Membrane structural biology with biochemical and biophysical foundations Second Edition2025|PDF|Epub|mobi|kindle电子书版本百度云盘下载

Membrane structural biology with biochemical and biophysical foundations Second EditionPDF格式电子书版下载

注意：本站所有压缩包均有解压码： 点击下载压缩包解压工具

1 INTRODUCTION1

General features of membranes1

Paradigm 1：the amphiphilic molecules in membranes assemble spontaneously due to the hydrophobic effect4

Paradigm 2：the Fluid Mosaic Model describes the membrane structure5

A shift in the paradigm：biomembranes have lateral domains that form “rafts”9

A view for the future：dynamic protein complexes crowd the membrane interior and extend its borders9

For further reading13

2 THE DIVERSITY OF MEMBRANE LIPIDS14

The acyl chains14

Complex lipids17

Phospholipids19

Sphingolipids20

Sterols and linear isoprenoids21

The lipid bilayer matrix22

Structure of bilayer lipids22

Diffusion of bilayer lipids24

Lipid asymmetry and membrane thickness27

Lipid polymorphism28

Lamellar phase28

Hexagonal phase and the amphiphile shape hypothesis29

Cubic phase30

Miscibility of bilayer lipids31

Lateral domains and lipid rafts34

Detergent-resistant membranes35

Diversity of lipids37

Conclusion39

For further reading41

3 TOOLS FOR STUDYING MEMBRANE COMPONENTS：DETERGENTS AND MODEL SYSTEMS42

Detergents43

Types of detergents43

Mechanism of detergent action46

Membrane solubilization49

Lipid removal51

Model membranes51

Monolayers52

Planar bilayers54

Patch clamps57

Supported bilayers57

Liposomes from SUVs to GUVs60

Multilamellar vesicles60

Small unilamellar vesicles61

Large unilamellar vesicles61

Short-chain/long-chain unilamellar vesicles62

Giant unilamellar vesicles62

Mixed micelles and bicelles63

Blebs and blisters64

Nanodiscs66

Conclusion67

For further reading67

4 PROTEINS IN OR AT THE BILAYER69

Classes of proteins that interact with the membrane69

Proteins at the bilayer surface70

Extrinsic/peripheral membrane proteins70

Amphitropic proteins74

Lipid-anchored proteins74

Reversible interactions of peripheral proteins with the lipid bilayer77

Effects of peripheral protein binding on membrane lipids77

Interactions between peripheral proteins and lipids78

Domains involved in binding the membrane81

Curvature83

Modulation of binding84

Proteins and peptides that insert into the membrane85

Toxins86

Colicins88

Peptides88

SecA：protein acrobatics90

Proteins embedded in the membrane91

Monotopic proteins91

Integral membrane proteins91

Protein-lipid interactions97

Hydrophobic mismatch101

For further reading103

5 BUNDLES AND BARRELS105

Helical bundles105

Bacteriorhodopsin105

Photosynthetic reaction center109

The proteins110

Lipids112

The cofactors112

Antennae113

The reaction cycle114

β-barrels115

Porins117

OmpF and OmpC118

VDAC，a mitochondrial porin122

Specific porins123

PhoE，the phosphoporin123

LamB，the maltoporin124

Other β-barrel transporters124

Iron receptors125

Outer membrane secretory proteins：not β-barrels126

Conclusion127

For further reading127

6 FUNCTIONS AND FAMILIES130

Membrane enzymes130

Diacylglycerol kinase132

Presenilin，an intra-membrane protease134

P450 cytochromes136

Transport proteins137

Transport classifcation system138

Superfamilies of ATPases139

ABC transporter superfamily140

Group translocation140

Symporters142

Antiporters142

Ion channels143

Membrane receptors144

Nicotinic acetylcholine receptor144

G protein-coupled receptors145

Bioinformatics tools for membrane protein families146

Predicting TM segments146

Hydrophobicity plots148

Orientation of membrane proteins149

The positive-inside rule150

Inverted repeats151

Genomic analysis of membrane proteins153

Helix-helix interactions162

Proteomics of membrane proteins163

Predicting β-barrels164

For further reading165

7 PROTEIN FOLDING AND BIOGENESIS168

Protein folding169

Folding α-helical membrane proteins170

bR folding studies173

Folding studies of β-barrel membrane proteins175

Other folding studies177

Whole protein hydrophobicity scale178

Biogenesis of membrane proteins178

Export from the cytoplasm180

The translocon187

The translocon structure187

TM insertion189

Biological hydrophobicity scale191

Topogenesis in membrane proteins195

Misfolding diseases198

For further reading201

8 DIFFRACTION AND SIMULATION203

Back to the bilayer203

Liquid crystallography204

Liquid crystal theory206

Joint refinement of x-ray and neutron diffraction data207

Modeling the bilayer209

Simulations of lipid bilayers209

Molecular dynamics209

Monte Carlo213

Lipids observed in x-ray structures of membrane proteins215

Crystallography of membrane proteins219

A multidisciplinary approach223

For further reading225

9 MEMBRANE ENZYMES226

Prostaglandin H2 synthase227

OMPLA230

Membrane proteases234

Omptins234

Intramembrane proteases235

Rhomboid protease236

Structure of the bacterial rhomboid GlpG237

Formate dehydrogenase239

P-type ATPases243

Ca2+ ATPases243

Na+，K+ ATPase250

Other P-type ATPases254

Conclusion255

For further reading255

10 MEMBRANE RECEPTORS257

G protein-coupled receptors258

Rhodopsin，a light-sensitive GPCR259

Ground state rhodopsin260

Activated rhodopsin261

Rhodopsin as prototype263

Adrenergic receptors267

β2AR structure268

β1AR structure270

Activated β2AR in complex with Gs270

Neurotransmitter receptors274

Glutamate receptors：GluA2274

Cys-loop receptors and GluCl278

Conclusion282

For further reading282

11 TRANSPORTERS284

Secondary transporters284

MFS transporters285

LacY，a scrutinized symporter285

GlpT，an MFS antiporter288

EmrD，an MFS exporter in an occluded conformation289

FucP，an MFS symporter in co conformation290

A paradigm for MFS transporters291

Mitochondrial ADP/ATP carrier291

AAC structure291

Neurotransmitter transporters294

Glutamate transporters and GltPh294

Neurotransmitter sodium symporters and LeuT296

LeuT structure298

Transport mechanism of LeuT300

The NSS family and the LeuT （APC-fold） superfamily300

BetP and osmoregulated transport303

ABC transporters and beyond306

Maltose transporter306

The vitamin B12 uptake system310

BtuCD-BtuF，an ABC transport system311

BtuB，an outer membrane transporter energized by TonB313

Drug efflux systems316

Sav1866 and P-glycoprotein，ABC exporters316

EmrE，an example of dual topology318

Tripartite drug efflux via a membrane vacuum cleaner320

AcrB，a peristaltic pump321

Alternating site mechanism of AcrB322

AcrA，a periplasmic adaptor protein323

TolC，the channel-tunnel323

Partners of TolC325

Conclusion325

For further reading326

12 CHANNELS328

Aquaporins and glyceroaquaporins329

Structure of aquaporins330

Glyceroaquaporins：GlpF331

Human aquaporins：AQP4333

Potassium channels335

KcsA structure and selectivity336

Gating and activation337

Voltage gating339

Gating in human potassium channels341

Chloride channels and the CLC family343

ClC-ec1344

CLC channels as “broken transporters”346

Mechanosensitive ion channels347

MscL349

MscS350

MS channel gating351

Gap junction channels354

Conclusion356

For further reading356

13 ELECTRON TRANSPORT AND ENERGY TRANSDUCTION358

Complexes of the respiratory chain359

Complex Ⅰ359

Conformational coupling mechanism363

Cytochrome bc1365

The Q cycle366

High-resolution structures366

Cytochrome c oxidase371

High-resolution structures371

Oxygen reduction373

Proton pathways374

F1F0-ATP synthase375

Subunit structure and function377

F1 Domain377

F0 Domain379

Regulation of the F1F0-ATPase379

Catalytic mechanism of a rotary motor380

Rotational catalysis380

Conclusions383

For further reading383

14 IN PURSUIT OF COMPLEXITY385

Complex formation386

Conformational changes and dynamics390

For further reading392

Appendix Ⅰ：Abbreviations393

Appendix Ⅱ：Single-Letter Codes for Amino Acids397

Index399