Structural Biology of Membrane Proteins

by Grisshammer, Reinhard; Buchanan, Susan K.

• ISBN13: 9780854043613
• ISBN10: 0854043616
• Format: Hardcover
• Copyright: 2006-06-30
• Publisher: Royal Society of Chemistry

Summary

In the last few years there have been many exciting and innovative developments in the field of membrane protein structure and this trend is set to continue. Structural Biology of Membrane Proteins is a new monograph covering a wide range of topics with contributions from leading experts in the field.The book will be split into three sections: the first will discuss topics such as expression, purification and crystallisation; the second will cover characterisation techniques and the final section will look at new protein structures. The book will hence have wide appeal to researchers working in and around the field and provide an up-to-date reference source. Introductory sections to each topic are accompanied by more detailed discussions for the more experienced biochemist. Detailed descriptions of experimental methods are included to demonstrate practical approaches to membrane protein structure projects. The book also offers an up-to-date reference source in addition to descriptions of new and emerging developments, including state-of-the-art techniques for solving membrane protein structures. Structural Biology of Membrane Proteins encompasses both basic introductions and detailed descriptions of themes and should appeal to a wide range of biochemical scientists, both experienced and beginner.

Table of Contents

Section 1 Expression and Purification of Membrane Proteins
Chapter 1 Refolding of G-Protein-Coupled Receptors	3	(12)
Jean-Louis Banères
1 Introduction	3	(1)
2 Refolding of Membrane Proteins	4	(2)
3 In Vitro Protein Refolding	6	(1)
4 GPCR In Vitro Refolding	6	(6)
4.1 Resolubilization from Inclusion Bodies	6	(1)
4.2 Refolding	7	(1)
4.3 Refolding of GPCR Fragments	8	(1)
4.4 Refolding of Intact GPCRs	9	(3)
5 Conclusion	12	(1)
References	13	(2)
Chapter 2 Expression of Genes Encoding Eukaryotic Membrane Proteins in Mammalian Cells	15	(14)
Philip J. Reeves
1 Introduction	15	(1)
2 Mammalian Cell Hosts and Gene Expression Vectors	16	(1)
3 Delivery and Maintenance of Expression Vectors in Mammalian Cells	16	(4)
3.1 Transient Transfection	17	(1)
3.2 Stable Transfection	17	(1)
3.2.1 A Procedure for Stable Transfection of HEK293S Cells	18	(1)
3.3 Stable Episomal Replication	19	(1)
3.4 Viral Infection	19	(1)
4 HEK293S Stable Cell Lines for High-Level Expression of Eukaryotic Membrane Proteins	20	(4)
4.1 Constitutive Expression	20	(1)
4.2 Tetracycline-Regulated Gene Expression	21	(1)
4.3 A Plasmid for Tetracycline-Regulated Expression of Opsin	22	(1)
4.3.1 Construction and Characterization of HEK293S Stable Cell Lines for Inducible Gene Expression	23	(1)
5 Scale Up of Culture Growth and Rhodopsin Purification	24	(1)
5.1 Growth of HEK293S Cells in Suspension Culture Using a Bioreactor	24	(1)
5.2 Immunoaffinity Purification of Rhodopsin	25	(1)
6 Preparation of Eukaryotic Membrane Proteins Containing Simple N-Glycans	25	(1)
7 Outlook for the Use of HEK293S Tetracycline-Inducible Cell Lines for Large-Scale Preparation of Other Eukaryotic Membrane Proteins	26	(2)
References	28	(1)
Chapter 3 Expression of Recombinant G-Protein Coupled Receptors for Structural Biology	29	(22)
Filippo Mancia and Wayne A. Hendrickson
1 Introduction	29	(5)
1.1 Signal Transduction through G-protein Coupled Receptors	29	(1)
1.2 Structural and Functional Characteristics of GPCRs	30	(2)
1.3 Structure Determination of GPCRs	32	(2)
2 Expression of Recombinant GPCRs	34	(10)
2.1 Overview	34	(1)
2.2 Bacteria as Hosts for the Production of Functional GPCRs	35	(4)
2.3 Production of GPCRs in Stably Transfected Mammalian Cells	39	(3)
2.4 Production of GPCRs via Transient Transfection or Viral Infection of Mammalian Cells	42	(1)
2.5 Production of GPCRs in Yeast	42	(1)
2.6 Production of GPCRs in Insect Cells	43	(1)
2.7 "In Vivo" Expression in the Eye	43	(1)
2.8 Extra-Membranous Expression Systems	44	(1)
3 Conclusions	44	(1)
Acknowledgments	45	(1)
References	45	(6)
Chapter 4 The Purification of G-Protein Coupled Receptors for Crystallization	51	(21)
Tony Warne and Gebhard F.X. Schertler
1 Introduction	51	(1)
1.1 Structural Studies of G-Protein Coupled Receptors	51	(1)
1.2 The Turkey Erythrocyte Beta-Adrenergic Receptor	52	(1)
2 Heterogeneity of Overexpressed Receptors	52	(3)
2.1 Heterogeneity of GPCRs due to Post-Translational Modifications	52	(1)
2.1.1 N-Glycosylation	52	(1)
2.1.2 Palmitoylation	53	(1)
2.1.3 Phosphorylation	54	(1)
2.2 Other Sources of Heterogeneity	54	(1)
3 Membrane Fractionation, Solubilization, and Detergent Selection	55	(5)
3.1 Detergents for Solubilization	56	(1)
3.2 Detergents for Final Purification Steps and Crystallization	57	(3)
4 Purification	60	(6)
4.1 Use of Purification Tags and Fusions	60	(3)
4.2 Removal of Tags and Fusions	63	(1)
4.3 Ligand Affinity Chromatography	63	(1)
4.4 Final Purification Steps before Crystallization and Assembly of Complexes	64	(2)
4.5 Lipid Content during Purification	66	(1)
5 Final Quality Control, Monitoring Protein Stability, Aggregational State, Lipid, and Bound Detergent	66	(2)
6 Conclusions	68	(1)
Acknowledgments	68	(1)
References	68	(4)
Chapter 5 An Introduction to Detergents and Their Use in Membrane Protein Studies	72	(27)
Fabien Walas, Hiroyoshi Matsumura and Ben Luisi
1 Introduction	72	(1)
2 Physical Properties of Detergents Used in Membrane Protein Studies	73	(6)
2.1 Properties and Classification of Detergents	74	(1)
2.1.1 Properties of Detergents	74	(1)
2.1.2 Ionic Detergents	75	(1)
2.1.3 Non-Ionic Detergents	76	(1)
2.1.4 Zwitterionic Detergents	77	(1)
2.1.5 Amphipols	77	(1)
2.2 Lipopeptide Detergents	78	(1)
2.3 Supplements and Additives for Detergents	78	(1)
3 Extraction and Purification Procedure Using Common Detergents	79	(3)
3.1 Choice of Detergent	79	(1)
3.2 Purification of Membrane Proteins in the Presence of Detergents	80	(1)
3.2.1 Strategy and Method	80	(1)
3.2.2 Detergent Exchange or Removal	81	(1)
4 Use of Detergents in Membrane Protein Crystallization	82	(7)
4.1 Introduction	82	(1)
4.2 Membrane Protein Crystallization in Lipid Cubic Phase	83	(1)
4.3 Crystal Lattice Organization	83	(1)
4.4 Example of Detergent Interactions with β-Sheet Membrane Proteins	84	(1)
4.4.1 Crystal Structure of VceC, an Outer Membrane Protein from Vibrio Cholerae	85	(1)
4.4.2 Detergent Organization in Crystals of Monomeric Outer Membrane Phospholipase A	85	(1)
4.5 Example of Detergent and α-Helical Type Membrane Protein Contact	85	(1)
4.5.1 Crystal Structure of Rotor Rings	85	(1)
4.5.2 Structure of Bovine Rhodopsin in a Trigonal Crystal Form	87	(1)
4.6 A Synopsis of Detergent–Protein Interactions in Crystals	87	(2)
5 Conclusion	89	(1)
Acknowledgements	90	(1)
References	90	(9)
Section 2 Methods for Structural Characterization of Membrane Proteins
Chapter 6 Solution NMR Approaches to the Structure and Dynamics of Integral Membrane Proteins	99	(19)
John H. Bushweller, Tomasz Cierpicki and Yunpeng Zhou
1 Introduction	99	(1)
2 Protein Production and Optimization for NMR Studies	100	(2)
2.1 Protein Production	100	(1)
2.2 Sample Optimization	101	(1)
3 NMR Methodology for the Study of Integral Membrane Proteins	102	(5)
3.1 High Level Deuteration and Assignment Strategies Using TROSY-Based Experiments	102	(2)
3.2 Carbon Detected Experiments: Breaking the Limit of Sensitivity	104	(1)
3.3 Use of Methyl Protonation to Increase the Number of Nuclear Overhauser Effect-Derived Distance Constraints	105	(1)
3.4 Application of Electron-Nuclear Relaxation for Long Range Distances	106	(1)
3.5 Residual Dipolar Couplings	106	(1)
4 Solution NMR Structures of Helical Integral Membrane Proteins	107	(2)
4.1 F1Fo ATP Synthase Subunit c from E. coli	107	(1)
4.2 MerF	108	(1)
4.3 Mistic	109	(1)
5 Solution NMR Structures of β-Barrel Membrane Proteins	109	(2)
5.1 OmpA	110	(1)
5.2 OmpX	110	(1)
5.3 PagP	111	(1)
6 Solution NMR Characterization of Membrane Protein Dynamics	111	(2)
6.1 OmpA	112	(1)
6.2 PagP	112	(1)
7 Future Directions	113	(1)
References	114	(4)
Chapter 7 Membrane Proteins Studied by Solid-State NMR	118	(13)
Adam Lange and Marc Baldus
1 Introduction	118	(1)
2 Sample Preparation and Methodology	118	(3)
2.1 Isotope Labelling and Solid-State NMR Sample Preparation	118	(2)
2.2 Resonance Assignments and Structure Determination	120	(1)
3 Applications	121	(4)
3.1 Membrane Protein Structure	121	(1)
3.2 Ligand Binding to Membrane Proteins	121	(3)
3.3 Membrane Protein Dynamics	124	(1)
4 Conclusions	125	(1)
Acknowledgements	126	(1)
References	126	(5)
Chapter 8 Assessing Structure and Dynamics of Native Membrane Proteins	131	(21)
W. Kukulski, T. Kaufmann, T. Braun, H. Remigy, D. Fotiadis and A. Engel
Abstract	131	(1)
1 Introduction	131	(1)
2 Assembly of 2D Crystals	132	(3)
3 Electron Microscopy	135	(7)
3.1 Image Formations	135	(3)
3.2 Electron Diffraction	138	(1)
3.3 Specimen Preparation	138	(1)
3.4 Data Processing	139	(3)
4. Atomic Force Microscopy	142	(5)
4.1 Image Formation	142	(1)
4.2 Sample Preparation	143	(1)
4.3 Optimized Imaging Conditions	143	(1)
4.4 Imaging Native Membranes	144	(1)
4.5 Nanodissection	144	(1)
4.6 Image Processing	145	(2)
5 Conclusion and Perspectives	147	(1)
References	147	(5)
Chapter 9 State-of-the-Art Methods in Electron Microscopy, including Single-Particle Analysis	152	(21)
Vinzenz M. Unger
1 Introduction	152	(1)
2 Sample Preparation	153	(1)
3 Low-Dose Microscopy	154	(5)
3.1 Sample Holders	154	(3)
3.2 Radiation Damage and Low-Dose Imaging	157	(2)
4 Applications of CryoEM	159	(11)
4.1 Single-Particle Approaches	159	(1)
4.1.1 Generating a Data Set	160	(1)
4.1.2 Particle Classification	160	(1)
4.1.3 Euler Angle Determination	163	(1)
4.1.4 Structure Calculation	163	(1)
4.2 Electron Crystallography	164	(1)
4.2.1 2D Crystallization and Advantages of Crystalline Samples over Single Particles	165	(1)
4.2.2 Image Filtering and Lattice Straightening	166	(1)
4.2.3 Impact of CTF on Images of 2D crystals and CTF–Correction	167	(1)
4.2.4 Projection Density Maps and Calculation of 3D Structures	168	(2)
5 Examples	170	(1)
5.1 Single-Particle Reconstructions	170	(1)
5.2 Electron Crystallography	170	(1)
6 Conclusion	170	(1)
References	171	(2)
Chapter 10 Atomic Resolution Structures of Integral Membrane Proteins Using Cubic Lipid Phase Crystallization	173	(22)
Hartmut Luecke
1 Introduction	173	(4)
1.1 Nuclear Magnetic Resonance Techniques	173	(1)
1.2 Crystallography	174	(1)
1.3 Crystallization Techniques	174	(1)
1.3.1 Vapor Diffusion	174	(1)
1.3.2 Microdialysis Crystallization	175	(1)
1.4 Special Issues of Membrane Protein Crystallization	175	(1)
1.5 History of Membrane Protein Crystallization	176	(1)
1.6 Aim of this Chapter	177	(1)
2 Membrane Protein Crystals and Crystallization	177	(9)
2.1 Vapor Diffusion of Detergent-Solubilized Membrane Proteins	177	(2)
2.2 The Cubic Lipid Phase (CLP) Crystallization Method	179	(6)
2.3 Crystallization from Bicelles	185	(1)
2.4 Crystallization from Spherical Micelles	186	(1)
3 Advantages of Structures in a Native Setting at High Resolution	186	(2)
4 Conclusions	188	(1)
References	188	(7)
Section 3 New Membrane Protein Structures
Chapter 11 Aquaporins: Integral Membrane Channel Proteins	195	(17)
Robert M. Stroud, William E.C. Harries, John Lee, Shahram Khademi and David Savage
1 Introduction	195	(4)
2 The Exclusion Barrier to Ions and Protons in Aquaporins	199	(2)
2.1 Global Orientational Tuning by the NPA Motif	199	(2)
2.2 Helix Dipole	201	(1)
2.3 Electrostatic Desolvation Penalty	201	(1)
3 Selectivity in the Aquaporin Family	201	(2)
4 Permeation of Substances Other than Water and Glycerol	203	(1)
4.1 Conductance of Other Molecules	203	(1)
5 Aquaporin Monomer Associations and their Functional Implications	204	(5)
5.1 The Eye Lens: A Brief History of Aquaporin 0 Research	204	(1)
5.2 Aquaporin 0 Monomer Structure and Organization	205	(3)
5.3 Extracellular Domain Interactions	208	(1)
Acknowledgment	209	(1)
References	209	(3)
Chapter 12 Gas Channels for Ammonia	212	(23)
Shahram Khademi and Robert M. Stroud
1 Introduction	212	(1)
2 The Structure of Ammonia Channel	213	(9)
2.1 Overall Structure of AmtB: A New Family of 11-Crossing Proteins	213	(4)
2.2 A Membrane Protein with In-Plane Quasi Twofold Symmetry	217	(1)
2.3 The Ammonia Pathway	218	(4)
3 Reconstituted into Liposomes AmtB Acts as a Channel that Conducts NH3	222	(2)
4 The Mechanism of Conduction	224	(3)
4.1 pH-Dependent Effects	224	(2)
4.2 Competitive Inhibition	226	(1)
4.3 Transmembrane Potential	226	(1)
5 The Rh Proteins	227	(1)
6 Comparison with Aquaporins	228	(2)
7 Comparison with K+ Channel	230	(1)
Acknowledgment	230	(1)
References	230	(5)
Chapter 13 Channels in the Outer Membrane of Mycobacter	235	(17)
Georg E. Schulz
1 Introduction	235	(1)
2 Structure Determination	236	(4)
2.1 Protein Production	236	(2)
2.2 Crystallization	238	(1)
2.3 X-Ray Analysis	239	(1)
3 Structure Description	240	(5)
3.1 The Channel	240	(2)
3.2 0-Barrels	242	(2)
3.3 Protein Properties	244	(1)
4 The Outer Membrane	245	(4)
4.1 Membrane Structure	245	(3)
4.2 Porin Localization	248	(1)
5 Conclusion	249	(1)
Acknowledgments	249	(1)
References	249	(3)
Chapter 14 The Structure of the SecY Protein Translocation Channel	252	(18)
Bert Van Den Berg and Ian Collinson
1 Introduction	252	(3)
1.1 The Sec61/SecY Complex	253	(1)
1.2 The Three Different Translocation Modes	253	(2)
2 Structure Determination of the SecY Complex by Electron Cryo-Microscopy	255	(2)
3 Determination of the X-ray Crystal Structure of the SecY Complex	257	(2)
4 Description of the Structure of the SecY Complex	259	(4)
5 Post-Translational Translocation in Bacteria	263	(2)
5.1 A Model for Post-Translational Protein Translocation in Bacteria	265	(1)
6 Conclusions and Outlook	265	(1)
References	266	(4)
Chapter 15 Structure and Function of the Translocator Domain of Bacterial Autotransporters	270	(18)
Peter Van Ulsen, Piet Gros and Jan Tommassen
1 Introduction	270	(1)
2 The NalP Autotransporter	271	(1)
3 The Translocator Domain of Autotransporters	272	(1)
4 Purification and In Vitro Folding of the Na1P Translocator Domain	273	(4)
5 The Structure of the NalP Translocator Domain	277	(2)
6 Comparison of the NalP Translocator Domain to Other Translocator Domains and to TolC	279	(4)
7 The Autotransporter Secretion Mechanism	283	(2)
References	285	(3)
Chapter 16 X-Ray Crystallographic Structures of Sarcoplasmic Reticulum Ca²+-ATPase at the Atomic Level	288	(19)
Jesper Vuust Møller, Poul Nissen and Thomas Lykke-Møller Sørensen
1 Introduction	288	(1)
2 The Transport Scheme and Thermodynamics of Ca²+ Transport	289	(1)
3 Overall structure of Ca²+-ATPase	290	(2)
4 Transport Models	292	(1)
5 Initialization of the Cycle: Phosphorylation and Calcium Ion Occlusion	293	(4)
6 The Dephosphorylation Step and Proton Counter Transport	297	(3)
7 Getting Ca²+ in and out of the Membrane	300	(2)
8 Compact vs. Open Conformations of SERCA	302	(1)
9 Conclusions and Perspectives	303	(1)
References	303	(4)
Chapter 17 Comparison of the Multidrug Transporter EmrE Structures Determined by Electron Cryomicroscopy and X-ray Crystallography	307	(13)
C.G. Tate
1 Introduction	307	(2)
2 The Oligomeric State of EmrE	309	(3)
3 Transport Activity of EmrE	312	(1)
4 Structure of EmrE Determined by Electron Cryomicroscopy	312	(3)
5 Comparison of the EmrE Structure Determined by Electron Crystallography with a 3.8 Å Resolution Structure Determined by X-ray Crystallography	315	(2)
6 Conclusions	317	(1)
References	317	(3)
Chapter 18 Structure of Photosystems I and II	320	(29)
Raimund Fromme, Ingo Grotjohann and Petra Fromme
1 Introduction to Oxygenic Photosynthesis	320	(4)
2 Photosystem II	324	(8)
2.1 Overview	324	(1)
2.2 The Protein subunits in Photosystem II	325	(1)
2.2.1 The Core Subunits D1 and D2 (PsbA and PsbD)	325	(1)
2.2.2 The Antenna Proteins CP47 and CP43 (PsbB and PsbC)	325	(1)
2.2.3 Cytochrome b559 (PsbE and PsbF)	325	(1)
2.2.4 The Small Membrane-Intrinsic Subunits	327	(1)
2.2.5 The Lumenal Subunits PsbO, PsbV, and PsbU	327	(1)
2.3 The Electron Transport Chain of Photosystem II	327	(1)
2.3.1 The Acceptor Site of the Electron Transport Chain in Photosystem II	328	(1)
2.3.2 The Donor Site of the Electron Transfer Chain of Photosystem II	329	(2)
2.4 The Antenna System of Photosystem II	331	(1)
3 Photosystem I	332	(12)
3.1 Overview	332	(1)
3.2 The Protein Subunits of Photosystem I	332	(1)
3.2.1 The Core of Photosystem I: The Large Subunits PsaA and PsaB	333	(1)
3.2.2 The Small Transmembrane Subunits in Photosystem I	336	(1)
3.2.3 The Stromal Hump of PSI: PsaC, PsaD, and PsaE	338	(1)
3.3 The Electron Transfer Chain of Photosystem I	339	(1)
3.3.1 P700: The Primary Electron Donor	340	(1)
3.3.2 A: The Initial Electron Acceptor	340	(1)
3.3.3 A0: The First Stable Electron Acceptor	341	(1)
3.3.4 A1: The Phylloquinone	341	(1)
3.3.5 Fx: The First FeS Cluster	342	(1)
3.3.6 FA and FB: The Terminal FeS Clusters	342	(1)
3.4 The Antenna System of Photosystem I	342	(1)
3.4.1 The Chlorophylls	343	(1)
3.4.2 The Carotenoids	343	(1)
3.4.3 The Lipids in Photosystem I	344	(1)
4 Conclusion and Outlook	344	(1)
References	344	(5)
Chapter 19 Glutamate Receptor Ion Channels: Structural Insights into Molecular Mechanisms	349	(24)
Avinash Gill and Dean R. Madden.
1 Introduction	349	(2)
1.1 Physiological and Pathophysiologieal Roles of the Ionotropic Glutamate Receptors	350	(1)
1.2 Medicinal Chemistry	351	(1)
1.3 Ionotropic Glutamate Receptor Subunits Are Modular	351	(1)
2 Studies of the Ligand-Binding Domain	351	(7)
2.1 Overall Structure	353	(1)
2.2 Pharmacological Specificity	353	(1)
2.3 Ligand-Binding Domain Conformational Changes	354	(1)
2.4 Correlation with Channel Activation	355	(1)
2.5 Dimerization	356	(1)
2.6 Desensitization and the Stability of the Dimer Interface	356	(2)
3 The Functional Architecture of a Glutamate Receptor Ion Channel	358	(4)
3.1 Structure of a Complete Ionotropic Glutamate Receptor	358	(2)
3.2 The Role of the N-Terminal Domain in Subunit Assembly	360	(1)
3.3 The Organization of the Transmembrane Domains	361	(1)
4 A Working Model of AMPA Receptor Function	362	(2)
4.1 LBD Mutations Affecting Binding and Gating	363	(1)
4.2 Subunit Gating Behavior	363	(1)
5 Open Questions	364	(3)
5.1 Different Models of Partial Agonism	364	(2)
5.2 Multistate Kinetic Models	366	(1)
5.3 Structural Prospects	366	(1)
5.4 Auxiliary Proteins	367	(1)
References	367	(6)
Chapter 20 The Mitochondrial ADP/ATP Carrier	373	(17)
Eva Pebay-Peyroula
1 Introduction	373	(1)
2 Mitochondrial Carriers and ADP/ATP Carrier	374	(1)
3 Crystallization	375	(3)
4 Diffraction, Phasing and Model Building	378	(2)
5 Structure Analysis	380	(4)
6 Functional Implications	384	(2)
6.1 Nucleotide Binding	384	(1)
6.2 Conformational Changes	385	(1)
6.3 Transport Regulation	386	(1)
7 Future Developments and Conclusions	386	(1)
Acknowledgments	387	(1)
References	387	(3)
Subject Index	390