Protein NMR spectroscopy: practical techniques and applications
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Format: | Buch |
Sprache: | English |
Veröffentlicht: |
Chicester
Wiley
2011
|
Ausgabe: | 1. publ. |
Schlagworte: | |
Online-Zugang: | Inhaltsverzeichnis Klappentext |
Beschreibung: | Literaturangaben |
Beschreibung: | XIV, 351 S. Ill., graph. Darst. |
ISBN: | 0470721936 9780470721933 9781119972006 |
Internformat
MARC
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020 | |a 0470721936 |9 0-470-72193-6 | ||
020 | |a 9780470721933 |9 978-0-470-72193-3 | ||
020 | |a 9781119972006 |c oBook |9 978-1-1199-7200-6 | ||
035 | |a (OCoLC)755165812 | ||
035 | |a (DE-599)BVBBV037286477 | ||
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084 | |a CHE 808f |2 stub | ||
245 | 1 | 0 | |a Protein NMR spectroscopy |b practical techniques and applications |c ed. by Lu-Yun Lian ; Gordon Roberts |
250 | |a 1. publ. | ||
264 | 1 | |a Chicester |b Wiley |c 2011 | |
300 | |a XIV, 351 S. |b Ill., graph. Darst. | ||
336 | |b txt |2 rdacontent | ||
337 | |b n |2 rdamedia | ||
338 | |b nc |2 rdacarrier | ||
500 | |a Literaturangaben | ||
650 | 0 | 7 | |a Proteine |0 (DE-588)4076388-2 |2 gnd |9 rswk-swf |
650 | 0 | 7 | |a NMR-Spektroskopie |0 (DE-588)4075421-2 |2 gnd |9 rswk-swf |
689 | 0 | 0 | |a NMR-Spektroskopie |0 (DE-588)4075421-2 |D s |
689 | 0 | 1 | |a Proteine |0 (DE-588)4076388-2 |D s |
689 | 0 | |5 DE-604 | |
700 | 1 | |a Lian, Lu-Yun |4 edt | |
700 | 1 | |a Roberts, Gordon C. |4 edt | |
776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, EPUB |z 978-1-1199-7282-2 |
776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, MOBI |z 978-1-1199-7288-4 |
776 | 0 | 8 | |i Erscheint auch als |n Online-Ausgabe, PDF |z 978-1-1199-7201-3 |
856 | 4 | 2 | |m Digitalisierung UB Bayreuth |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021199149&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
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999 | |a oai:aleph.bib-bvb.de:BVB01-021199149 |
Datensatz im Suchindex
_version_ | 1804143918641577984 |
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adam_text | Contents
Ust
of Contributors
Introduction
Lu-Yun
Lian
and Gordon Roberts
References
1
Sample Preparation, Data Collection and Processing
Frederick W. Muskett
1
.1
Introduction
1
.2
Sample Preparation
1.2.1
Initial Considerations
1.2.2
Additives
1.2.3
Sample Conditions
1.2.4
Special Cases
1.2.5
NMR Sample Tubes
1.2.5.1 3
mm Tubes
1
.3
I
Data
Collection
1.3.1
Locking
1.3.2
Tuning
.3.3
Shimming
.3.4
Calibrating Pulses
.3.5
Acquisition Parameters
.3.6
Fast Acquisition Methods
1
4
Data
Processing
References
Xlii
1
4
5
5
5
6
7
7
8
9
10
11
11
11
12
13
14
16
17
20
2
Isotope Labelling
Milsuhiro Takeda and Masatsune Kainosho
2.1
Introduction
2.2
Production Methods for Isotopically Labelled Proteins
2.2.1
Recombinant
Protein Expression in Living Organisms
2.2.1.1
Escherichia
coli
2.2.1.2
Yeast Cells
2.2.1.3
Other Host Cells
23
23
24
24
24
25
25
vi
Contents
2.2.2
Cell-Free Synthesis
25
Protocol
1:
Preparation of the
Amino
Acid Free
S30 Extract
26
Protocol
2:
Cell-Free Reaction on a Small Scale
28
2.3
Uniform Isotope Labelling of Proteins
29
2.3.1
Uniform 15N Labelling
29
2.3.2
Uniform 13C, 15N Labelling
30
2.3.3
2H Labelling
30
2.4
Selective Isotope Labelling of Proteins
32
2.4.1
Amino
Acid Type-Selective Labelling
32
2.4.2
Reverse Labelling
34
2.4.3
Stereo-Selective Labelling
36
2.5
Segmental
Labelling
37
2.6
SAIL Methods
38
2.6.1
Concept of SAIL
38
2.6.2
Practical Procedure for the SAIL Method
41
Protocol
3:
Production of SAIL Proteins by the
E. coli
Cell-Free Method
41
2.6.3
Residue-Selective SAIL Method
42
Protocol
4:
Optimisation of the Amount of SAIL
Amino
Acids for
the Production of Calmodulin Selectively Labelled
by SAIL Phenylalanine
45
2.7
Concluding Remarks
45
Acknowledgements
46
References
46
3
Resonance Assignments
55
Lu-Yun
Lian
and Igor
L Borsukov
3.1
Introduction
55
3.2
Resonance Assignment of Unlabelled Proteins
56
3.2.1
Spin System Assignments
57
3.2.2
Sequence-Specific Assignments
59
3.2.3
Possible Difficulties
60
3.3
15N-Edited Experiments
60
3.4
Triple Resonance
62
3.4.1 3D
Triple Resonance
62
3.4.1.1
Identification of Spin Systems
64
3.4.1.2
Sequential Assignment
68
3.4.1.3
Proline
Residues
74
3.4.2
4D Triple Resonance
74
3.4.3
Computer-Assisted Backbone Assignments
76
3.4.4
Unstructured Proteins
76
3.4.5
Large Proteins
77
3.5
Side-Chain Assignments
77
References
81
Contents
vii
4
Measurement of Structural Restraints
83
Geerten W.
Vuister, Nico Tjandra,
Yang Shen, Alex Grishaev
and
Stephan
Grzesiek
4.1
Introduction
83
4.2
NOE-Based Distance Restraints
84
4.2.1
Physical Background
84
4.2.2
NMR Experiments for Measuring the
NOE
86
4.2.3
Set-up of NOESY Experiments
87
4.2.3.1
Estimation of T2s
87
Recipe
4.1: 1-1
Echo Experiment
88
Recipe
4.2:
Set-up of Optimal Acquisition Times
89
Recipe
4.3:
Set-up of a
3D
15N-Edited NOESY
Experiment (Figure 4.2a)
90
Recipe
4.4:
Set-up of a
3D
13C-Edited NOESY
Experiment
91
4.2.4
Deriving Structural Information from
NOE
Cross-peaks
92
Recipe
4.5:
Extraction of Distances Using Classes
95
Recipe
4.6:
Extraction of Distances Using the
Two-Spin Approximation
95
4.2.5
Information Content of
NOE
Restraints
95
4.3
Dihedral Restraints Derived from /-Couplings
96
4.3.1
Physical Background
96
4.3.2
NMR Experiments for Measuring /-Couplings
97
Recipe
4.7:
E.COSY Experiment
98
Recipe
4.8:
Quantitative /-Correlation
100
4.3.3
Deriving Structural Information from /-Couplings
102
4.4
Hydrogen Bond Restraints
103
4.4.1
NMR
Н
-Bond
Observables
103
4.4.2
Detection of N-H·
·
O=C
Н
-Bonds in Proteins
104
Recipe
4.9:
Setting up a Long-Range HNCO Experiment
for
Н
-Bond
Detection
106
4.5
Orientational Restraints
107
4.5.1
Physical Background
108
4.5.1.1
Dipolar Couplings in
Anisotropie
Solution
108
4.5.1.2
The Alignment Tensor
109
4.5.1.3
Chemical Shifts in
Anisotropie
Solution 111
4.5.2
Alignment Methods
112
4.5.2.1
Intrinsic Molecular Alignment
112
4.5.2.2
Indirect Alignment by External Media
113
4.5.3
Measurements and Data Analysis
116
4.5.4
Determination of the Alignment Tensor
118
4.5.4.1
Degeneracy of Solutions
121
4.5.4.2
Prediction of the Alignment Tensor from the Structure
121
4.5.5
RDCs in Structure Validation
122
4.5.5.1
Q-Factor
122
viii Contents
4.5.5.2
Using RDC Values for Database Screening
122
4.5.6
RDCs in Structure Determination
122
4.5.6.1
Structure Refinement
122
4.5.6.2
Domain Orientation
125
4.5.6.3
De Novo
Structure Determination
128
4.5.7
Conclusion
129
4.6
Chemical Shift Structural Restraints
129
4.6.1
Origin of Chemical Shifts and Its Relation to Protein Structure
129
4.6.2
Obtaining Chemical Shifts
131
4.6.3
Backbone Dihedral Angle Restraints from Chemical
Shifts
(TALOS)
132
Recipe
4.10:
Using the
TALOS
+
Program (for details see
http://spin.niddk.nih.gov/bax/software/TALOS
+ /) 132
4.6.4
Protein Structure Determination from Chemical
Shifts (CS-Rosetta)
134
Recipe
4.11:
CS-Rosetta Structure Calculation
136
4.7
Solution Scattering Restraints
137
4.7.1
Physical Background
137
4.7.2
Shape Reconstructions from Solution Scattering Data
139
4.7.3
Use of SAXS in High-Resolution Structure Determination
140
4.7.4
Sample Preparation
141
4.7.5
Data Collection
142
4.7.6
Data Processing and Initial Analysis
145
Acknowledgement
147
References
147
5
Calculation of Structures from NMR Restraints
159
Peter Guntert
5.1
Introduction
159
5.2
Historical Development
161
5.3
Structure Calculation Algorithms
164
5.3.1
Molecular Dynamics Simulation versus NMR Structure
Calculation
164
5.3.2
Potential Energy
-
Target Function
165
5.3.3
Torsion Angle Dynamics
166
5.3.3.1
Tree Structure
167
5.3.3.2
Kinetic Energy
167
5.3.3.3
Forces
=
Torques
=—
Gradient of the Target Function
169
5.3.3.4
Equations of Motion
169
5.3.3.5
Torsionai
Accelerations
170
5.3.3.6
Time Step
171
5.3.4
Simulated Annealing
172
Protocol for Simulated Annealing
172
5.4
Automated
NOE
Assignment
173
5.4.1
Ambiguity of Chemical Shift Based NOESY Assignment
174
Contents ix
5.4.2
Ambiguous Distance Restraints
175
5.4.3
Combined Automated
NOE
Assignment and Structure
Calculation with CYANA
175
5.4.4
Network-Anchoring I77
5.4.5
Constraint Combination I77
5.4.6
Structure Calculation Cycles I77
5.5
Nonclassical Approaches
178
5.5.1
Assignment-Free Methods
178
5.5.2
Methods Based on Residual Dipolar Couplings
179
5.5.3
Chemical Shift-Based Structure Determination
180
5.6
Fully Automated Structure Analysis
181
References
185
6
Paramagnetic Tools in Protein NMR
193
Peter H.J.
Keizers
and
Marcellus Ubbink
6.1
Introduction
193
6.2
Types of Restraints I94
6.2.1
Paramagnetic Dipolar Relaxation Enhancement
194
6.2.2
Other Types of Relaxation
197
6.2.3
Residual Dipolar Couplings
197
6.2.4
Contact and Pseudocontact Shifts
199
6.3
What Metals to Use?
200
6.4
Paramagnetic Probes
203
6.4.1
Substitution of Metals
203
6.4.2
Free Probes
204
6.4.3
Nitroxide Labels
204
6.4.4
Metal Binding Peptides
205
6.4.5
Synthetic Metal Chelating Tags
206
Protocol for the Application of Paramagnetic NMR
on Diamagnetic Proteins
207
6.5
Examples
209
6.5.1
Structure Determination of Paramagnetic Proteins
209
6.5.2
Structure Determination Using Artificial Paramagnets
209
6.5.3
Structures of Protein Complexes
210
6.5.4
Studying Dynamics with Paramagnetism
211
6.6
Conclusions and Perspective
212
References
213
7
Structural and Dynamic Information on Ligand Binding
221
Gordon Roberts
7.1
Introduction
221
7.2
Fundamentals of Exchange Effects on NMR Spectra
222
7.2.1
Definitions
222
7.2.2
Lineshape
225
7.2.3
Identification of the Exchange Regime
227
χ
Contents
7.3
Measurement of Equilibrium and Rate Constants
229
7.3.1
Lineshape Analysis
229
7.3.1.1
Slow Exchange
229
7.3.1.2
Fast Exchange
230
7.3.2
Magnetisation Transfer Experiments
231
7.3.2.1
Saturation Transfer
233
7.3.2.2
Inversion Transfer
233
7.3.2.3
Two-Dimensional Exchange Spectroscopy
233
7.3.3
Relaxation Dispersion Experiments
235
7.4
Detecting Binding
-
NMR Screening
238
7.4.1
Detecting Binding by Changes in Rotational and
Translation^ Mobility of the Ligand
239
7.4.2
Detecting Binding by Magnetisation Transfer
240
7.4.2.1
Saturation Transfer Difference (STD) Spectroscopy
240
7.4.2.2
Water-LOGSY
241
7.5
Mechanistic Information
241
7.5.1
Problems of Fast Exchange
242
7.5.2
Identification of Kinetic Mechanisms
242
7.5.2.1
Slow Exchange
243
7.5.2.2
Fast Exchange
243
7.6
Structural Information
246
7.6.1
Ligand Conformation
-
the Transferred
NOE
246
7.6.1.1
Exchange Rate
248
7.6.1.2
Contributions from Other Species
249
7.6.1.3
Spin Diffusion
250
7.6.1.4
Structure Calculation
251
7.6.2
Interligand Transferred NOEs
251
7.6.2.1
Two Ligands Bound Simultaneously
252
7.6.2.2
Competitive Ligands
-
INPHARMA
252
7.6.3
Ligand Conformation
-
Transferred Cross-Correlated
Relaxation
253
7.6.4
Chemical Shift Mapping
-
Location of the Binding Site
253
7.6.5
Paramagnetic Relaxation Experiments
254
7.6.6
Isotope-Filtered and -Edited Experiments
256
References
259
8
Macromolecular Complexes
269
Paul
С
Driscoll
8.1
Introduction
269
8.2
Spectral Simplification through Differential Isotope Labelling
270
8.3
Basic NMR Characterisation of Complexes
273
Protocol for Protein-Protein Titrations
273
8.4 3D
Structure Determination of Macromolecular Protein-Ligand
Complexes
277
8.4.1
NOEs
277
8.5
Contents
xi
8.4.2 Saturation Transfer
282
8.4.3 Residual
Dipolar Couplings
286
8.4.4
Paramagnetic
Relaxation
Enhancements
289
8.4.5
Pseudo-Contact Shifts
291
8.4.6
Data-Driven
Docking
293
8.4.7
Small Angle
Х
-Ray Scattering (SAXS)
296
Literature Examples
297
8.5.1
Protein-Protein Interactions
297
8.5.2
Protein-DNA Interactions
301
8.5.3
Protein-RNA Interaction
303
8.5.3.1
Protein-dsRNA
303
8.5.3.2
Protein-ssRNA
305
tices
310
9
Studying Partially Folded and Intrinsically Disordered
Proteins Using NMR Residual Dipolar Couplings
319
Malene
Ringkj0bing Jensen,
Valéry
Ozenne,
Loie
Salmon,
Gábriellé Nődet,
Phineus Markwick,
Pau
Bernadó
and Martin Blackledge
9.1
Introduction
319
9.2
Ensemble Descriptions of Unfolded Proteins
320
9.3
Experimental Techniques for the Characterisation of IDPs
320
9.4
NMR Spectroscopy of Intrinsically Disordered Proteins
321
9.4.1
Chemical Shifts
321
9.4.2
Scalar Couplings
322
9.4.3
Nuclear Overhauser Enhancements
322
9.4.4
Paramagnetic Relaxation Enhancements
322
9.4.5
Residual Dipolar Couplings
323
9.5
Residual Dipolar Couplings
323
9.5.1
Interpretation of RDCs in Disordered Proteins
324
9.5.2
RDCs in Highly Flexible Systems: Explicit Ensemble Models
327
9.5.3
RDCs to Detect Deviation from Random Coil
Behaviour in IDPs
329
9.5.4
Multiple RDCs Increase the Accuracy of Determination
of Local Conformational Propensity
333
9.5.5
Quantitative Analysis of Local Conformational Propensities
from RDCs
335
9.5.6
Conformational Sampling in the Disordered Transactivation
Domain of p53
339
9.6
Conclusions
340
References
340
Index
347
Protein NMR Spectroscopy:
Principal
Techniques
and
Applications
Editors
LU
~
Y U
Π
LI d
Π
Institute of
Integrative
Biology, University of Liverpool, UK
KODGľlS
Department of Biochemistry, University of Leicester, UK
Nuclear Magnetic Resonance (NMR) spectroscopy, a physical phenomenon based upon
the magnetic properties of certain atomic nuclei, has found a wide range of applications
in life sciences over recent decades. The dramatic advances in NMR techniques have led
to corresponding advances in the ability of NMR to study the structure, dynamics and
interactions of biological macromolecules in solution under close to physiological conditions.
This volume focuses on the use of NMR to study proteins.
NMR can be used to determine detailed three-dimensional structures of proteins in
solution. Furthermore, it provides information about conformational or chemical
exchange, internal mobility and dynamics at timescales varying from picoseconds to
seconds. It is the primary technique used to obtain information on intrinsically disordered
(unfolded) proteins, since these proteins will not crystallize easily. NMR is also a very
powerful method for the study of interactions of proteins with other molecules,
whether small molecules (including drugs), nucleic acids or other proteins.
This up-to-date volume covers NMR techniques and their application to proteins, with
a focus on practical details. This book will provide a newcomer to NMR with the practical
guidance in order to carry out successful experiments with proteins and to analyze the
resilWng spectra. Those who are familiar with the chemical applications of NMR will
alsq fifid it useful in understanding the special requirements of protein NMR.
Enjoyed this book?
|
any_adam_object | 1 |
author2 | Lian, Lu-Yun Roberts, Gordon C. |
author2_role | edt edt |
author2_variant | l y l lyl g c r gc gcr |
author_facet | Lian, Lu-Yun Roberts, Gordon C. |
building | Verbundindex |
bvnumber | BV037286477 |
classification_rvk | UP 9400 WC 2600 |
classification_tum | CHE 820f CHE 244f CHE 808f |
ctrlnum | (OCoLC)755165812 (DE-599)BVBBV037286477 |
dewey-full | 572.6 |
dewey-hundreds | 500 - Natural sciences and mathematics |
dewey-ones | 572 - Biochemistry |
dewey-raw | 572.6 |
dewey-search | 572.6 |
dewey-sort | 3572.6 |
dewey-tens | 570 - Biology |
discipline | Physik Biologie Chemie |
edition | 1. publ. |
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id | DE-604.BV037286477 |
illustrated | Illustrated |
indexdate | 2024-07-09T22:55:18Z |
institution | BVB |
isbn | 0470721936 9780470721933 9781119972006 |
language | English |
oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-021199149 |
oclc_num | 755165812 |
open_access_boolean | |
owner | DE-11 DE-91G DE-BY-TUM DE-20 DE-703 DE-19 DE-BY-UBM |
owner_facet | DE-11 DE-91G DE-BY-TUM DE-20 DE-703 DE-19 DE-BY-UBM |
physical | XIV, 351 S. Ill., graph. Darst. |
publishDate | 2011 |
publishDateSearch | 2011 |
publishDateSort | 2011 |
publisher | Wiley |
record_format | marc |
spelling | Protein NMR spectroscopy practical techniques and applications ed. by Lu-Yun Lian ; Gordon Roberts 1. publ. Chicester Wiley 2011 XIV, 351 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Literaturangaben Proteine (DE-588)4076388-2 gnd rswk-swf NMR-Spektroskopie (DE-588)4075421-2 gnd rswk-swf NMR-Spektroskopie (DE-588)4075421-2 s Proteine (DE-588)4076388-2 s DE-604 Lian, Lu-Yun edt Roberts, Gordon C. edt Erscheint auch als Online-Ausgabe, EPUB 978-1-1199-7282-2 Erscheint auch als Online-Ausgabe, MOBI 978-1-1199-7288-4 Erscheint auch als Online-Ausgabe, PDF 978-1-1199-7201-3 Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021199149&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis Digitalisierung UB Bayreuth application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021199149&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA Klappentext |
spellingShingle | Protein NMR spectroscopy practical techniques and applications Proteine (DE-588)4076388-2 gnd NMR-Spektroskopie (DE-588)4075421-2 gnd |
subject_GND | (DE-588)4076388-2 (DE-588)4075421-2 |
title | Protein NMR spectroscopy practical techniques and applications |
title_auth | Protein NMR spectroscopy practical techniques and applications |
title_exact_search | Protein NMR spectroscopy practical techniques and applications |
title_full | Protein NMR spectroscopy practical techniques and applications ed. by Lu-Yun Lian ; Gordon Roberts |
title_fullStr | Protein NMR spectroscopy practical techniques and applications ed. by Lu-Yun Lian ; Gordon Roberts |
title_full_unstemmed | Protein NMR spectroscopy practical techniques and applications ed. by Lu-Yun Lian ; Gordon Roberts |
title_short | Protein NMR spectroscopy |
title_sort | protein nmr spectroscopy practical techniques and applications |
title_sub | practical techniques and applications |
topic | Proteine (DE-588)4076388-2 gnd NMR-Spektroskopie (DE-588)4075421-2 gnd |
topic_facet | Proteine NMR-Spektroskopie |
url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021199149&sequence=000003&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=021199149&sequence=000004&line_number=0002&func_code=DB_RECORDS&service_type=MEDIA |
work_keys_str_mv | AT lianluyun proteinnmrspectroscopypracticaltechniquesandapplications AT robertsgordonc proteinnmrspectroscopypracticaltechniquesandapplications |