Cell Boundaries: How Membranes and Their Proteins Work

Description

The central themes of Cell Boundaries concern the structural and organizational principles underlying cell membranes, and how these principles enable function. By building a biological and biophysical foundation for understanding the organization of lipids in bilayers and the folding, assembly, stability, and function of membrane proteins, the book aims to broaden the knowledge of bioscience students to include the basic physics and physical chemistry that inform us about membranes. In doing so, it is hoped that physics students will find familiar territory that will lead them to an interest in biology. Our progress toward understanding membranes and membrane proteins depends strongly upon the concerted use of both biology and physics. It is important for students to know not only what we know, but how we have come to know it, so Cell Boundaries endeavours to bring out the history behind the central discoveries, especially in the early chapters, where the foundation is laid for later chapters. Science is far more interesting if, as students, we can appreciate and share in the adventures―and misadventures―of discovering new scientific knowledge. Cell Boundaries was written with advanced undergraduates and beginning graduate students in the biological and physical sciences in mind, though this textbook will likely have appeal to researchers and other academics as well. Highlights the history of important central discoveries Early chapters lay the foundation for later chapters to build on, so knowledge is amassed High-quality line diagrams illustrate key concepts and illuminate molecular mechanismsBox features and spreads expand on topics in main text, including histories of discoveries, special techniques, and applications Cover Half Title Title Page Table of Contents Preface Acknowledgements Chapter 0 The “E” Words: A Concise Guide to Thermodynamics 0.1 Work, Heat, and Energy 0.2 First Law of Thermodynamics 0.2.1 The First Law Accounts for the Observations of Count Rumford 0.2.2 The Thermodynamics of Ideal Gases Reveal Quantitative Insights into the First Law 0.2.3 Enthalpy Is the Most Convenient Measure of Heat in the Laboratory 0.3 Second Law of Thermodynamics 0.3.1 ΔS Is Always Positive for Spontaneous Reactions at Constant Temperature 0.4 The Second Law and Statistical Thermodynamics 0.5 Gibbs Energy 0.6 Chemical Potential 0.7 Boltzmann Principle 0.8 The Nernst Equation 0.9 Generalized Equations of Thermodynamics 0.10 Perspective Chapter 1 Foundations of Membrane Structure 1.1 Membranes Define Cell Anatomy 1.1.1 Prokaryotes Have a Minimum Complement of Membranes 1.1.2 Eukaryotic Cells Have Many Compartments 1.1.3 Compartments Are Shaped by Proteins 1.2 Plasma Membranes Are Composed of Surface-Active Lipids 1.2.1 The Existence of Plasma Membranes Was Inferred from the Osmotic Properties of Plant Cells 1.2.2 The Lipidic Nature of Membranes Was Inferred from the Osmotic Behavior of Cells 1.2.3 Membrane Phospholipids Are Surface Active and Form Monolayers at the Air/Water Interface 1.2.4 Red Blood Cells Are Covered by a Layer of Lipids Two Molecules Thick 1.3 Lipid Bilayers Are the Fabric of Cell Membranes 1.3.1 Membranes and Lipid Dispersions Have a Trilaminar Structure When Viewed by Electron Microscopy (EM) 1.3.2 X-Ray Diffraction Proves the Existence of Lipid Bilayers 1.3.3 Single Planar Bilayers Can Be Easily Constructed in the Laboratory 1.3.4 Calorimetry and X-Ray Diffraction Demonstrate the Existence of Lipid Bilayers in Membranes 1.4 Proteins Penetrate the Membrane Bilayer and Are Mobile in the Membrane Plane 1.4.1 Freeze-Fracture EM Suggests Proteins within the Bilayer Fabric 1.4.2 Chemical Labeling of Membrane Proteins Shows That They Span Membranes 1.4.3 Proteins in Plasma Membranes Are α-Helical 1.4.4 Proteins Diffuse Freely in the Plane of Plasma Membranes 1.4.5 Electron Crystallography Reveals the First Structure of a Transmembrane Protein 1.4.6 X-Ray Crystallography Reveals the Structure of a Membrane at Atomic Resolution Key Concepts Further Reading Key Literature Exercises Chapter 2 Lipid Bilayers 2.1 Biological Membrane Lipids Spontaneously Form Bilayers 2.1.1 Hydrophobic Interactions Arise from Hydrogen Bonding in Water 2.1.2 The Hydrophobic Effect Drives Non-Polar Molecules out of Aqueous Solution 2.1.3 Amphiphiles Are Molecules That Have a Non-Polar Part Separated from a Polar Part 2.1.4 Micelles Have Different Shapes and Sizes 2.1.5 Many Membrane Lipids Are Two-Chain Amphiphiles 2.1.6 Membrane Lipids Form Bilayers in Water 2.1.7 Bilayers Spontaneously Form Closed Compartments: Liposomes and Vesicles 2.1.8 Lipids Can Form Structures Other than Bilayers 2.1.9 Phospholipids with Added Detergents Can Form Bilayered Micelles (Bicelles) 2.1.10 Lipid and Protein Composition of Membranes Varies Widely 2.2 Diffraction Methods Give Key Insights for Understanding Bilayer Structure and Membranes 2.2.1 Bilayer Profiles Obtained from Lamellar Diffraction Patterns Reveal Thermal Motion 2.2.2 Diffraction Patterns Can Be Obtained from Single Bilayers 2.2.3 Headgroup Layer Spacing Shows That Lipid Area per Molecule Is Conserved 2.2.4 Bilayer Scattering Can Be Seen in Natural Membranes 2.2.5 Bilayer Dynamics Can Be Inferred from Bilayer Profiles 2.2.6 The Transbilayer Distribution of the Principal Lipid-Component Groups Provide a Detailed View of Bilayer Structure 2.2.7 Bilayer Dynamics Can Be Explored Computationally 2.2.8 NMR Order Parameters Reveal the Nature of Chain Disorder in the Hydrocarbon Core 2.2.9 Cholesterol Affects the Packing of Lipid Chains, Keeping Them in a Fluid State 2.3 Macroscopic Descriptions of Bilayers Define Fundamental Properties of Biological Membranes 2.3.1 Lipid Bilayers Can Be Described Grossly Using a Simple Macroscopic Model 2.3.2 The Bilayer Is a Capacitor with Capacitance Cm 2.3.3 Lipid Bilayers Have a Very High Electrical Resistance Rm 2.3.4 Bilayers Are More Permeable to Anions than Cations Because of the Membrane Dipole Potential 2.4 Lipid Interactions Shape Membrane Properties 2.4.1 Lipids Diffuse Rapidly in the Plane of a Bilayer but Slowly across the Bilayer: Bilayer Lipid Asymmetry 2.4.2 A Bilayer Can Be Curved If Its Monolayers Differ in Area 2.4.3 Lipid Interactions in the Plane of a Bilayer Can Generate Regions of Different Composition 2.4.4 Bilayer Fluidity Allows Deformation When Strained Key Concepts Further Reading Key Literature Exercises Chapter 3 Interactions of Peptides with Lipid Bilayers 3.1 Gibbs Partitioning Energies Provide a Foundation for Describing Lipid–Protein Interactions 3.1.1 Partitioning Free Energies of Amino Acids Provide Hydrophobicity Scales 3.1.2 The Cost of Partitioning Peptide Bonds into Bulk Non-Polar Phases Is Very High 3.1.3 Partitioning of Pentapeptides Provides Whole-Residue Amino Acid Hydrophobicities 3.2 Lipid Bilayers Have Distinct Properties Compared with Bulk Organic Phases 3.2.1 Lipid Bilayers Are Not Equivalent to Bulk Non-Polar Phases 3.2.2 Partitioning of Pentapeptides Provides Whole-Residue Amino Acid Hydrophobicities for Neutral Bilayer Interfaces 3.2.3 Aromatic Amino Acids Have a Special Affinity for the Membrane Interface 3.2.4 The Interfacial Partitioning Free Energies of Unstructured Peptides Can Be Computed Accurately Using Interfacial Hydrophobicity Scales 3.3 Charged Peptides Interact Strongly, and Predictably, with Charged Interfaces 3.3.1 Electrostatic Properties of Charged Lipid Bilayers Are Described by Gouy–Chapman Theory 3.3.2 Gouy–Chapman Theory Describes the Behavior of Simple Charged Peptides in the Vicinity of Charged Membranes 3.3.3 Partitioning of Charged Hydrophobic Peptides into Membranes Reveals the Non-Additivity of Electrostatic and Hydrophobic Interactions 3.3.4 Some Physiologically Important Proteins Bind to Membranes with the Help of Covalently Linked Lipids 3.4 Membrane-active Peptides Provide Clues to Secondary Structure Formation at Membrane Interfaces 3.4.1 The Bilayer Interface Induces Secondary Structure Formation 3.4.2 The High Cost of Partitioning Peptide Bonds into the Interface Explains Partitioning–Folding Coupling 3.4.3 The Hydrophobic Moment of Structured Peptides Is of Little Energetic Importance in Interfacial Partitioning 3.4.4 Amphiphilic Helices Can Be Used as Scaffolds for Forming Nanodisc Membranes 3.4.5 The Stability of Transmembrane Helices Results from the High Cost of Partitioning Peptide Bonds into Lipid Bilayers 3.4.6 pHLIP Peptides Can Partition Spontaneously as Transmembrane Helices 3.4.7 Hydrophobic Mismatch and the Single Helix 3.4.8 Side Chain Snorkeling Is Important in Transmembrane Helix–Bilayer Interactions Key Concepts Further Reading Key Literature Exercises Chapter 4 Membrane Protein Folding and Stability 4.1 Interactions between α-Helices Are Central to 3D Structure Formation 4.1.1 van der Waals Interactions Underlie Favorable Helix–Helix Interactions in α-Helical MPs 4.1.2 Transmembrane Helix Dimers Are Stabilized by Close Packing 4.1.3 A Small Number of Structural Motifs Describe the Majority of Helix–Helix Interactions in Membrane Proteins 4.1.4 Hydrogen Bonds between Polar Residues Can Stabilize Transmembrane Helix–Helix Interactions 4.1.5 Helix Connecting Links Are Not Necessary for the Formation of Native Structures 4.1.6 Proline Residues Permit Kinks in Transmembrane Helices 4.2 α-Helical Membrane Proteins Can Be Destabilized Using Heat, Detergents, and Denaturants 4.2.1 Calorimetric Measurements Reveal the High Stability of Transmembrane α-Helices 4.2.2 α-Helical Proteins Can Be Denatured and Refolded Using Detergents and Lipids 4.2.3 α-Helical Membrane Proteins Can Be Unfolded Using Atomic Force Microscopy 4.3 β-Barrel Membrane Proteins Can Be Reversibly Unfolded Using Denaturants 4.3.1 β-Barrels Can Fold Reversibly into Membranes with the Help of Urea or Guanidinium Hydrochloride 4.3.2 Reversible Refolding of OmpLA Can Be Used to Derive an Amino Acid Hydrophobicity Scale 4.4 Lipid Bilayers and Membrane Proteins Adapt to Each Other 4.4.1 The Refolding of β-Barrels Depends upon Lipid Bilayer Properties 4.4.2 Hydrophobic Mismatch Is a General Feature of Protein–Bilayer Interactions Key Concepts Further Reading Key Literature Exercises Chapter 5 Protein Trafficking in Cells 5.1 Translocases Mediate the Transport of Proteins across the Endoplasmic Reticulum Membrane 5.1.1 Proteins Selected for Transport Are Identified by N-Terminal Signal Peptides: The Signal Hypothesis 5.1.2 Proteins Are Transported across the ER Membrane through the SRP/Sec61 Pathway 5.1.3 The SRP and the SR Ensure Proper Targeting of the Ribosome to the Sec61/SecYEG Translocons 5.1.4 Signal Peptidase (SPase) Cleaves Signal Peptides 5.1.5 Most Secretory Proteins in Bacteria Are Translocated Post-Translationally across the Inner Membrane 5.2 Bacteria Have Many Systems for Exporting Proteins 5.2.1 Bacterial Lipoproteins Are Sorted between the Inner and Outer Membranes 5.2.2 Fully Folded Proteins Can Be Exported by the Bacterial Twin-Arginine Translocation System 5.2.3 Some Bacterial Proteins Require Specialized Secretion Systems 5.2.4 Usher Proteins Secrete Bacterial Pili 5.3 Proteins Are Imported into Mitochondria, Chloroplasts, and Peroxisomes 5.3.1 Proteins Are Imported into Mitochondria through the TOM and TIM Translocases 5.3.2 Proteins Are Imported into Chloroplasts through the TOC and TIC Translocons 5.3.3 Proteins Are Imported into Peroxisomes by a “Piggy-Back” Mechanism 5.4 Proteins Are Transported in and out of the Nucleus through the Nuclear Pore Complex Key concepts Further reading Key Literature exercises Chapter 6 Biosynthesis and Assembly of Membrane Proteins 6.1 Cellular Mechanisms of Membrane Protein Assembly 6.1.1 How Do Cells Make Integral Membrane Proteins? 6.1.2 Bacterial Toxins Can Insert Spontaneously into Membranes 6.1.3 Most Membrane Proteins Are Co-translationally Inserted into the Membrane 6.1.4 Tail-Anchored Membrane Proteins Use a Distinct Insertion Machinery in the ER 6.1.5 GPI-Anchored Proteins Are Synthesized with a Hydrophobic C-Terminal Tail 6.1.6 β-Barrel Membrane Proteins Are Chaperoned to the Outer Membrane in Gram-Negative Bacteria 6.1.7 Mitochondrial Membrane Proteins Are Either Imported from the Cytosol or Made In Situ 6.2 Energetics of Membrane Protein Assembly 6.2.1 Membrane-Insertion Propensities Can Be Measured In Vivo 6.2.2 Some Transmembrane Helices Cannot Insert by Themselves 6.2.3 Many Membrane Proteins Form Homo- or Hetero-Oligomeric Complexes, but Multi-domain Architectures Are Rare 6.3 Membrane Protein Topology 6.3.1 Most Membrane Proteins Have a Unique Topology 6.3.2 The Distribution of Positively Charged Residues Correlates with Membrane Orientation 6.3.3 Membrane Orientation Can Be Manipulated by Sequence Alterations 6.3.4 The Translocon, the Membrane Potential, and Lipid Composition Can All Affect Protein Topology 6.3.5 Membrane Proteins Can Evolve by Gene Duplication and Addition/Deletion of Terminal Helices 6.3.6 Some Proteins Have a Dual Topology 6.3.7 Membrane Proteins Can Have Multiple Topologies 6.3.8 Membrane Proteins Can Undergo Dynamic Changes in Topology 6.3.9 Misfolded Membrane Proteins Are Degraded Key Concepts Further Reading Key Literature Exercises Chapter 7 How Proteins Shape Membranes 7.1 The Cytoskeleton Provides a Framework for Cell Shape and Vesicle Transport 7.1.1 How the Red Blood Cell Gets Its Shape 7.1.2 Cytoskeletal Filaments Organize Cells Spatially and Determine Mechanical Properties 7.1.3 Microtubules Formed from α- and β-tubulin Are Polarized 7.1.4 The Molecular Motors Kinesin and Dynein “Walk” along Microtubules to Transport Membrane Vesicles 7.2 Many Different Proteins Act Together to Create Vesicular Compartments in Cells 7.2.1 Clathrins Form Membrane Vesicles from the Plasma Membrane for Endocytosis 7.2.2 Caveolins also Carry Out Endocytosis but May Be More Important as Membrane-Status Sensors 7.2.3 COPI and COPII Vesicles Maintain the Endoplasmic Reticulum and the Golgi Apparatus 7.2.4 COPII Coats Are Adaptable to Cargos of Odd Shapes 7.2.5 COPI-Coated Vesicles Are Constructed from Preassembled Coatamers 7.3 Surface-Binding Proteins Modulate Membrane Curvature and Cause Vesicle Scission 7.3.1 BAR Domains Shape Vesicle Curvature 7.3.2 Dynamins Pinch Off Vesicles Shaped by BAR Domains 7.3.3 SNARE Complexes Control Fusion of Vesicles with Membranes Key Concepts Further Reading General Background BAR domains Erythrocyte Membranes Cytoskeleton Molecular Motors & Trafficking Caveolae & Caveolin Clathrin-Coated Vesicles COPI & COPII Vesicles Key literature BAR domains Erythrocyte Membranes Cytoskeleton Molecular Motors & Trafficking Caveolae & Caveolin Clathrin-Coated vesicles COPI & COPII vesicles Exercises Chapter 8 Membrane Protein Bioinformatics 8.1 Evolution of Protein Amino Acid Sequences Provides a Basis for Bioinformatics 8.1.1 The Statistical Variations among Related Protein Amino Acid Sequences Provide Insights into Evolutionary Processes 8.1.2 Sequence Alignment Algorithms Are Central to Bioinformatics 8.1.3 Structurally Similar Proteins Can Have Dramatically Different Sequences 8.1.4 Statistical Analysis Can Reveal Motifs in Membrane Helices, Such as GxxxG 8.2 Prediction Methods Allow Identification of Functional and Structural Features of Membrane Proteins 8.2.1 The Subcellular Localization of Proteins Can Be Predicted 8.2.2 Membrane Proteins Can Be Identified in Genomic Data 8.2.3 Topology Can Be Predicted for Both Helix-Bundle and β-Barrel Proteins 8.2.4 Interfacial Helices, Reentrant Loops, and Kinks 8.2.5 GPI Anchors Can Be Predicted 8.2.6 Prediction of Membrane Protein 3-D Structure Is Possible Key concepts Further reading Key literature Exercises Chapter 9 Primer on Biomolecular Structure Determination 9.1 Microscopy and Crystallography Depend upon Diffraction and Fourier Transformation 9.1.1 Understanding How Lenses Magnify Objects Reveals That Fourier Transformation of Images Is an Inherent Feature of Image Formation 9.1.2 Radiation Wavelength Limits What We Can See 9.2 Electron Microscopy Is a Versatile Tool for Molecular Structure Determination 9.2.1 Electron Microscopes Can Produce Direct Images of Biological Molecules 9.2.2 Images Can Be Formed from Single Molecules 9.3 X-Ray Crystallography Is the Mainstay of Structural Biology 9.3.1 Why Crystals of Proteins? 9.3.2 Diffraction from a Crystal Combines the Influence of the Contents of the Unit Cell with the Influence of the Crystal Lattice 9.4 What Is the “Phase Problem,” and How Do We Conquer It? 9.5 Crystallographic Models of Proteins Are Derived from Electron Density Maps 9.6 Electron Crystallography Is Useful for Diffraction from Small Crystals Key Concepts Further Reading Exercises Chapter 10 Small-Molecule Channels 10.1 Water Can Cross Membranes Either by Diffusion through the Lipid Bilayer or through Channels 10.1.1 Water Diffuses through Lipid Bilayers but with a High Activation Energy 10.1.2 Water Diffuses through Pores in Erythrocyte Membranes 10.2 Water and Other Small Molecules Move across Membranes Using Channels: Aquaporins and Aquaglyceroporins 10.2.1 Aquaporins and Aquaglyceroporins Facilitate the Passage of Water and a Few Small Molecules, Such as Glycerol, across Membranes 10.2.2 The Structure of an Aquaglyceroporin Reveals Tetramers with a Transport Pore in Each Subunit 10.2.3 Sequence Analysis of the Family Reveals Key Features of Aquaglyceroporins 10.2.4 The Charge Distribution in GlpF Is in Accord with the “Positive-Inside Rule” 10.2.5 An Ancient Gene Duplication Resulted in the Present Structure 10.3 Aquaporin Structure Reveals Structure–Function Relationships 10.3.1 Ions Are Blocked from the Channel by Their Hydration 10.3.2 Ideas for the Block of Proton Transport Are under Investigation 10.4 Gating and Control of Aquaporin Function 10.4.1 Plant Aquaporins Reveal Gating Mechanisms for Control 10.5 Ammonia Channels Have Many Roles across Phyla but Similar Structures 10.6 Specialized Mechanosensitive Channels Relieve Osmotic Stress 10.6.1 Mechanosensitive Channels Respond to Mechanical Forces by Opening to Allow Transmembrane Flow of Osmolytes 10.6.2 Mechanosensitive Channels Couple Lateral Membrane Tension to Channel Area 10.6.3 McsL Opens in a Squashed Iris Motion 10.6.4 McsS Also Gates by Helix Rearrangement 10.6.5 Non-specific Porins Allow Solute Passage Based Mostly on Molecular Weight 10.6.6 Metabolically Important Sugars Use Specialized Porins for Gaining Access to the Periplasm of Gram-Negative Bacteria 10.6.7 Why Are Beta-Barrels not Used in the Plasma Membrane Instead of Helical Bundles? 10.7 β-Barrels in Outer Membranes Reveal Diverse Strategies for Solute Permeation Key Concepts Further Reading Key Literature Exercises Chapter 11 Ion Channels 11.1 Ionic Currents across Membranes Underlie Nerve Action Potentials 11.1.1 Measurements of Macroscopic Electrical Properties of Nerves Reveal the Essential Features of Action Potentials 11.1.2 Excitability of Membranes Is Revealed by I–V Curves 11.1.3 I–V Curves and Chemical Agents Show That Ions Flow across Membranes through Channels 11.1.4 Noise in Voltage-clamp Experiments Suggests Stochastic Opening and Closing of Ion Channels 11.1.5 Patch Clamping Reveals Individual Ion Channels 11.1.6 Cloning and Expression of Sodium Channels Provide the First Glimpse of Channel Structure 11.1.7 Sodium, Potassium, and Calcium Channels Share Common Structural Motifs and Are Found in All Kingdoms of Life 11.2 Potassium Channels Are Highly Selective and Permit Diffusion-Limited Ion Transport 11.2.1 Dehydration and Ion Selectivity Result from the Properties of the Selectivity Filter 11.2.2 Cyclic Peptide Ionophores hint at the Selectivity Mechanism of Potassium Channels 11.2.3 The Carbonyl Groups of the Filter Determine Selectivity 11.2.4 The Energy Barrier for Ion Passage Is Lowered by Helix-end Polarity and a Water Chamber 11.2.5 High Ion Flux Is Facilitated by Cooperative Ion Movement 11.3 Ligands Can Control the Opening and Closing of Channels 11.3.1 Gating Energy Determines Regulatory Specificity 11.3.2 Gating by Ligand Binding Can Pull a Channel Open by Lateral Forces 11.4 Changes In Transmembrane Voltage Can Gate Channels Rapidly by Changing Charge Exposure across the Membrane Barrier 11.4.1 Voltage Gating Is Needed for Fast Responses 11.4.2 Voltage Gating Builds on the Theme of K+ Channels, with Added Domains for Voltage Sensing 11.4.3 Determination of the Structure of Voltage-Gated Ion Channels Presents Many Challenges 11.4.4 Channel Structures Lead to Mechanistic Ideas about Voltage Sensing 11.4.5 Lipid Composition and Mechanical Distortions Can Affect Channel Function 11.5 Voltage-Gated Na+ Channel Mechanism and Hydrated-Ion Selection 11.5.1 The NaV Channel Is Similar to the KcsA Channel but Selects Hydrated Na+ Ions 11.5.2 The Structure and Environment of the Gating Helix Suggest a Mechanism for Nav 11.6 A Voltage-Gated Porin in the Outer Membrane of Mitochondria Controls Exchange of Metabolites with the Cytoplasm of Eukaryotes 11.7 Conclusion Key Concepts Further Reading Key Literature Exercises Chapter 12 Primary Transporters: Transport against Electrical and Chemical Gradients 12.1 P-Type ATPases 12.1.1 A P-Type ATPase Is Responsible for Na+/K+ Active Transport 12.1.2 The Complete Pump Cycle of the Ca2+-ATPase Is Understood Structurally 12.1.3 P-type ATPases Are Structurally Similar but Serve Many Different Transport Functions 12.2 The Transport Principles of ABC Transporters Differ from Those of the P-Type ATPases 12.2.1 ABC Importers: The Maltose Transporter 12.2.2 ABC Exporters: P-glycoprotein 12.3 Energy-Coupling Factor Transporters Couple ATP Hydrolysis to “Toppling” of the Substrate-Binding Subunit Key Concepts Further Reading Key Literature Exercises Chapter 13 Secondary Transport 13.1 Requirements for Secondary Transporters 13.2 Rocker-Switch Transporters: Major Facilitator Superfamily (MFS) Symporters 13.2.1 The MFS Family Is Large 13.2.2 Structures of the Proton-Lactose Symporter, LacY, and the Proton-Fucose Symporter, FucP, Can Be Combined to Give a View of MFS Function 13.2.3 Structures of the Substrate-Free LacY at Different PHs Imply an Induced-Fit Mechanism 13.2.4 The Fucose Symporter, FucP, Is Outward, Open, and Supports a Rocker-Switch Alternating-Access Mechanism 13.3 Rocking-Bundle Transporters: Neurotransmitter Sodium Symporters 13.3.1 Key Topology Theme of LeuT Is an Inverted Repeat 13.3.2 The LeuT Structure in the Outward-Facing, Closed State Reveals Binding Sites for Na+ and Leucine 13.3.3 Ion- and Substrate-Binding Sites Use Principles Seen in Ion Channels 13.3.4 LeuT Is Active in Crystals Used in Structure Determination 13.3.5 Structures of the Outward-Open and Inward-Open States Have Been Determined 13.3.6 The Substrate-Free, Outward-Open State Reveals the Chemistry of the Outward-Open to Outward-Closed Transition 13.3.7 The Inward-Open Structure of LeuT Allows the Structural Conformation Change and Internal Gating to Be Understood 13.3.8 Combining the Three Structures of LeuT Gives a View of the Sequence of Events That Lead to Symport 13.4 Elevator-Like Transporters: Structural Studies of a Glutamate Transporter, GltPh, Reveal Similar Principles 13.4.1 FRET studies of GltPh reveal the dynamic nature of protein function 13.5 The ADP/ATP Transporter from Mitochondria 13.5.1 Mitochondrial Membranes Transport Key Metabolites, Including ATP and ADP 13.5.2 The Bovine ADP/ATP Transporter 13.5.3 The Structure of a Monomer of the Bovine ATP/ADP Transporter Has Been Determined 13.5.4 Is the Transporter a Monomer or a Dimer? 13.6 Uniporters (aka Facilitators) Facilitate Transport without Chemical Gradients 13.6.1 The Erythrocyte Glucose Transporter Resembles the MFS Proteins LacY and GlpT. 13.7 Conclusion Key Concepts Further Reading Key Literature Exercises Chapter 14 Bioenergetics 14.1 The Chemiosmotic Theory Is the Foundation of Bioenergetics 14.1.1 Redox Potentials Provide a Quantitative Foundation for Bioenergetics 14.1.2 Quantum Mechanical Tunneling Allows Long-Range Transfer of Electrons 14.2 Electrons Move along a Chain of Protein Complexes 14.2.1 Complex I (NADH Dehydrogenase) 14.2.2 Complex II (Succinate Dehydrogenase) 14.2.3 Complex III (Cytochrome c Reductase) 14.2.4 Complex IV (Cytochrome c Oxidase) 14.2.5 The Mitochondrial Electron Transport Chain Components Form Supercomplexes 14.3 ATP Synthase Produces ATP Using the Proton Gradient 14.3.1 ATP Synthase Is a Rotary Enzyme 14.3.2 Mechanism of ATP Synthesis 14.3.3 The H+/ATP Ratio Varies between Different Organisms 14.3.4 ATP Synthase Dimers Are Organized into Rows in Mitochondria 14.4 Photosynthesis Harvests Light to Produce Oxygen 14.4.1 Light-Harvesting Complex II 14.4.2 Photosystem II 14.4.3 The Cytochrome b6f Complex and Plastocyanin 14.4.4 Photosystem I Key Concepts Further Reading Key Literature Exercises Chapter 15 Information Transfer:: Signaling in Cells 15.1 Bacteria Sense Their Environment by Two-Component Signaling Systems 15.1.1 General Design of Two-Component Systems 15.1.2 Phosphoryl Transfer Is Carried out by the Kinase Core 15.1.3 Phosphorylation of the Receiver Domain Activates the Output Domain 15.1.4 Bacteria Seek Nutrients by Chemotaxis Using Two-Component Signaling 15.1.5 Bacteria Respond to Osmotic Stress by Regulating the Expression of OmpF and OmpC Porins in the Outer Membrane 15.2 Eukaryotic Cells Coordinate Their Interactions Using Receptor Tyrosine Kinases 15.2.1 Ligand Binding Induces Receptor Dimerization or Dimer Reorganization 15.2.2 Phosphorylation of the “Activation Loop” Activates the Kinase 15.3 G Protein Receptors Transmit Signals across the Plasma Membrane in Response to Hormones and Other Compounds 15.3.1 GPCRs Bind a Vast Variety of Ligands 15.3.2 Signaling Begins with Stabilization of an Active Conformation of the GPCR Induced by Agonist Binding 15.3.3 β2 Adrenergic Receptor and Bound G Proteins Change Conformation in Response to Ligand Binding 15.3.4 Rhodopsin’s Photocycle Underlies Vision 15.3.5 Crystal Structures Reveal General Principles of GPCR Activation 15.4 Cadherins and Integrins Mediate Mechanical Interactions with Neighboring Cells and the Extracellular Matrix 15.4.1 Cadherins Mediate Cell-Cell Contacts 15.4.2 Integrins Mediate Two-Way Signaling between Cells and the Surrounding Extracellular Matrix 15.4.3 Two-Way Signaling Mediated by Integrins Allows Cells to Shape the Extracellular Matrix, and Vice Versa Key Concepts Further Reading Key Literature G Protein Coupled Receptors, Including Rhodopsin Two-Component Signaling Systems Bacterial Motility Receptor Tyrosine Kinases Cahderins and Integrins Exercises Electrostatics Appendix Index