell Membranes 136
7.3.1 Organization and Dynamics of Cell Membranes 136
7.3.2 Techniques 137
7.4 Investigating Kinetics and Thermodynamics of Ligand-Receptor
Interactions by FCS 138
7.4.1 Principles 338
7.4.2 FCS at High Fluorophore Concentrations 150
7.5 Modulation of Ion Channel Current by ligand Binding 151
7.5.1 Iigand-activated Ion Channels: Decoupling Ligand Binding and
Channel Gating with Single-molecule Patch-clamp 151
7.5.2 The Nicotinic Acetylcholine Receptor as a Prototypical Example 151
7.5.3 Chemical Gating by Specifk Ligand Binding inside Ion
Channels 153
7.5.4 Facilitated Translocation of Sugars through Bacterial Porins 154
7.5.5 Combined Electrical and Fluorescence Measurements 157
7.6 Forces of Ligand-Receptor Interactions in Iiving Cells 157
7.6.1 Principles of Single-molecule Dynamic Force Spectroscopy and
Applications to Cell Surface Receptors 157
7.6.2 Novel AFM-based Techniques 159
References 166
8 RNA in cells 171
Valeria de Tunis and Robert H. Singer
8.1 Why Study RNA' 171
8.2 RNA Visualization inside Cells 172
8.2.1 Techniques to Label RNA 172
8.2.2 Advancements in Imaging Technologies 175
8.3 RNA Dynamics in the Nudeus 175
8.3.1 Dynamics in Transcription 176
8.3.2 A Journey from the Transcription Site to the Nudear Envelope 177
8.3.3 Transport through the Nudear Pore Complex 179
8.4 RNA Dynamics in the Cytoplasm 181
8.4.1 Non-localizing RNA 181
8.4.2 RNA Localization 182
Contents IX
8.4.2.1 Some Examples of Localization in Mammalian Cells and
Drosophila 183
8.5 Condusion 185
References 185
9 Protein Dynamics and Interactions 191
Ted A. Laurence and Shimon Wehs
9.1 Introduction 191
9.1.1 The Single-molecule Approach to Protein Dynamics and
Interactions 191
9.1.1.1 Distributions of Subpoupulations 192
9.1.1.2 Dynamics of Unsynchronized Trajectories 192
9.1.1.3 Order of Events/States 192
9.1.2 Example Biological Systems 193
9.2 Fluorescence Spectroscopy as a Tool for Dynamic Measurements
of Molecular Conformation and Interactions 194
9.2.1 Jablonski Diagram (Intensity, Spectrum, lifetime, Polarization) 194
9.2.2 Point Emission-Localization Measurements 196
9.2.3 Fluorescence Polarization-Measures Rotational Movement and Freedom
ofMovement 197
9.2.4 Fluorescence Resonance Energy Transfer-nm-scale Ruler 197
9.2.5 Single-molecule Electron Transfer-Angstrom-scale Ruler 199
9.3 Single-molecule Data Acquisition and Analysis Methods 200
9.3.1 Choosing a Labeling Configuration: What is the
Observable? 200
9.3.2 Should a Freely-diffusing or Immobilized Format be used? 202
9.3.3 What Excitation/Optical Isolation Format should be used? 203
9.3.3.1 Optical Isolation ofa Single Point 205
9.3.3.2 Multiple Points 207
9.3.3.3 How many Excitation Lasers? 207
9.3.3.4 Pulsed Laser Excitation 209
9.3.4 What Detection Format should be used? 209
9.3.5 Data Reduction and Analysis Methods 210
9.3.5.1 Photon Streams and Films 210
9.3.5.2 TimeTraces 211
9.3.5.3 Single-molecule Identification 211
9.3.5.4 Histogram-based Analysis (Induding Correlation Analysis) 212
9.3.5.5 Analysis of Histograms of Single Molecules 213
9.3.5.6 Single-molecule Sorting 213
9.3.5.7 Trajectory Analysis of Single Molecules 214
9.3.6 Modeling and Simulations of Single-molecule Experiments 214
9.4 Examples 214
9.4.1 Single-molecule Fluorescence Studies of Protein Folding and
Conformations 215
9.4.1.1 Observables for Protein Folding 215
X Contents
9.4.1.2 Labeling Schemes for Protein Folding 215
9.4.1.3 Equüibrium Unfolding Studies on Simple Model Two-state
Folders 217
9.4.1.4 Single-molecule Protein Folding under Non-equilibrium
Conditions 219
9.4.1.5 Monitoring Conformational Dynamics using Fluorescence
Lifetime 220
9.4.1.6 Single-pair FRET Studies on Immobilized Proteins 222
9.4.1.7 Probing Biomolecular Dynamics via Fluorescence Quenching and
Electron Transfer 223
9.4.2 Single-molecule Measurements ofDNA-processing Enzymes 225
9.4.2.1 RNAP - Retention of Sigma 227
9.4.2.2 RNAP - Abortive Initiation 229
9.4.2.3 Future Directions 230
9.5 Condusion 231
References 231
10 Two Rotary Motors of ATP Synthase 237
Ryota Uno and Hiroyuki Noji
10.1 Introduction 237
10.1.1 ATP Synthase: a Significant and Ubiquitous Enzyme in the Cell 237
10.1.2 Boyer's Proposal and Walker's Crystal Structure 238
10.2 Rotation of ATP Synthase 240
10.2.1 Single-molecule Imaging of Rotation of Fj Driven by ATP
Hydrolysis 240
10.2.1.1 Strategy for Visualization of Rotation 240
10.2.1.2 large Torque Generated by Fj 240
10.2.1.3 Steps in Rotation 242
10.2.1.4 A Model of Cooperative Chemo-mechanical Coupling in
Rotating Fi 243
10.2.2 Single-molecule Manipulation of Fi Rotation 244
10.2.2.1 Mechanical Activationof PausingFj 244
10.2.2.2 Highly Coupled ATP Synthesis by F! Forced to Rotate in the
Reverse Direction 246
10.2.3 Rotation of FOF, or Fo 249
10.2.3.1 Steps in the Rotation of FoFj driven by ATP hydrolysis 249
10.2.3.2 Ratchet versus Power Stroke as the Driving Force of Fo Rotation 249
10.2.3.3 Rotation of FoFj Driven by the Proton Motive Force 250
10.3 Perspectives 252
References 252
11 Single-molecule FRET Studies of Helicases and Holliday
Junctions 257
Taekjip Ha
11.1 Introduction 257
Contents XI
11.2 Single-molecule FRET 258
11.2.1 Non-perturbative Immobilization: BSA and PEG Surfaces, and
Vesicle Encapsulation 258
11.3 smFRETStudiesofRep Helicase 259
11.3.1 Helicase: Essential Motor Proteins on the Nudeic Acid Highway 260
11.3.2 Single-molecule Techniques Applied to Helicase Studies 261
11.3.3 Different Types of smFRET Approaches to Probe Helicase
Mechanisms 262
11.3.3.1 DNA-DNA FRET 262
11.3.3.2 Protein-DNA FRET 263
11.3.3.3 Repetitive Shuttling 263
11.3.3.4 ssDNA Flexibility 264
11.4 SmFRET Studies of Holliday Junction 265
11.4.1 StructureandFunctionofHJ 265
11.4.2 Conformer Transitions of Non-migratable HJ 266
11.4.2.1 Single-molecule Three-color FRET onHJ 268
11.4.3 Spontaneous Branch Migration Observed with a Single Step
Resolution 269
11.5 Outlook 271
References 271
12 High-speed Atomic Force Microscopy for Nano-visualization
of Biomolecu lar Processes 277
Toshio Ando, Takayuki Uchihashi, Noriyuki Kodera, Daisuke Yamamoto,
Masaaki Taniguchi, Atsushi Miyagi, and Hayato Yamashita
12.1 Introduction 277
12.2 AFM Set-up and Operation 278
12.3 Imaging Rate and Feedback Bandwidth 279
12.4 Feedback Operation and Parachuting 280
12.5 Key Devices for High-Speed AFM 281
12.5.1 Small Cantilevers and Related Devices 282
12.5.2 Scanner 282
12.5.3 Dynamic PID Control 284
12.6 Bioimaging 284
12.7 Other Type of Imaging 289
12.7.1 Phase-contrast Imaging 289
12.7.2 Recognition Imaging 290
12.8 Substratum 290
12.9 Future Prospects 291
References 294
13 Force-clamp Spectroscopyof Single Proteins 297
Lorna Dougan,Jasna Brujic, andjulio M. Femandez
13.1 Introduction 297
13.2 Single-protein AFM Techniques 298
XII Contents
13.2.1 Force-extension Spectroscopy 299
13.2.2 Force-damp Spectroscopy 300
13.3 Order Statistics in Unfolding 303
13.4 Disordered Free Energy Landscape 305
13.5 Protein Folding 306
13.5.1 The Force Quench Experiment 307
13.5.2 Developing a Model for Protein Folding 309
13.6 Force as a Probe of Protein Chemistry 313
13.7 Condusions 315
References 315
Index 323 |
| any_adam_object | 1 |
| author2 | Yanagida, Toshio Ishii, Yoshiharu |
| author2_role | edt edt |
| author2_variant | t y ty y i yi |
| author_GND | (DE-588)136889395 |
| author_facet | Yanagida, Toshio Ishii, Yoshiharu |
| building | Verbundindex |
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| callnumber-first | Q - Science |
| callnumber-label | QH317 |
| callnumber-raw | QH317 |
| callnumber-search | QH317 |
| callnumber-sort | QH 3317 |
| callnumber-subject | QH - Natural History and Biology |
| classification_rvk | VG 5150 WC 1200 WC 2050 WE 5460 |
| classification_tum | CHE 808f |
| ctrlnum | (OCoLC)271770315 (DE-599)DNB987897306 |
| dewey-full | 570.78 572.8 572.330154354 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 570 - Biology 572 - Biochemistry |
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| dewey-search | 570.78 572.8 572.330154354 |
| dewey-sort | 3570.78 |
| dewey-tens | 570 - Biology |
| discipline | Chemie / Pharmazie Biologie Chemie |
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| id | DE-604.BV035454126 |
| illustrated | Illustrated |
| indexdate | 2024-07-20T10:08:34Z |
| institution | BVB |
| isbn | 9783527312887 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-017374106 |
| oclc_num | 271770315 |
| open_access_boolean | |
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| owner_facet | DE-703 DE-11 DE-19 DE-BY-UBM DE-91G DE-BY-TUM |
| physical | XVIII, 328 S. Ill., graph. Darst. |
| publishDate | 2009 |
| publishDateSearch | 2009 |
| publishDateSort | 2009 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Single molecule dynamics in life science ed. by Toshio Yanagida and Yoshiharu Ishii Weinheim Wiley-VCH 2009 XVIII, 328 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Biology Laboratory manuals Models, Molecular Molecular Biology methods Molecular Structure Molecules Einzelmolekülspektroskopie (DE-588)4396226-9 gnd rswk-swf Biomolekül (DE-588)4135124-1 gnd rswk-swf Biomolekül (DE-588)4135124-1 s Einzelmolekülspektroskopie (DE-588)4396226-9 s DE-604 Yanagida, Toshio (DE-588)136889395 edt Ishii, Yoshiharu edt text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3080367&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017374106&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Klappentext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017374106&sequence=000006&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Single molecule dynamics in life science Biology Laboratory manuals Models, Molecular Molecular Biology methods Molecular Structure Molecules Einzelmolekülspektroskopie (DE-588)4396226-9 gnd Biomolekül (DE-588)4135124-1 gnd |
| subject_GND | (DE-588)4396226-9 (DE-588)4135124-1 |
| title | Single molecule dynamics in life science |
| title_auth | Single molecule dynamics in life science |
| title_exact_search | Single molecule dynamics in life science |
| title_full | Single molecule dynamics in life science ed. by Toshio Yanagida and Yoshiharu Ishii |
| title_fullStr | Single molecule dynamics in life science ed. by Toshio Yanagida and Yoshiharu Ishii |
| title_full_unstemmed | Single molecule dynamics in life science ed. by Toshio Yanagida and Yoshiharu Ishii |
| title_short | Single molecule dynamics in life science |
| title_sort | single molecule dynamics in life science |
| topic | Biology Laboratory manuals Models, Molecular Molecular Biology methods Molecular Structure Molecules Einzelmolekülspektroskopie (DE-588)4396226-9 gnd Biomolekül (DE-588)4135124-1 gnd |
| topic_facet | Biology Laboratory manuals Models, Molecular Molecular Biology methods Molecular Structure Molecules Einzelmolekülspektroskopie Biomolekül |
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| work_keys_str_mv | AT yanagidatoshio singlemoleculedynamicsinlifescience AT ishiiyoshiharu singlemoleculedynamicsinlifescience |