Membrane proteins: engineering, purification and crystallization:
Saved in:
| Format: | Book |
|---|---|
| Language: | English |
| Published: |
Amsterdam [u.a.]
Elsevier, Acad. Press
2015
|
| Edition: | 1. ed. |
| Series: | Methods in enzymology
557 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | XX, 624 S., [9] Bl. Ill., graph. Darst. |
| ISBN: | 9780128021835 |
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MARC
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| 245 | 1 | 0 | |a Membrane proteins: engineering, purification and crystallization |c ed. by Arun K. Shukla |
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| 264 | 1 | |a Amsterdam [u.a.] |b Elsevier, Acad. Press |c 2015 | |
| 300 | |a XX, 624 S., [9] Bl. |b Ill., graph. Darst. | ||
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Record in the Search Index
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|---|---|
| adam_text | CONTENTS
Contributors
xiii
Preface
xix
Section I
Membrane Protein Engineering, Soiubiiization
and Purification
1.
Multicolor Fluorescence-Based Screening Toward Structural
Analysis of Multiprotein Membrane Complexes
3
Simon Trowitzsch and Robert
Tampé
1.
Introduction
4
2.
Production of Fluorescently Labeled TAP Complexes in P.
pastoris
12
3.
Production of Fluorescently Labeled TAP Complexes in Mammalian Cells
16
4.
Multicolor Fluorescence-Based Screening Approaches
17
5.
Summary
21
Acknowledgments
21
References
21
2.
A Novel Screening Approach for Optimal and Functional
Fusion of T4 Lysozyme in GPCRs
27
Elizabeth Mathew and Mark E. Dumont
1.
Introduction
28
2.
Overall Strategy
30
3.
PSasmids, Yeast Strains, and Media
32
4.
Library Construction
33
5.
Expression Screening and Functional Assays
37
6.
Results for the Yeast oc-Factor Receptor Ste2p
39
Acknowledgments
40
References
40
3.
Membrane Preparation and Soiubiiization
45
Ankita Roy
1.
introduction
46
2.
iViembrane
Preparatson
¿7
3.
Solubiäizatíon
50
References
55
vi
Contents
4.
Amphipathic
Agents
for Membrane Protein Study
57
Aiman Sadaf, Kyung Ho Cho,
Bernadette
Byrne, and
Pii Seok
Chae
1.
Introduction
58
2.
MP Stability in Membrane Architecture
58
3.
Conventional Detergents
60
4.
Novel Amphipathic Systems
65
5.
Summary of Detergent Properties
85
6.
Detergent Selection
86
7.
Future Direction
87
References
88
5.
Quantification of Detergent Using
Colorimetrie
Methods
in Membrane Protein Crystallography
95
CheJsy Prince and Zongchao Jia
1.
Detergent in Membrane Protein Crystallography
96
2.
2,6-Di methyl phenol Assay for Sugar-Based Detergents
97
3.
Molybdate Assay for Total Phosphate
103
4.
Assay of Bile Salt with
Sulfuric Acid
106
5.
Applications of Detergent Measurement
108
6.
Concluding Remarks
113
Acknowledgments
114
References
114
6.
Solubilization of
G
Protein-Coupled Receptors: A Convenient
Strategy to Explore Lipid-Receptor Interaction
117
Amitabha Chattopadhyay, Bhagyashree D. Rao, and Md. Jafurulla
1.
G
Protein-Coupled Receptors
118
2.
Membrane Lipids in GPCR Organization and Function
118
3.
Cholesterol: An Important Modulator of GPCR Function
119
4.
Membrane Protein Soiubilization: An Essential Step Toward Purification
120
5.
Solubilization as a Strategy to Monitor Lipid-Protein Interactions
125
6.
Conclusions and Future Perspectives
129
Acknowledgments
130
References
130
7.
Overexpression, isolation. Purification, and Crystallization
ofNhaA
135
Etana Padan
and Manish Dwivedi
1.
Introduction
136
2.
Overexpression
138
Contents
vii
3.
Isolation
of
Membranes
from Strain Expressing His-tagged NhaA
140
4.
Affinity Purification of His-tagged NhaA
141
5.
Analysis of Protein Quality
142
6.
Crystallization of His-tagged NhaA
143
7.
Functional Assay
143
8.
Preparation of Solutions
145
Acknowledgments
146
References
146
8.
Purification, Refolding, and Crystallization of the Outer
Membrane Protein OmpG from Escherichia
coli
149
Stefan
Köster, Katharina
van Pee, and
Özkan Yildiz
1.
Introduction
150
2.
OmpG Production and Purification
15?
3.
Protein Analysis
155
4.
Crystallization of OmpG
158
5.
Summary
64
References
164
9.
Biophysical Approaches to the Study of LeuT, a Prokaryotic
Homolog
of
Neurotransmitter
Sodium Symporters
167
Satinder K.
Singh and Aritra Pal
1.
Introduction
168
2.
LeuT Expression, Purification, Crystallization, and Structure Determination
169
3.
Functional Characterization
183
4.
Transport Mechanism Unveiled from Structure, Function, and
Computationai Biology
192
5.
Summary
194
Acknowledgments
194
References
195
Section
11
Generation and Use of Antibody Fragments
Against Membrane Proteins
10.
Generation of
Recombinant
Antibody Fragments for
Membrane Protein Crystallization
201
Syed H. Mir, Claudia
Escher,
Wei-Chun
Kao,
Dominic Birth,
Christophe
Wirth,
and
Carola
Hunte
1.
introduction
20?
Vill
Contents
2.
Generation
of Antibodies for Structural Characterization
of Membrane Proteins
206
Ackno wledg
ments
215
References
215
П.
Phage Display Selections for Affinity Reagents to Membrane
Proteins in Nanodiscs
219
Pawel
К.
Dominik
and Anthony A. Kossiakoff
Ί.
introduction
220
2.
Materials and Equipment
222
3.
Methods
224
4.
Notes
241
Acknowledgments
244
References
244
12.
Antibody Fragments for Stabilization and Crystallization
of
G
Protein-Coupled Receptors and Their Signaling
Complexes
247
Arun K. Shukla, Charu Gupta, Ashish Srivastava, and Deepika Jaiman
1.
Introduction
248
2.
The Genesis of Antibody Fragment-Mediated Membrane Protein
Crystallization
249
3.
Nanobody Technology -Trapping Active GPCR Conformations
252
4.
Antibody Fragments in Visualizing GPCR Signaling Complexes
254
5.
Conclusion and Future Perspective
256
Acknowledgments
257
References
257
Section III
Biophysical Studies of Membrane Proteins
13.
Conformational Analysis of
G
Protein-Coupled Receptor
Signaling by Hydrogen/Deuterium Exchange Mass
Spectrometry
261
Sheng
Li, Su
Youn Lee, and Ka Young Chung
1.
introduction
262
2.
Experimental Procedure
266
3.
Conclusion and Perspectives
275
Acknowledgments
276
References
276
Contents
ix
14.
EPR
Studies of Gating Mechanisms in Ion Channels
279
Sudha Chakrapani
1.
SDSL and EPR Spectroscopy to Study Gating Mechanisms in Ion Channels
281
2.
Voltage-Gated Ion Channels
284
3.
Ligand-Gated Ion Channels
291
4.
Future Directions
299
Acknowledgments
300
References
300
15.
Magic-Angle-Spinning Solid-State NMR of Membrane Proteins
307
Lindsay A. Baker,
Gert E.
Folkers,
Tessa
Sinnige, Klaartje Houben,
Mohammed Kaplan, Elwin A.W. van
der
Cruijsen, and Marc Baldus
1.
Introduction
308
2.
Production of
Recombinant
Proteins in Escherichia
coli
310
3.
Isolation of Cells and Cellular Membranes
3-6
4.
Purification and
Reconstitution
of MPs for ssNMR
318
5.
Dedicated ssNMR Experiments J?2
6.
Conclusions
375
Acknowledgments 3> 5
References
Ώ5
16.
Solution NMR Structure Determination of Polytopic
α
-Helical
Membrane Proteins: A Guide to Spin Label Paramagnetic
Relaxation Enhancement Restraints
329
Linda Columbus and Brett Kroncke
1.
Site-Directed Spin Labeling
332
2.
PRE
Measurements
336
3.
Structure Calcufation with
PRE
Restraints
338
4.
Assessment of Structure Quality
341
5.
Future Developments
342
6.
Summan/
343
References
343
Section IV
Crystallization of Membrane Proteins
17.
Inducing Two-Dimensional Crystallization of Membrane
Proteins by Dialysis for Electron Crystallography
351
Yusuf M. Uddin and
Ingeborg Schmidt-Krey
1.
introduction
351
x
Contents
2. 2D
Crystallization by Dialysis
353
3.
EM Screening of 2D Crystallization Conditions
356
4.
Optimization of 2D Crystallization and Protein Purification
358
5.
Conclusion
360
References
360
18.
Crystallization of Membrane Proteins by Vapor Diffusion
363
Jared A. Deimar,
Jani
Reddy
Bolla, Chih-Chia Su,
and Edward W. Yu
1.
Introduction
364
2.
Membrane Protein Expression
365
3.
Membrane Protein Purification
368
4.
Membrane Protein Crystallization via Vapor Diffusion
372
5.
Case Studies
377
6.
Concluding Remarks
388
Acknowledgment
388
References
388
19.
Bicelles Coming of Age: An Empirical Approach to Bicelle
Crystallization
393
Sandra Poulos, Jacob LW. Morgan,
Jochen Zimmer,
and Salem Faham
1.
Introduction
394
2.
Protein Function and Folding in
Lipid
Bicelles
396
3.
Bicelle Crystallization of MPs
398
4.
User Guide to Bicelle Crystallization
398
5.
Bicelle Crystallization General Protocol
401
6.
Successful Crystallization Conditions
403
7.
Case Study of Cellulose Synthase Crystallization
409
8.
Alternative Approaches
411
9.
Summary
411
Acknowledgments
412
References
412
20.
Fluorescence Recovery After Photobleaching in
Lipidie
Cubic
Phase (LCP-FRAP): A Precrystailization Assay for Membrane
Proteins
417
Gustavo Fenalti, Enrique E.
Abola,
Chong Wang,
Beili Wu,
and
Vadim
Cherezov
1.
introduction
418
2.
Experimental Components and Considerations for LCP-FRAP Assays
419
Contents
x¡
3.
Examples of Using LCP-FRAP to Guide GPCR Crystallization
¿28
4.
Protocols for LCP-FRAP Assays
430
Acknowledgments
435
References
435
21.
Crystallization of Proteins from Crude Bovine Rod
Outer Segments
439
Bo Y. Baker, Sahil Gulati, Wuxian Shi, Benlian Wang, Phoebe
L
Stewart,
and
Krzysztof
Paiczewski
1.
Introduction
440
2.
Experimental Procedures
442
3.
Pilot Experimental Results
446
4.
Conclusions
454
Acknowledgments
455
References
456
22.
Crystallization of
Photosystem
M
for Time-Resolved Structural
Studies Using an X-ray Free Electron Laser
459
Jesse
Coe,
Christopher Kupitz, Shibom
Basu,
Chelsie E. Conrad,
Shatabdi
Roy-Chowdhury, Raimund Fromme,
and
Petra Fromme
1.
Introduction
460
2.
Isolation of
Photosystem
II
462
3.
Crystallization for Studies with FELs
463
4.
Detection and Characterization of
Nano-
and Microcrystals
466
5.
Time-Resolved Crystallography of PSI1 Using FELs
468
6.
Summary
478
Acknowledgments
4/9
References
479
Section V
Computational Approaches to Understand
Membrane Proteins
23.
Major Intrinsic Protein Superfamily: Channels with Unique
Structural Features and Diverse Selectivity Filters
485
Ravi Kumar Verma, Anjali Bansal Gupta, and Ramasubbu
Sanka
raramakrishnan
1.
Introduction
486
2.
Structural Biology of M!P Channels
489
xii Contents
3. MIPModDB
Database: A Database of
МІР
Models
496
4.
Unique Structural Features Within the TM Region
498
5.
Residues Forming
Ar/R SF
are Diverse
504
6.
Conclusion
512
Acknowledgments
512
References
512
24.
Comparative Sequence-Function Analysis of the Major
Facilitator Superfamily: The Mix-and-Match Method
521
M.
Gregor
Madej
1.
Introduction
522
2.
Helix-Triplets
526
3.
Detection of Functionally Homologous Positions
528
4.
Examples
533
5.
Conclusion
543
Acknowledgments
544
References
544
25.
Elucidating Ligand-Modulated Conformationat Landscape
of GPCRs Using Cloud-Computing Approaches
551
Diwakar Shukla, Morgan Lawrenz, and Vijay S.
Pande
1.
Introduction
552
2.
What are Markov State Models?
554
3.
How Do MSMs Enable Novel Insight?
560
4.
How Can MSMs Be Used for Improved Drug Design?
564
5.
Conclusions
569
Acknowledgments
570
References
570
Author Index
573
Subject Index
611
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| indexdate | 2024-07-10T07:05:45Z |
| institution | BVB |
| isbn | 9780128021835 |
| language | English |
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| series | Methods in enzymology |
| series2 | Methods in enzymology |
| spelling | Membrane proteins: engineering, purification and crystallization ed. by Arun K. Shukla 1. ed. Amsterdam [u.a.] Elsevier, Acad. Press 2015 XX, 624 S., [9] Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods in enzymology 557 Membranproteine (DE-588)4130026-9 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Membranproteine (DE-588)4130026-9 s DE-604 Shukla, Arun K. 1981- Sonstige (DE-588)131837397 oth Methods in enzymology 557 (DE-604)BV000000938 557 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=028038494&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Membrane proteins: engineering, purification and crystallization Methods in enzymology Membranproteine (DE-588)4130026-9 gnd |
| subject_GND | (DE-588)4130026-9 (DE-588)4143413-4 |
| title | Membrane proteins: engineering, purification and crystallization |
| title_auth | Membrane proteins: engineering, purification and crystallization |
| title_exact_search | Membrane proteins: engineering, purification and crystallization |
| title_full | Membrane proteins: engineering, purification and crystallization ed. by Arun K. Shukla |
| title_fullStr | Membrane proteins: engineering, purification and crystallization ed. by Arun K. Shukla |
| title_full_unstemmed | Membrane proteins: engineering, purification and crystallization ed. by Arun K. Shukla |
| title_short | Membrane proteins: engineering, purification and crystallization |
| title_sort | membrane proteins engineering purification and crystallization |
| topic | Membranproteine (DE-588)4130026-9 gnd |
| topic_facet | Membranproteine Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028038494&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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