Biophysical analysis of membrane proteins: investigating structure and function
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Weinheim
WILEY-VCH
2008
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| Online Access: | Inhaltstext Inhaltsverzeichnis |
| Physical Description: | XX, 347 S. Ill., graph. Darst. 240 mm x 170 mm |
| ISBN: | 9783527316779 3527316779 |
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| 245 | 1 | 0 | |a Biophysical analysis of membrane proteins |b investigating structure and function |c ed. by Eva Pebay-Peyroula |
| 264 | 1 | |a Weinheim |b WILEY-VCH |c 2008 | |
| 300 | |a XX, 347 S. |b Ill., graph. Darst. |c 240 mm x 170 mm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Membranproteine - Struktur-Aktivitäts-Beziehung | |
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| 650 | 0 | 7 | |a Biophysik |0 (DE-588)4006891-2 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Membranproteine |0 (DE-588)4130026-9 |2 gnd |9 rswk-swf |
| 689 | 0 | 0 | |a Membranproteine |0 (DE-588)4130026-9 |D s |
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| 700 | 1 | |a Pebay-Peyroula, Eva |e Sonstige |4 oth | |
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Contents
Preface XIII
The Editor
XV
List of Contributors
XVII
Part I Introduction
1
High-Resolution Structures of Membrane Proteins:
From
Х
-Ray Crystallography to an Integrated Approach
of Membranes
3
Eva Pebay-Peyrouia
1.1
Membranes: A Soft Medium?
3
1.2
Current Knowledge on Membrane Protein Structures
4
1.2.1
An Overview of the Protein Data Bank
4
1.2.2
Protein Sources for Structural Studies
5
1.2.3
The Diversity of Membrane Protein Topologies
6
1.2.4
Genome Analyses
8
1.3
Х
-Ray Crystallography
8
1.3.1
Crystallization of Membrane Proteins
9
1.3.2
General Aspects of Crystallography
11
1.3.3
Determining the Phases Associated with Diffracted Waves
13
1.3.4
Structure Determination of Membrane Proteins
14
1.3.4.1
Crystal Quality
14
1.3.4.2
Phase Determination
14
1.3.4.3
Crystal Freezing
14
1.4
Recent Examples
16
1.4.1
Bacterial Rhodopsins
16
1.4.2
ADP/ATP Carrier
17
1.4.3
Oligomerization of Membrane Proteins in their Natural
Environment
22
1.5
Future Developments in
Х
-Ray Crystallography of Membrane
Proteins
23
1.6
Conclusions
25
VI
Contents
Part II Structural Approaches
2
Membrane Protein Structure Determination by Electron
Cryo-Microscopy
31
Christopher C.
Tate
and John
L
Rubinstein
2.1
Introduction
32
2.1.1
The Electron Microscope
33
2.2
Single-Particle Electron Microscopy
33
2.2.1
Sample Preparation and Requirements
35
2.2.1.1
Negative Staining of Specimens
36
2.2.1.2
Cryo-EM of Unstained Specimens
36
2.2.1.3
Choice of detergent
38
2.2.2
Image Analysis
38
2.2.2.1
Classification of Images
38
2.2.2.2
Model Building and Refinement
39
2.2.2.3
Assessing Resolution
40
2.2.3
Future Perspectives
41
2.3
Structure Determination from 2-Dimensional Crystals
41
2.3.1
Two-Dimensional Crystallization of Membrane Proteins
44
2.3.2
Image Acquisition and Structure Determination
46
2.3.3
Future Perspectives
49
2.4
Helical Analysis of Tubes
49
2.5
Conclusions
51
3
Introduction to Solid-State NMR and its Application to Membrane
Protein-Ligand Binding Studies
55
Krisztina
Varga
and Anthony Watts
3.1
Introduction
55
3.1.1
Membrane Proteins: A Challenge
55
3.1.2
Why Solid-State NMR?
56
3.2
Solid-State NMR
57
3.2.1
Sample Preparation: What is an Ideal Sample?
58
3.2.1.1
Availability
58
3.2.1.2
Stability
58
3.2.1.3
Secondary Structure
59
3.2.1.4
Sample Form: Local Order
59
3.2.2
NMR Active Isotopes and Labeling
60
3.2.3
Assignment and Structure Determination
62
3.2.4
NMR Techniques: Solution- versus Solid-State NMR
63
3.2.4.1
Isotropie
Liquids
63
3.2.4.2 Anisotropie
Liquids
63
3.2.4.3
Solids
64
3.3
Examples: Receptor-Ligand Studies by Solid-State NMR
70
3.3.1
Transport Proteins
71
3.3.1.1
LacS
71
Contents
VII
3.3.2 G-Protein-Coupled
Receptors and Related Proteins
71
3.3.2.1
Bacteriorhodopsin, Rhodopsin, and Sensory Rhodopsin (NpSRII)
72
3.3.2.2
Human Hj Receptor
74
3.3.2.3
Neurotensin Receptor
74
3.3.3
Ion Channels
74
3.3.3.1
Nicotinic Acetylcholine Receptor
74
3.3.3.2
K+ Ion Channel, KcsA
75
3.3.4
P-type ATPases
75
3.3.5
Membrane Protein Soluble Alternatives
78
Part III Molecular Interaction and Large Assemblies
4
Analytical Ultracentrifugation: Membrane Protein Assemblies in the
Presence of Detergent
91
Christine
Ebei,
Jesper
V.
М0ІІег
and Marc
le Maire
4.1
Introduction
91
4.2
Instrumentation and the Principle of Typical Experiments
92
4.3
General Theoretical Background
93
4.3.1
Equation of the Transport
93
4.3.2
The Macromolecular Parameters: Rs, Mh, M, and
v
95
4.3.3
The
Svedberg
Equation
96
4.3.3.1
Mean values of Mb and
s
96
4.3.4
Non-Ideality
96
4.4
Membrane Proteins: Measurement of Rs, Mj, M, and
v
97
4.4.1
Composition and Molar Mass
97
4.4.2
Values of
v
98
4.4.3
Buoyant Mass for Detergent-Solubilized Membrane Proteins,
MÇk
99
4.4.4
Stokes Radius, Frictional Ratio
100
4.4.5
The Example of the Membrane Protein BmrA
101
4.5
Sedimentation Equilibrium Data Analysis
103
4.5.1
Equation of Sedimentation Equilibrium and Comments on the
Experimental Set-Up
103
4.5.2
Simulation of Sedimentation Equilibrium for a Mixture of
Particles
104
4.5.3
Analysis of Data
105
4.5.4
Matching of Surfactant and Solvent Densities
106
4.5.5
Determining the Association States and Dissociation Constant in the
Presence of Non-Density-Matched Detergent
107
4.5.6
Dependency of Association Constants on Detergent
Concentration
107
4.6
Sedimentation Velocity Data Analysis
108
4.6.1
Numerical Solutions of the Lamm Equation
108
4.6.2
Analysis in Terms of Non-Interacting Species: Principle
109
4.6.3
Analysis in Terms of Non-Interacting Species: Applications to
Detergent and the Membrane Protein EmrE
109
VIII Contents
4.6.4
c(s)
Analysis: Principle
110
4.6.5
Sedimentation Velocity Simulation and c(s) Analysis for a
Hypothetical Sample of Membrane Proteins 111
4.6.6
Example of Characterization of a Membrane Protein by Sedimentation
Velocity
113
4.6.6.1
Association State of Na+-K+-ATPase Expressed in Pichia
pastoris
and of
Sarcoplasmic
Ca2ł-ATPase
113
4.6.6.2
Complex Behavior in Solution of New Amphiphilic
Compounds
114
4.6.6.3
The Sh/sd Method
114
4.6.7
General Potentials of the c(s) Analysis per
se as a
Prelude to more
Sophisticated Analysis
115
4.7
Analytical Ultracentrifugation and
SANS/SAXS
116
4.8
Conclusions
116
5
Probing Membrane Protein Interactions with
Real-Time
Biosensor
Technology
121
lva Navrátilova,
David
С.
Myszka
and Rebecca
L
Rich
5.1
Introduction
121
5.2
Interactions of Extracellular Domains
123
5.3
Interactions of Soluble Proteins with
Lipid
Layers
124
5.4
Interactions of Proteins Embedded in
Lipid
Layers
129
5.4.1
On-Surface
Reconstitution
of G-Protein-Coupled Receptor
129
5.4.2
Capture/Reconstitution
of GPCRs
131
5.5
Interactions of Membrane-Solubilized Proteins
131
5.6
Summary
138
6
Atomic Force Microscopy: High-Resolution Imaging of Structure and
Assembly of Membrane Proteins
141
Simon
Scheuring,
Nikolay Buzhynskyy,
Rui
Pedro
Concalves
and
Szymon Jaroslawski
6.1
Atomic Force Microscopy
141
6.1.1
Sample Preparation
141
6.1.2
Equipment and Experimental Procedure
141
6.1.3
Experimental Rationales
142
6.2
Combined Imaging and Force Measurements by AFM
145
6.2.1
Imaging and Force Measurement of a Bacterial Surface Layer
(S-Layer)
145
6.3
High-Resolution Imaging by AFM
147
6.3.1
High-Resolution AFM of Aquaporin-Z (AQPZ)
147
6.3.2
High-Resolution AFM of Aquaporin-0 (AQPO)
148
6.3.3
Comparison Between AQPZ and AQPO Topographies
350
6.3.4
The Supramolecular Assembly of Photosynthetic Complexes
in Native Membranes of
Rhodospiríllum photometricum
by AFM
150
Contents
IX
6.3.5 AQPO-Connexon
Junction Platforms in Native Sheep Lens
Membranes
152
6.4
Conclusions
153
6.5
Feasibilities, Limitations, and Outlook
153
Part IV Dynamics
7
Molecular Dynamics Studies of Membrane Proteins: Outer Membrane
Proteins and Transporters
161
Syma Khalid, John Holyoake and Mark S. P.
Šansom
7.1
Introduction
161
7.1.1
Molecular Dynamics Simulations
161
7.2
Outer Membrane Proteins
163
7.2.1
OmpA
163
7.2.2
Simulations of OMPs in Diverse Environments
265
7.2.3
Porins
167
7.2.4
More Complex Outer Membrane Transporters
167
7.2.4.1
TonB-Dependent Transporters
168
7.2.4.2 Autotransporters 169
7.2.4.3
TolC
170
7.3
Cytoplasmic Membrane Transport Proteins
172
7.3.1
Simulated State Transitions
172
7.3.1.1
BtuCD
173
7.3.1.2
LacY
175
7.3.2
Intrinsic Flexibilities
176
7.3.3
Non-Equilibrium Methods
178
7.3.4
Homology Models
178
7.4
Conclusions
179
8
Understanding Structure and Function of Membrane Proteins Using Free
Energy Calculations
187
Christophe
Chĺpot
and Klaus
Schulten
8.1
Introduction
387
8.2
Theoretical Underpinnings of Free Energy Calculations
188
8.2.1
Alchemical Transformations
188
8.2.1.1
What is Usually Implied by Small Changes?
189
8.2.1.2
How is the Coupling Parameter Defined?
190
8.2.1.3
Thermodynamic Integration
192
8.2.2
Free Energy Changes Along a Reaction Coordinate
192
8.2.2.1
Umbrella Sampling or Stratification?
193
8.2.2.2
Adaptive Biasing Force
194
8.2.2.3
Non-Equilibrium Simulations for Equilibrium Free Energies
194
8.3
Point Mutations in Membrane Proteins
196
8.3.1
Why Have Free Energy Calculations Been Applied only Sparingly to
Membrane Proteins?
196
X
Contents
8.3.2
Gaining New Insights into Potassium Channels
197
8.3.3
Tackling the Assisted Transport of Ammonium Using FEP
198
8.3.4
How Relevant are Free Energy Calculations in Models of Membrane
Proteins?
198
8.4
Assisted Transport Phenomena Across Membranes
199
8.4.1
Gramicidin: A Paradigm for Assisted Transport Across
Membranes
199
8.4.2
Free Energy Calculations and Potassium Channels
200
8.4.3
Non-Equilibrium Simulations for Understanding Equilibrium
Phenomena
201
8.4.4
Deciphering Transport Mechanisms in Aquaporins
202
8.4.5
Non-Equilibrium Simulations and Potassium Channels
203
8.5
Recognition and Association in Membrane Proteins
204
8.5.1
The "Two-Stage" Model
204
8.5.2
Glycophorin A: A Paradigmatic System for Tackling Recognition and
Association in Membranes
205
8.6
Conclusions
206
9
Neutrons to Study the Structure and Dynamics of Membrane
Proteins
213
Kathleen Wood and Giuseppe Zaccai
9.1
General Introduction
213
9.2
Introduction to Neutrons
213
9.2.1
Production and Properties of the Neutron
213
9.2.2
Interaction Between Neutrons and Matter
214
9.2.3
Scattering Law
216
9.2.4
Coherent and Incoherent scattering
216
9.2.5
Instruments
218
9.3
Introduction to Bacteriorhodopsin and the Purple Membrane
219
9.4
Methods for Labeling
221
9.4.1
Biosynthetic Labeling
221
9.4.2
Reconstitution
221
9.5
Neutrons for Structural Studies of Membrane Proteins
222
9.5.1
Neutron Diffraction
222
9.5.1.1
Bacteriorhodopsin
222
9.5.1.2
Lipids
223
9.5.1.3
Water
224
9.5.2
Low-Resolution Studies
224
9.5.2.1
Small-Angle Neutron Scattering of Membrane Proteins in
D-Vesicles
224
9.5.2.2
Low-Resolution Single-Crystal Studies
227
9.5.2.3
Reflectivity
227
9.6
Neutrons for Dynamical Studies of Membrane Proteins
231
9.6.1
Energy-Resolved Experiments
231
9.6.1.1
Time and Space Scales
232
Contents
XI
9.6.2
Elastic
Scattering and Atomic Mean Square Displacements
233
9.6.3
Quasi-Elastic Scattering
235
9.6.4
Inelastic Scattering
235
9.6.5
Other Types of Measurement
235
9.7
Take-Home Message
237
Part V Spectroscopies
Ί0
Circular Dichroism: Folding and Conformational Changes of Membrane
Proteins
243
Nadège
Jamin and
Jean-Jacques bucapere
10.1
Introduction
243
10.2
Secondary Structure Composition
244
10.3
Tertiary Structure Fingerprint
250
10.4
Extrinsic Chromophores
252
10.5
Conformational Changes upon Ligand Binding
252
10.6
Folding/Unfolding
254
10.7
Conclusion and Perspectives
255
Π
Membrane Protein Structure and Conformational Change Probed using
Fourier Transform Infrared Spectroscopy
259
John E. Baenziger and Come
J. B. daCosta
11.1
Introduction
259
11.2
FTIR Spectroscopy
260
11.2.1
Attenuated Total Reflectance FTIR Spectroscopy
260
11.2.2
Detecting Changes in Side Chain Structure/Environment During
Protein Conformational Change
263
11.2.3
Probing the Orientation of Functional Groups
266
11.3
Vibrational Spectra of Membrane Proteins
267
11.3.1
Lipid
Vibrations
268
11.3.1.1
Lipid
Ester C=O
268
11.3.1.2
Lipid Methylene
C
-Н
269
11.3.2
Protein Backbone Vibrations
269
11.3.2.1
Amide I
269
11.3.2.2
Amide II
272
11.3.3
Protein Side-Chain Vibrations
272
11.4
Applications of FTIR To Membrane Proteins
273
11.4.1
Testing Protein Structural Models and Validating the Structures of
Mutant Proteins
273
11.4.2
Lipid-Protein Interactions
276
11.4.3
Receptor-Drug Interactions
278
11.4.4
Chemistry of Receptor-Ligand Interactions
281
11.4.5
Changes in Orientation of Functional Groups During Conformational
Change
282
11.4.6
A Tool in the Crystallization of Integral Membrane Proteins
284
11.5
Conclusions and Future Directions
286
XII
I Contents
12
Resonance Raman Spectroscopy of a Light-Harvesting Protein
289
Andrew Aaron Pascal and Bruno Robert
12.1
Introduction
289
12.2
Principles of Resonance Raman Spectroscopy
289
12.3
Primary Processes in Photosynthesis
291
12.4
Photosynthesis in Plants
292
12.5
The Light-Harvesting System of Plants
293
12.6
Protection against Oxidative Stress: Light-Harvesting Regulation in
Plants
294
12.7
Raman studies of
ШСИ
297
12.8
Crystallographic Structure of LHCII
301
12.9
Properties of LHCII in Crystal
302
12.10
Recent Developments and Perspectives
305
Part VI Exploring Structure-Function Relationships in Whole Cells
13
Energy Transfer Technologies to Monitor the Dynamics and Signaling
Properties of G-Protein-Coupled Receptors in Living Cells
311
Jean-Philippe Pin, Mohammed-Akli Ayoub, Damien
Maurei,
Julie Perroy
and
Eric Trinquet
13.1
Introduction
311
13.2
Fluorescence Resonance Energy Transfer (FRET)
312
13.3
FRET Using GFP and its Various Mutants
314
13.4
BRET as an Alternative to FRET
315
13.5
Time-Resolved FRET (TR-FRET) and Homogeneous Time-Resolved
Fluorescence (HTRF)
318
13.6
New Developments in Fluorescent Labeling of Membrane
Proteins
320
13.7
Ligand-Receptor Interaction Monitored by FRET
322
13.8
Fast GPCR Activation Process Monitored in Living Cells
323
13.9
FRET and BRET Validated the Constitutive Oligomerization of GPCR
in Living Cells
324
13.10
FRET and BRET Changed the Concept of G-Protein Activation
326
13.11
GPCRs as Part of Large Signaling Complexes
327
13.12
Conclusion and Future Prospects
328
Index
335 |
| adam_txt |
Contents
Preface XIII
The Editor
XV
List of Contributors
XVII
Part I Introduction
1
High-Resolution Structures of Membrane Proteins:
From
Х
-Ray Crystallography to an Integrated Approach
of Membranes
3
Eva Pebay-Peyrouia
1.1
Membranes: A Soft Medium?
3
1.2
Current Knowledge on Membrane Protein Structures
4
1.2.1
An Overview of the Protein Data Bank
4
1.2.2
Protein Sources for Structural Studies
5
1.2.3
The Diversity of Membrane Protein Topologies
6
1.2.4
Genome Analyses
8
1.3
Х
-Ray Crystallography
8
1.3.1
Crystallization of Membrane Proteins
9
1.3.2
General Aspects of Crystallography
11
1.3.3
Determining the Phases Associated with Diffracted Waves
13
1.3.4
Structure Determination of Membrane Proteins
14
1.3.4.1
Crystal Quality
14
1.3.4.2
Phase Determination
14
1.3.4.3
Crystal Freezing
14
1.4
Recent Examples
16
1.4.1
Bacterial Rhodopsins
16
1.4.2
ADP/ATP Carrier
17
1.4.3
Oligomerization of Membrane Proteins in their Natural
Environment
22
1.5
Future Developments in
Х
-Ray Crystallography of Membrane
Proteins
23
1.6
Conclusions
25
VI
Contents
Part II Structural Approaches
2
Membrane Protein Structure Determination by Electron
Cryo-Microscopy
31
Christopher C.
Tate
and John
L
Rubinstein
2.1
Introduction
32
2.1.1
The Electron Microscope
33
2.2
Single-Particle Electron Microscopy
33
2.2.1
Sample Preparation and Requirements
35
2.2.1.1
Negative Staining of Specimens
36
2.2.1.2
Cryo-EM of Unstained Specimens
36
2.2.1.3
Choice of detergent
38
2.2.2
Image Analysis
38
2.2.2.1
Classification of Images
38
2.2.2.2
Model Building and Refinement
39
2.2.2.3
Assessing Resolution
40
2.2.3
Future Perspectives
41
2.3
Structure Determination from 2-Dimensional Crystals
41
2.3.1
Two-Dimensional Crystallization of Membrane Proteins
44
2.3.2
Image Acquisition and Structure Determination
46
2.3.3
Future Perspectives
49
2.4
Helical Analysis of Tubes
49
2.5
Conclusions
51
3
Introduction to Solid-State NMR and its Application to Membrane
Protein-Ligand Binding Studies
55
Krisztina
Varga
and Anthony Watts
3.1
Introduction
55
3.1.1
Membrane Proteins: A Challenge
55
3.1.2
Why Solid-State NMR?
56
3.2
Solid-State NMR
57
3.2.1
Sample Preparation: What is an Ideal Sample?
58
3.2.1.1
Availability
58
3.2.1.2
Stability
58
3.2.1.3
Secondary Structure
59
3.2.1.4
Sample Form: Local Order
59
3.2.2
NMR Active Isotopes and Labeling
60
3.2.3
Assignment and Structure Determination
62
3.2.4
NMR Techniques: Solution- versus Solid-State NMR
63
3.2.4.1
Isotropie
Liquids
63
3.2.4.2 Anisotropie
Liquids
63
3.2.4.3
Solids
64
3.3
Examples: Receptor-Ligand Studies by Solid-State NMR
70
3.3.1
Transport Proteins
71
3.3.1.1
LacS
71
Contents
VII
3.3.2 G-Protein-Coupled
Receptors and Related Proteins
71
3.3.2.1
Bacteriorhodopsin, Rhodopsin, and Sensory Rhodopsin (NpSRII)
72
3.3.2.2
Human Hj Receptor
74
3.3.2.3
Neurotensin Receptor
74
3.3.3
Ion Channels
74
3.3.3.1
Nicotinic Acetylcholine Receptor
74
3.3.3.2
K+ Ion Channel, KcsA
75
3.3.4
P-type ATPases
75
3.3.5
Membrane Protein Soluble Alternatives
78
Part III Molecular Interaction and Large Assemblies
4
Analytical Ultracentrifugation: Membrane Protein Assemblies in the
Presence of Detergent
91
Christine
Ebei,
Jesper
V.
М0ІІег
and Marc
le Maire
4.1
Introduction
91
4.2
Instrumentation and the Principle of Typical Experiments
92
4.3
General Theoretical Background
93
4.3.1
Equation of the Transport
93
4.3.2
The Macromolecular Parameters: Rs, Mh, M, and
v
95
4.3.3
The
Svedberg
Equation
96
4.3.3.1
Mean values of Mb and
s
96
4.3.4
Non-Ideality
96
4.4
Membrane Proteins: Measurement of Rs, Mj, M, and
v
97
4.4.1
Composition and Molar Mass
97
4.4.2
Values of
v
98
4.4.3
Buoyant Mass for Detergent-Solubilized Membrane Proteins,
MÇk
99
4.4.4
Stokes Radius, Frictional Ratio
100
4.4.5
The Example of the Membrane Protein BmrA
101
4.5
Sedimentation Equilibrium Data Analysis
103
4.5.1
Equation of Sedimentation Equilibrium and Comments on the
Experimental Set-Up
103
4.5.2
Simulation of Sedimentation Equilibrium for a Mixture of
Particles
104
4.5.3
Analysis of Data
105
4.5.4
Matching of Surfactant and Solvent Densities
106
4.5.5
Determining the Association States and Dissociation Constant in the
Presence of Non-Density-Matched Detergent
107
4.5.6
Dependency of Association Constants on Detergent
Concentration
107
4.6
Sedimentation Velocity Data Analysis
108
4.6.1
Numerical Solutions of the Lamm Equation
108
4.6.2
Analysis in Terms of Non-Interacting Species: Principle
109
4.6.3
Analysis in Terms of Non-Interacting Species: Applications to
Detergent and the Membrane Protein EmrE
109
VIII Contents
4.6.4
c(s)
Analysis: Principle
110
4.6.5
Sedimentation Velocity Simulation and c(s) Analysis for a
Hypothetical Sample of Membrane Proteins 111
4.6.6
Example of Characterization of a Membrane Protein by Sedimentation
Velocity
113
4.6.6.1
Association State of Na+-K+-ATPase Expressed in Pichia
pastoris
and of
Sarcoplasmic
Ca2ł-ATPase
113
4.6.6.2
Complex Behavior in Solution of New Amphiphilic
Compounds
114
4.6.6.3
The Sh/sd Method
114
4.6.7
General Potentials of the c(s) Analysis per
se as a
Prelude to more
Sophisticated Analysis
115
4.7
Analytical Ultracentrifugation and
SANS/SAXS
116
4.8
Conclusions
116
5
Probing Membrane Protein Interactions with
Real-Time
Biosensor
Technology
121
lva Navrátilova,
David
С.
Myszka
and Rebecca
L
Rich
5.1
Introduction
121
5.2
Interactions of Extracellular Domains
123
5.3
Interactions of Soluble Proteins with
Lipid
Layers
124
5.4
Interactions of Proteins Embedded in
Lipid
Layers
129
5.4.1
On-Surface
Reconstitution
of G-Protein-Coupled Receptor
129
5.4.2
Capture/Reconstitution
of GPCRs
131
5.5
Interactions of Membrane-Solubilized Proteins
131
5.6
Summary
138
6
Atomic Force Microscopy: High-Resolution Imaging of Structure and
Assembly of Membrane Proteins
141
Simon
Scheuring,
Nikolay Buzhynskyy,
Rui
Pedro
Concalves
and
Szymon Jaroslawski
6.1
Atomic Force Microscopy
141
6.1.1
Sample Preparation
141
6.1.2
Equipment and Experimental Procedure
141
6.1.3
Experimental Rationales
142
6.2
Combined Imaging and Force Measurements by AFM
145
6.2.1
Imaging and Force Measurement of a Bacterial Surface Layer
(S-Layer)
145
6.3
High-Resolution Imaging by AFM
147
6.3.1
High-Resolution AFM of Aquaporin-Z (AQPZ)
147
6.3.2
High-Resolution AFM of Aquaporin-0 (AQPO)
148
6.3.3
Comparison Between AQPZ and AQPO Topographies
350
6.3.4
The Supramolecular Assembly of Photosynthetic Complexes
in Native Membranes of
Rhodospiríllum photometricum
by AFM
150
Contents
IX
6.3.5 AQPO-Connexon
Junction Platforms in Native Sheep Lens
Membranes
152
6.4
Conclusions
153
6.5
Feasibilities, Limitations, and Outlook
153
Part IV Dynamics
7
Molecular Dynamics Studies of Membrane Proteins: Outer Membrane
Proteins and Transporters
161
Syma Khalid, John Holyoake and Mark S. P.
Šansom
7.1
Introduction
161
7.1.1
Molecular Dynamics Simulations
161
7.2
Outer Membrane Proteins
163
7.2.1
OmpA
163
7.2.2
Simulations of OMPs in Diverse Environments
265
7.2.3
Porins
167
7.2.4
More Complex Outer Membrane Transporters
167
7.2.4.1
TonB-Dependent Transporters
168
7.2.4.2 Autotransporters 169
7.2.4.3
TolC
170
7.3
Cytoplasmic Membrane Transport Proteins
172
7.3.1
Simulated State Transitions
172
7.3.1.1
BtuCD
173
7.3.1.2
LacY
175
7.3.2
Intrinsic Flexibilities
176
7.3.3
Non-Equilibrium Methods
178
7.3.4
Homology Models
178
7.4
Conclusions
179
8
Understanding Structure and Function of Membrane Proteins Using Free
Energy Calculations
187
Christophe
Chĺpot
and Klaus
Schulten
8.1
Introduction
387
8.2
Theoretical Underpinnings of Free Energy Calculations
188
8.2.1
Alchemical Transformations
188
8.2.1.1
What is Usually Implied by Small Changes?
189
8.2.1.2
How is the Coupling Parameter Defined?
190
8.2.1.3
Thermodynamic Integration
192
8.2.2
Free Energy Changes Along a Reaction Coordinate
192
8.2.2.1
Umbrella Sampling or Stratification?
193
8.2.2.2
Adaptive Biasing Force
194
8.2.2.3
Non-Equilibrium Simulations for Equilibrium Free Energies
194
8.3
Point Mutations in Membrane Proteins
196
8.3.1
Why Have Free Energy Calculations Been Applied only Sparingly to
Membrane Proteins?
196
X
Contents
8.3.2
Gaining New Insights into Potassium Channels
197
8.3.3
Tackling the Assisted Transport of Ammonium Using FEP
198
8.3.4
How Relevant are Free Energy Calculations in Models of Membrane
Proteins?
198
8.4
Assisted Transport Phenomena Across Membranes
199
8.4.1
Gramicidin: A Paradigm for Assisted Transport Across
Membranes
199
8.4.2
Free Energy Calculations and Potassium Channels
200
8.4.3
Non-Equilibrium Simulations for Understanding Equilibrium
Phenomena
201
8.4.4
Deciphering Transport Mechanisms in Aquaporins
202
8.4.5
Non-Equilibrium Simulations and Potassium Channels
203
8.5
Recognition and Association in Membrane Proteins
204
8.5.1
The "Two-Stage" Model
204
8.5.2
Glycophorin A: A Paradigmatic System for Tackling Recognition and
Association in Membranes
205
8.6
Conclusions
206
9
Neutrons to Study the Structure and Dynamics of Membrane
Proteins
213
Kathleen Wood and Giuseppe Zaccai
9.1
General Introduction
213
9.2
Introduction to Neutrons
213
9.2.1
Production and Properties of the Neutron
213
9.2.2
Interaction Between Neutrons and Matter
214
9.2.3
Scattering Law
216
9.2.4
Coherent and Incoherent scattering
216
9.2.5
Instruments
218
9.3
Introduction to Bacteriorhodopsin and the Purple Membrane
219
9.4
Methods for Labeling
221
9.4.1
Biosynthetic Labeling
221
9.4.2
Reconstitution
221
9.5
Neutrons for Structural Studies of Membrane Proteins
222
9.5.1
Neutron Diffraction
222
9.5.1.1
Bacteriorhodopsin
222
9.5.1.2
Lipids
223
9.5.1.3
Water
224
9.5.2
Low-Resolution Studies
224
9.5.2.1
Small-Angle Neutron Scattering of Membrane Proteins in
D-Vesicles
224
9.5.2.2
Low-Resolution Single-Crystal Studies
227
9.5.2.3
Reflectivity
227
9.6
Neutrons for Dynamical Studies of Membrane Proteins
231
9.6.1
Energy-Resolved Experiments
231
9.6.1.1
Time and Space Scales
232
Contents
XI
9.6.2
Elastic
Scattering and Atomic Mean Square Displacements
233
9.6.3
Quasi-Elastic Scattering
235
9.6.4
Inelastic Scattering
235
9.6.5
Other Types of Measurement
235
9.7
Take-Home Message
237
Part V Spectroscopies
Ί0
Circular Dichroism: Folding and Conformational Changes of Membrane
Proteins
243
Nadège
Jamin and
Jean-Jacques bucapere
10.1
Introduction
243
10.2
Secondary Structure Composition
244
10.3
Tertiary Structure Fingerprint
250
10.4
Extrinsic Chromophores
252
10.5
Conformational Changes upon Ligand Binding
252
10.6
Folding/Unfolding
254
10.7
Conclusion and Perspectives
255
Π
Membrane Protein Structure and Conformational Change Probed using
Fourier Transform Infrared Spectroscopy
259
John E. Baenziger and Come
J. B. daCosta
11.1
Introduction
259
11.2
FTIR Spectroscopy
260
11.2.1
Attenuated Total Reflectance FTIR Spectroscopy
260
11.2.2
Detecting Changes in Side Chain Structure/Environment During
Protein Conformational Change
263
11.2.3
Probing the Orientation of Functional Groups
266
11.3
Vibrational Spectra of Membrane Proteins
267
11.3.1
Lipid
Vibrations
268
11.3.1.1
Lipid
Ester C=O
268
11.3.1.2
Lipid Methylene
C
-Н
269
11.3.2
Protein Backbone Vibrations
269
11.3.2.1
Amide I
269
11.3.2.2
Amide II
272
11.3.3
Protein Side-Chain Vibrations
272
11.4
Applications of FTIR To Membrane Proteins
273
11.4.1
Testing Protein Structural Models and Validating the Structures of
Mutant Proteins
273
11.4.2
Lipid-Protein Interactions
276
11.4.3
Receptor-Drug Interactions
278
11.4.4
Chemistry of Receptor-Ligand Interactions
281
11.4.5
Changes in Orientation of Functional Groups During Conformational
Change
282
11.4.6
A Tool in the Crystallization of Integral Membrane Proteins
284
11.5
Conclusions and Future Directions
286
XII
I Contents
12
Resonance Raman Spectroscopy of a Light-Harvesting Protein
289
Andrew Aaron Pascal and Bruno Robert
12.1
Introduction
289
12.2
Principles of Resonance Raman Spectroscopy
289
12.3
Primary Processes in Photosynthesis
291
12.4
Photosynthesis in Plants
292
12.5
The Light-Harvesting System of Plants
293
12.6
Protection against Oxidative Stress: Light-Harvesting Regulation in
Plants
294
12.7
Raman studies of
ШСИ
297
12.8
Crystallographic Structure of LHCII
301
12.9
Properties of LHCII in Crystal
302
12.10
Recent Developments and Perspectives
305
Part VI Exploring Structure-Function Relationships in Whole Cells
13
Energy Transfer Technologies to Monitor the Dynamics and Signaling
Properties of G-Protein-Coupled Receptors in Living Cells
311
Jean-Philippe Pin, Mohammed-Akli Ayoub, Damien
Maurei,
Julie Perroy
and
Eric Trinquet
13.1
Introduction
311
13.2
Fluorescence Resonance Energy Transfer (FRET)
312
13.3
FRET Using GFP and its Various Mutants
314
13.4
BRET as an Alternative to FRET
315
13.5
Time-Resolved FRET (TR-FRET) and Homogeneous Time-Resolved
Fluorescence (HTRF)
318
13.6
New Developments in Fluorescent Labeling of Membrane
Proteins
320
13.7
Ligand-Receptor Interaction Monitored by FRET
322
13.8
Fast GPCR Activation Process Monitored in Living Cells
323
13.9
FRET and BRET Validated the Constitutive Oligomerization of GPCR
in Living Cells
324
13.10
FRET and BRET Changed the Concept of G-Protein Activation
326
13.11
GPCRs as Part of Large Signaling Complexes
327
13.12
Conclusion and Future Prospects
328
Index
335 |
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| any_adam_object_boolean | 1 |
| building | Verbundindex |
| bvnumber | BV023015337 |
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| dewey-search | 570 |
| dewey-sort | 3570 |
| dewey-tens | 570 - Biology |
| discipline | Physik Biologie |
| discipline_str_mv | Physik Biologie |
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| id | DE-604.BV023015337 |
| illustrated | Illustrated |
| index_date | 2024-07-02T19:11:02Z |
| indexdate | 2024-07-20T09:27:32Z |
| institution | BVB |
| isbn | 9783527316779 3527316779 |
| language | English |
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| physical | XX, 347 S. Ill., graph. Darst. 240 mm x 170 mm |
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| spelling | Biophysical analysis of membrane proteins investigating structure and function ed. by Eva Pebay-Peyroula Weinheim WILEY-VCH 2008 XX, 347 S. Ill., graph. Darst. 240 mm x 170 mm txt rdacontent n rdamedia nc rdacarrier Membranproteine - Struktur-Aktivitäts-Beziehung Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd rswk-swf Biophysik (DE-588)4006891-2 gnd rswk-swf Membranproteine (DE-588)4130026-9 gnd rswk-swf Membranproteine (DE-588)4130026-9 s Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 s DE-604 Biophysik (DE-588)4006891-2 s Pebay-Peyroula, Eva Sonstige oth text/html http://deposit.dnb.de/cgi-bin/dokserv?id=2945672&prov=M&dok_var=1&dok_ext=htm Inhaltstext Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016219503&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Biophysical analysis of membrane proteins investigating structure and function Membranproteine - Struktur-Aktivitäts-Beziehung Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd Biophysik (DE-588)4006891-2 gnd Membranproteine (DE-588)4130026-9 gnd |
| subject_GND | (DE-588)4183784-8 (DE-588)4006891-2 (DE-588)4130026-9 |
| title | Biophysical analysis of membrane proteins investigating structure and function |
| title_auth | Biophysical analysis of membrane proteins investigating structure and function |
| title_exact_search | Biophysical analysis of membrane proteins investigating structure and function |
| title_exact_search_txtP | Biophysical analysis of membrane proteins investigating structure and function |
| title_full | Biophysical analysis of membrane proteins investigating structure and function ed. by Eva Pebay-Peyroula |
| title_fullStr | Biophysical analysis of membrane proteins investigating structure and function ed. by Eva Pebay-Peyroula |
| title_full_unstemmed | Biophysical analysis of membrane proteins investigating structure and function ed. by Eva Pebay-Peyroula |
| title_short | Biophysical analysis of membrane proteins |
| title_sort | biophysical analysis of membrane proteins investigating structure and function |
| title_sub | investigating structure and function |
| topic | Membranproteine - Struktur-Aktivitäts-Beziehung Struktur-Aktivitäts-Beziehung (DE-588)4183784-8 gnd Biophysik (DE-588)4006891-2 gnd Membranproteine (DE-588)4130026-9 gnd |
| topic_facet | Membranproteine - Struktur-Aktivitäts-Beziehung Struktur-Aktivitäts-Beziehung Biophysik Membranproteine |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=2945672&prov=M&dok_var=1&dok_ext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=016219503&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT pebaypeyroulaeva biophysicalanalysisofmembraneproteinsinvestigatingstructureandfunction |