Comprehensive Biophysics

Editorial Board

Preface

Permission Acknowledgments

Volume 1 Biophysical Techniques for Structural Characterization of Macromolecules

1.1 Volume Introduction

Overview and Historical

1.2 Cantor and Schimmel – 30 Years Later

Protein Production Strategies for High-Throughput Structure Determination

1.3 Efficient Strategies for Production of Eukaryotic Proteins

Glossary

1.3.1 Introduction

1.3.2 Selection of Expression Platform

1.3.3 Cloning

1.3.4 Expression and Recovery of Target Protein

1.3.5 Facility

1.3.6 Rescue and Optimization Strategies

1.3.7 Conclusion

Acknowledgments

REFERENCES

X-ray Crystallography

1.4 X-Ray Crystallography: Crystallization

Glossary

1.4.1 Introduction

1.4.2 Structure Determination Process Overview

1.4.3 Precrystallization Studies

1.4.4 Crystallization Process

1.4.5 High-Throughput Crystallization

REFERENCES

1.5 X-Ray Crystallography: Data Collection Strategies and Resources

Glossary

1.5.1 Basic Concepts in X-Ray Crystal Diffraction

1.5.2 X-Ray Sources and Instrumentation

1.5.3 Data Collection Strategies

REFERENCES

1.6 Phasing of X-ray Data

1.6.1 The Phase Problem or What Can Go Wrong?

1.6.2 Direct Methods: What We Know About the Unmeasured Phases?

1.6.3 The Patterson Function: Who Needs the Phases?

1.6.4 Dual-Space Recycling: Enforcing Atomicity in Real and Reciprocal Space

1.6.5 Experimental Phasing: Divide and Conquer

1.6.6 Density Modification: Improving Experimental Phases

1.6.7 Molecular Replacement: Exploiting Previous Structural Information

1.6.8 Frontier Methods: Not General – Yet?

1.6.9 Multiple Beam Interference: But It Is Possible to Measure Phases

1.6.10 Multisolution Combination of Location of Model Fragments and Density Modification

1.6.11 Molecular Replacement with Homology Models

Appendix: Web Phasing

Acknowledgments

REFERENCES

1.7 Refinement of X-ray Crystal Structures

Glossary

1.7.1 Introduction

1.7.2 Target Functions for Refinement

1.7.3 The Model

1.7.4 Cross-Validation

1.7.5 Optimization Methods

1.7.6 Special Considerations at Low Resolution

1.7.7 Conclusions and Outlook

Acknowledgments

REFERENCES

1.8 Structure Validation and Analysis

Glossary

1.8.1 Introduction

1.8.2 Validation of Crystallographic Models

1.8.3 Structural Biology in a High-Throughput Environment

1.8.4 Concluding Remarks

1.8.5 Software and Tools for Structure Validation and Analysis

Acknowledgment

REFERENCES

NMR Spectroscopy

1.9 Introduction to Solution State NMR Spectroscopy

1.9.1 Introduction

1.9.2 Introduction to the NMR Experiment

1.9.3 Multidimensional NMR Spectroscopy

1.9.4 Features of the NMR Spectrum

1.9.5 Relaxation Processes and Their Mechanisms

1.9.6 Samples

1.9.7 Resonance Assignments

1.9.8 Heteronuclear Multidimensional NMR Spectra

1.9.9 Problems with Large Molecules

1.9.10 Qualitative Structural Information from the NMR Spectrum

1.9.11 Structure Determination by NMR

1.9.12 Examples of Structures Calculated by NMR

REFERENCES

1.10 Solid State NMR Methods

1.10.1 Introduction

1.10.2 High-Resolution ssNMR

1.10.3 Sample Preparation

1.10.4 From High Resolution to 3-D Structure

1.10.5 Dynamics and Time-Resolved Experiments

1.10.6 Applications to Amyloids and Membrane Proteins

1.10.7 Larger Systems and Hybrid Approaches

1.10.8 Conclusion and Future Directions

Acknowledgments

REFERENCES

1.11 The Hybrid Solution/Solid-State NMR Method for Membrane Protein Structure Determination

1.11.1 Overview

1.11.2 Solution NMR Approach for Membrane Proteins in Micelles

1.11.3 Solid-State NMR Approach for Uniaxially Aligned Membrane Proteins

1.11.4 Computational Approach: Hybrid Energy Function and Virtual Membrane

1.11.5 Examples: High-Resolution Structures and Topologies of Phospholamban (Monomer and Pentamer) and Sarcolipin in Lipid Membranes

1.11.6 Sensitivity and Resolution Enhancement in Separated Local Field Experiments

1.11.7 Conclusions and Perspectives

REFERENCES

1.12 Labeling Techniques

Glossary

1.12.1 Introduction

1.12.2 Basic Isotope Labeling Strategies

1.12.3 Stereo-Array Isotope Labeling Principle

1.12.4 Stereo-Array Isotope Labeling Technologies

1.12.5 SAIL NMR Spectroscopy

1.12.6 Conclusion and Outlook

Acknowledgments

REFERENCES

1.13 NMR Spectroscopy: NMR Relaxation Methods

1.13.1 Introduction

1.13.2 Spin Relaxation and Dynamic Effects on NMR Spectra

1.13.3 Experimental Methods for Solution Laboratory Frame Relaxation Measurements

1.13.4 Experimental Methods for Solution Chemical Exchange Measurements

1.13.5 Methods for Nucleic Acids

1.13.6 Applications

1.13.7 Conclusion

Acknowledgments

REFERENCES

Electron Microscopy

1.14 Structure Determination of Macromolecular Complexes by Cryo-Electron Microscopy in vitro and in situ

Glossary

1.14.1 Introduction

1.14.2 3-D Cryo-EM

1.14.3 Automated Data Acquisition

1.14.4 SPA

1.14.5 CET

1.14.6 Electron Crystallography

1.14.7 Interpretation of EM Maps at the Molecular Level

1.14.8 Conclusions

Acknowledgments

REFERENCES

1.15 Analysis of 2-D Crystals of Membrane Proteins by Electron Microscopy

Glossary

1.15.1 Introduction

1.15.2 Membrane Protein 2-D Crystallization

1.15.3 EM Data Collection for 2-D Crystals

1.15.4 Image Processing for 2-D Crystals

1.15.5 Conclusion

REFERENCES

1.16 Cryo-Electron Microscopy and Tomography of Virus Particles

Glossary

1.16.1 Introduction

1.16.2 Single Particle Reconstruction

1.16.3 Tomography

1.16.4 Data Collection

1.16.5 Data Storage

1.16.6 Data Preprocessing

1.16.7 Single Particle Reconstruction

1.16.8 Tomographic Reconstruction

1.16.9 Data Interpretation

1.16.10 Biological Examples

1.16.11 Future Prospects

Acknowledgments

REFERENCES

Mass Spectrometry

1.17 Mass Spectrometry

Glossary

1.17.1 Introduction

1.17.2 Mass Spectrometry Technology

1.17.3 Functional Proteomics

1.17.4 Structural Proteomics

1.17.5 Characterization of Post-Translational Modifications

1.17.6 Chemical Labeling Approaches

1.17.7 Structural Mass Spectrometry

1.17.8 Conclusion and Future Directions

REFERENCES

SAXS

1.18 Small and Wide Angle X-ray Scattering from Biological Macromolecules and their Complexes in Solution

1.18.1 Introduction

1.18.2 Scattering Basics

1.18.3 Effects of Hydration

1.18.4 Three-Dimensional Reconstruction of Low Resolution Density Maps from SAXS Data

1.18.5 Disordered Peptides and Proteins in Solution: Free Energy Landscape for Denaturation

1.18.6 Calculation of SAXS Profiles for Detergent Micelles and Protein–Detergent Complexes

1.18.7 Combination of SAXS and NMR for Structure Determination of Multi-Domain Proteins

1.18.8 Solution Structure of Small Functional RNAs

1.18.9 Use of Nanogold Markers for SAXS Determination of Intramolecular Distance Distributions

Acknowledgments

REFERENCES

Ultrafast Spectroscopic Techniques

1.19 Ultrafast Structural Dynamics of Biological Systems

1.19.1 Introduction

1.19.2 Time and Length Scales

1.19.3 Principles and Methods of Ultrafast Laser Spectroscopy

1.19.4 Principles and Methods of Ultrafast Structural Dynamics

1.19.5 Applications

1.19.6 Outlook

REFERENCES

EPR and Other Electron Spectroscopies

1.20 Electron Magnetic Resonance

Glossary

1.20.1 A Simple Definition of Electron Spin Resonance and Its Spectroscopic Origins

1.20.2 Basic Elements of a Continuous Wave EMR Spectrum

1.20.3 Biophysical Applications of Electron Magnetic Resonance

1.20.4 Magnetochemistry and Electron Resonance

1.20.5 Magnetic Resonance Transitions and Justification of an Independent Spin Hamiltonian

1.20.6 The Lineshape Model and the Physical Interpretation of Relaxation Times

1.20.7 Further Details Concerning Resonance Spectrometers and the Generation of Spectra

1.20.8 Magnetic Effects in Three Dimensions: Anisotropy and Recovery of Information

1.20.9 Electron-Electron Double Resonance and Saturation Transfer

1.20.10 Pulse Methods

1.20.11 Concluding Remarks: Where One Goes from Here

REFERENCES

Computation

1.21 Computation of Structure, Dynamics, and Thermodynamics of Proteins

1.21.1 Introduction

1.21.2 Force Fields

1.21.3 Techniques

1.21.4 Use of Experimental Information in Simulations

1.21.5 Summary and Future Directions

REFERENCES

Fast Flow

1.22 Rapid Mixing Techniques for the Study of Enzyme Catalysis

1.22.1 Background

1.22.2 The Design of Rapid Mixers

1.22.3 Specialized Stopped-Flow and Continuous-Flow Instruments

1.22.4 Rapid Freeze Quenching Techniques

1.22.5 Conclusions and Outlook

Acknowledgments

REFERENCES

Other Spectroscopy – UV-Vis, CD, Raman, Vibrational CD Applied in Biophysical Research

1.23 Optical Spectroscopy

1.23.1 Introduction

1.23.2 Theory

1.23.3 Applications of Absorption and Electronic Circular Dichroism Spectroscopy

1.23.4 IR and Vibrational Circular Dichroism Spectroscopy

1.23.5 Epilogue

REFERENCES

FRET/Fluorescence

1.24 Fluorescence and FRET: Theoretical Concepts 101

1.24.1 Introduction

1.24.2 A Historical Synopsis of the Beginnings of Fluorescence and the Emergence of a Quantitative Physical Model

1.24.3 Fluorescence Background Important for FRET

1.24.4 Pathways of Excited States

1.24.5 FRET History and the Theoretical Basis of FRET

1.24.6 Methods of Data Acquisition and Analysis of FRET (Steady State and Dynamic Time and Frequency Domain)

1.24.7 Postscript

REFERENCES

Volume 2 Biophysical Techniques for Characterization of Cells

2.1 Volume Introduction

Elucidating Cellular Structures

2.2 Confocal Microscopy

2.2.1 Introduction

2.2.2 Flying-Spot Microscopes

2.2.3 Beam Scanning Confocal Microscopes

2.2.4 Scanning and Descanning the Beam

2.2.5 Confocal Imaging at Different Wavelengths

2.2.6 Detector Aperture

2.2.7 Resolution in an Ideal Confocal Microscope

2.2.8 Photon Statistics

2.2.9 Direct View

2.2.10 General Testing of Environmental Effects

2.2.11 Test Slides

Optical Appendix

REFERENCES

2.3 Fluorescence Lifetime Microscopy: The Phasor Approach

2.3.1 Introduction

2.3.2 Methods for the Determination of Fluorescence Lifetime on a Pixel Basis

2.3.3 Methods of Data Analysis

2.3.4 Examples of Application of Phasor Analysis in FLIM

2.3.5 FRET Biosensors

REFERENCES

2.4 Super-Resolution Microscopy

Glossary

2.4.1 Introduction

2.4.2 Super-Resolution Fluorescence Microscopy

2.4.3 Practical Considerations

2.4.4 Conclusions

REFERENCES

2.5 Studying the Macromolecular Machinery of Cells in situ by Cryo-Electron Tomography

Glossary

2.5.1 Introduction

2.5.2 Theoretical Aspects of Three-Dimensional Cryo-Electron Microscopy

2.5.3 From TEM Images to Tomogram

2.5.4 Sample Preparation

2.5.5 Post-Processing and Analysis of Tomograms

2.5.6 CET Studies of Cells and Cellular Fractions in toto

2.5.7 Genetic, Pharmacological and Related Manipulations Integrated with CET

2.5.8 Identification Based on Labeling

2.5.9 Conclusions

Acknowledgments

REFERENCES

2.6 Visualizing Sub-cellular Organization Using Soft X-ray Tomography

Glossary

2.6.1 Introduction

2.6.2 Soft X-Ray Microscopy

2.6.3 Soft X-Ray Tomography: Theory

2.6.4 Soft X-Ray Tomography: Practice

2.6.5 Application of Soft X-Ray Tomography in Cell Biology

2.6.6 Localizing Molecules Using Correlated Light and X-Ray Microscopy

2.6.7 Summary and Future Prospects

REFERENCES

2.7 Atomic Force Microscopy

2.7.1 Cell Sample Preparation Methods

2.7.2 Atomic Force Microscopy Imaging

2.7.3 Molecular Recognition Force Spectroscopy

2.7.4 Recognition Imaging

2.7.5 Fluorescence Guided Molecular Force Spectroscopy and Combined Fluorescent/Simultaneous Topography and Recognition Imaging

REFERENCES

2.8 Super-Resolution Near-Field Optical Microscopy

Glossary

2.8.1 Optical Microscopy Beyond the Diffraction Limit of Light

2.8.2 The Near-Field Concept

2.8.3 Technical Implementation

2.8.4 Applications on Cellular Structures

2.8.5 Future Directions

2.8.6 Summary

REFERENCES

2.9 CARS Microscopy

2.9.1 Label-Free Optical Microscopy

2.9.2 Theoretical Basics of Coherent Anti-Stokes Raman Scattering

2.9.3 CARS Microscopy Excitation Geometries

2.9.4 Excitation Schemes for CARS Microscopy

2.9.5 Applications of CARS Microscopy

2.9.6 Outlook

REFERENCES

Elucidating Cellular Dynamics

2.10 Quantitative Fluorescent Speckle Microscopy

2.10.1 Introduction

2.10.2 What Is a Speckle and How Is It Formed?

2.10.3 Practical Requirements for Speckle Imaging

2.10.4 Algorithms for Image Analysis

2.10.5 Applications of FSM in Cell Biological Experiments

2.10.6 Conclusions

REFERENCES

2.11 Fluorescence Correlation Spectroscopy

Glossary

2.11.1 Introduction

2.11.2 Basic Principles of FCS

2.11.3 The Correlation Function

2.11.4 Extending Correlation Functions

2.11.5 Theoretical Approaches

2.11.6 Practical Aspects

2.11.7 Artifacts

2.11.8 Advanced FCS Techniques

2.11.9 Applications

2.11.10 Outlook

REFERENCES

2.12 Image Correlation Spectroscopy

2.12.1 Introduction

2.12.2 Principles and Theory of Image Correlation Spectroscopy

2.12.3 Variants of ICS

2.12.4 Experimental Considerations for ICS

2.12.5 Conclusion

REFERENCES

2.13 The Basics and Potential of Single-Molecule Tracking in Cellular Biophysics

2.13.1 Introduction

2.13.2 Single-Molecule Detection

2.13.3 Analysis of Single-Molecule Data

2.13.4 Applications

2.13.5 Conclusion

Acknowledgments

REFERENCES

Volume 3 The Folding of Proteins and Nucleic Acids

Protein Folding

3.1 Combining Simulation and Experiment to Map Protein Folding

Glossary

3.1.1 Introduction

3.1.2 Case Studies

3.1.3 Conclusions

REFERENCES

Globular Proteins

3.2 Energetics of Protein Folding

3.2.1 Introduction

3.2.2 Hydrophobic Effect

3.2.3 Hydrogen Bond

3.2.4 Electrostatic Interaction

3.2.5 Conformational Entropy

3.2.6 Strategies to Improve Protein Stability

Acknowledgment

REFERENCES

3.3 Fast Events in Protein Folding

3.3.1 Introduction

3.3.2 Simulating the Fast Events

3.3.3 Capturing the Fast Events Experimentally

3.3.4 An Archetypal Ultrafast Folding Protein: BdpA

3.3.5 Fast Folding Measurements of BdpA

3.3.6 Comparison of Experiments with Simulations

Acknowledgments

REFERENCES

3.4 Intermediates in Protein Folding

Glossary

3.4.1 Perspective

3.4.2 Equilibrium Intermediates

3.4.3 Kinetic Intermediates

3.4.4 Development of Quaternary Structure

3.4.5 Biological Significance

Acknowledgments

REFERENCES

3.5 Characterization of the Denatured State

Glossary

3.5.1 Introduction and Historical Perspective

3.5.2 Theoretical Approaches to Characterizing the DSE

3.5.3 Structural Methods for Analyzing the DSE

3.5.4 Thermodynamic Characterization of the DSE

3.5.5 Kinetics of Contact Formation in the DSE

3.5.6 Summary and Perspectives

REFERENCES

3.6 Single-Molecule Spectroscopy of Protein Folding

Glossary

3.6.1 Introduction

3.6.2 History and Principles of Single-Molecule Detection

3.6.3 Kinetics: From Ensembles to single-Molecules

3.6.4 Correlation Analysis

3.6.5 Single-Molecule Förster Resonance Energy Transfer

3.6.6 Experimental Aspects

3.6.7 Single-Molecule Spectroscopy of Protein Folding

3.6.8 Current Developments and Future Directions

3.6.9 Conclusion

Acknowledgments

REFERENCES

3.7 Simulation Studies of Force-Induced Unfolding

Glossary

3.7.1 Introduction

3.7.2 Force Probe Experiments and Their Interpretation

3.7.3 Mechanical Unfolding of Single Domain Proteins

3.7.4 Conclusions and Perspectives

Acknowledgments

REFERENCES

3.8 Protein and Nucleic Acid Folding: Domain Swapping in Proteins

Glossary

3.8.1 Introduction

3.8.2 General Aspects

3.8.3 Instructive Examples and Biological Implications

3.8.4 Conclusions

Acknowledgments

REFERENCES

3.9 Intrinsically Disordered Proteins

Glossary

3.9.1 Introduction

3.9.2 Structural Properties and Conformational Behavior of IDPs and IDPRs

3.9.3 Functional Repertoire of IDPs

3.9.4 Methods for Structural Characterization of IDPs

Acknowledgments

REFERENCES

3.10 Chaperones and Protein Folding

Glossary

3.10.1 Hsp70 Chaperones

3.10.2 Chaperonin Ring Assemblies

3.10.3 Small Heat Shock Proteins

3.10.4 Hsp90 Chaperones

REFERENCES

3.11 Protein Switches

3.11.1 Introduction

3.11.2 Engineered Switches

3.11.3 Synthetic Polymer–Protein Hybrids

3.11.4 Conclusions

Acknowledgments

REFERENCES

Repeat/Non-Globular Proteins

3.12 The Folding of Repeat Proteins

3.12.1 Repeat Proteins: Simplified Frameworks in which to Deconstruct Protein Folding

3.12.2 Equilibrium Stability of Repeat Proteins

3.12.3 Linear Statistical Mechanics Models to Describe the Stability of Repeat Proteins

3.12.4 Exploring the Presence of Partially Unfolded Species at the Equilibrium: Ising Model Predictions

3.12.5 The Basis and Limits of Cooperativity in Repeat Proteins

3.12.6 Unfolding Kinetics of Repeat Proteins

3.12.7 Denatured State in Repeat Proteins

3.12.8 Repeat Protein Folding: Roles in the Regulation of Biological Function

3.12.9 Conclusions

REFERENCES

Membrane Proteins

3.13 The Membrane Factor: Biophysical Studies of Alpha Helical Transmembrane Protein Folding

3.13.1 Introduction and Membrane Complexity

3.13.2 Solubilizing Systems and Refolding Methods

3.13.3 Folding Kinetics

3.13.4 Comparing Membrane and Water-Soluble Protein Folding

3.13.5 Co-translational Folding and Membrane Integration

3.13.6 Conclusions

REFERENCES

Nucleic Acid Folding

3.14 Effect of Protein Binding on RNA Folding

Glossary

3.14.1 Introduction

3.14.2 Why Does RNA Need Protein?

3.14.3 Protein-Assisted RNA Folding in the Ribosome

3.14.4 DExD/H Helicases and RNA Folding

3.14.5 Proteins That Fold Group I Introns

3.14.6 Summary

REFERENCES

Volume 4 Molecular Motors and Motility

4.1 Introduction

REFERENCES

General Theoretical Considerations

4.2 Microscopic Reversibility and Free-Energy Transduction by Molecular Motors and Pumps

Glossary

4.2.1 Introduction – Molecular Motors at and Away from Equilibrium

4.2.2 Microscopic Reversibility and Ligand Binding to Myoglobin

4.2.3 Cycles of Molecular Machines

4.2.4 Molecular Machines in a Thermal Environment

4.2.5 How Does the Chemical Reaction Drive Conformational Cycling?

4.2.6 A Two-Headed Motor that Walks Down a Track

4.2.7 Microscopic Reversibility and Dynamic Disorder

4.2.8 Conclusion

REFERENCES

Actin

4.3 Structure and Dynamic States of Actin Filaments

Glossary

4.3.1 Introduction

4.3.2 Bacterial Actin Homologs

4.3.3 Polymerization

4.3.4 Actin in Muscle

4.3.5 Development of an F-actin Model

4.3.6 Variable Twist in F-Actin

4.3.7 Variable Tilt in F-Actin

4.3.8 Allostery and Cooperativity

4.3.9 Higher Order Structures

REFERENCES

4.4 Actin Filament Nucleation and Elongation

4.4.1 Introduction

4.4.2 Biochemical Bases of Actin Polymerization

4.4.3 Actin Filament Nucleators

4.4.4 Formins

4.4.5 The W Domain and Actin Filament Nucleation

4.4.6 Tandem W Domain-Based Filament Nucleators

4.4.7 Role of Oligomerization on the Activities of Filament Nucleators

4.4.8 Filament Nucleation by NPFs-Arp2/3 Complex

4.4.9 Lmod and the Nucleation of Actin Filaments in Muscle Cells

4.4.10 Ena/VASP Proteins as Dedicated Elongation Factors

4.4.11 Profilin and the Pro-Rich Regions of Nucleation and Elongation Factors

4.4.12 Concluding Remarks

Acknowledgments

Appendix A Supporting Materials

Appendix A Supporting materials

REFERENCES

4.5 Mechanical Properties of Actin Networks

4.5.1 Introduction

4.5.2 Rheology

4.5.3 Reconstituted Crosslinked Actin Networks

4.5.4 Reconstituted Contractile F-Actin Networks

4.5.5 Reconstituted Protrusive F-Actin Networks

4.5.6 Summary and Outlook

Acknowledgments

REFERENCES

Microtubles

4.6 Tubulin and Microtubule Structure: Mechanistic Insights into Dynamic Instability and Its Biological Relevance

Glossary

4.6.1 Introduction to Microtubules and Dynamic Instability

4.6.2 Tubulin Structure

4.6.3 Microtubule Lattice Structure

4.6.4 Alternative Conformational States of Tubulin

4.6.5 Biological Roles of Structural Intermediates in Microtubule Assembly and Disassembly

REFERENCES

4.7 Force Generation by Dynamic Microtubule Polymers

Glossary

4.7.1 Microtubules Are Ubiquitous Cytoskeletal Polymers, Essential for Cell Health and Viability

4.7.2 Growing MTs Can Push

4.7.3 Shortening MTs Can Pull on a Load in at Least Two Ways

4.7.4 Theoretical and Experimental Analysis of an MT Depolymerization Motor

4.7.5 Molecular Devices to Couple MT Depolymerization to Processive Cargo Motion

4.7.6 Summary

REFERENCES

Myosin

4.8 Myosin Motors: Structural Aspects and Functionality

4.8.1 Introduction

4.8.2 Structural Features of the Myosin Motor Domain

4.8.3 Allosteric Communication

4.8.4 Summary and Conclusions

REFERENCES

4.9 Myosin Motors: Kinetics of Myosin

Glossary

4.9.1 Introduction

4.9.2 Early Studies of Myosin

4.9.3 The Paradox

4.9.4 Kinetic Measurements

4.9.5 The Kinetic Pathway is Conserved for Most Characterized Myosins

4.9.6 ADP Release and Force Sensitivity

4.9.7 Kinetic Diversity of the Myosin Family

4.9.8 Summary

Acknowledgments

REFERENCES

4.10 Single Molecule Fluorescence Techniques for Myosin

Glossary

4.10.1 Introduction

4.10.2 A Description of the Major Techniques that Use Fluorescence to Study Single Molecules

4.10.3 Early Single Molecule and Polarization Studies

4.10.4 Some Myosins Move Processively Along Actin

4.10.5 Single Molecule Fluorescence Studies of Myosin-5a

4.10.6 Regulation of Processive Myosins

4.10.7 Unconventional Myosins – Single-Headed or Double-Headed?

4.10.8 Visualizing Single Molecules in Cells

4.10.9 Conclusions

REFERENCES

Muscle

4.11 Cell-Based Studies of the Molecular Mechanism of Muscle Contraction

Glossary

4.11.1 Introduction

4.11.2 The Sarcomere: Structural and Functional Unit of Striated Muscle

4.11.3 Structure of Thick and Thin Filaments

4.11.4 The Isometric Twitch: Unitary Response of an Intact Muscle Cell

4.11.5 Skinned Muscle Fibers

4.11.6 Muscle Mechanics and Energetics in the Steady State

4.11.7 The Cross-Bridge Paradigm: Cycles and Strokes

4.11.8 Myosin as a Motor Protein: A.F. Huxley′s (1957) Model

4.11.9 Stiffness of Sarcomeres, Filaments and Myosin Motors

4.11.10 Inside the Cross-Bridge Cycle: Mechanical Kinetics

4.11.11 Mechano-Chemical Coupling

4.11.12 Methods for Studying Molecular Structural Dynamics in Muscle

4.11.13 Structure of Myosin Filaments and Myosin Head Conformations in Reference States

4.11.14 Structure of Myosin Filaments and Myosin Head Conformations during Isometric Contraction

4.11.15 Mechano-Structural Coupling and its Kinetics

4.11.16 Structural Dynamics of Muscle Regulation

4.11.17 Resistance to Stretch: Muscle as a Brake

4.11.18 Summary and Perspective

REFERENCES

4.12 Spectroscopic Probes of Muscle Proteins

Glossary

4.12.1 Introduction

4.12.2 Case Studies

4.12.3 Summary

REFERENCES

4.13 Thin Filament Regulation

Glossary

4.13.1 Introduction

4.13.2 The Players Tropomyosin and Troponin

4.13.3 Structural Changes within the Regulated Actin Filaments

4.13.4 Biochemical Studies of the Thin Filament Regulation

4.13.5 Co-operativity

4.13.6 The Myosin ATPase

4.13.7 In vitro Motility Assays and Regulation

4.13.8 Fibers and Myofibrils

REFERENCES

4.14 Smooth Muscle and Myosin Regulation

4.14.1 Background

4.14.2 Folded-to-Extended Conformational Transition

4.14.3 Mutational Studies of the RLC

4.14.4 Rod Mutations

4.14.5 Motor Domain Mutations

4.14.6 Structural Basis of Regulation: The Lever Arm

4.14.7 Structural Basis of Regulation: Asymmetric Head-Head Interactions

4.14.8 Features of the Rod in the 10S State

4.14.9 Head-Head Interactions in Striated Muscle Myosins

4.14.10 What Happens Upon Activation?

4.14.11 Properties of Myosin with One of its Two Heads Phosphorylated

4.14.12 Does the Folded Form of Smooth Muscle Myosin Exist In Vivo?

4.14.13 Unique Features of Smooth Muscle Myosin

4.14.14 Unique Features of Smooth Muscle

4.14.15 Smooth Muscle Isoforms

4.14.16 Smooth Muscle Myosin Mutations Implicated in Disease

4.14.17 Future Goals

Acknowledgments

REFERENCES

Non-Muscle Motility

4.15 Intracellular Transport: Relating Single-Molecule Properties to In Vivo Function

Glossary

4.15.1 Overview

4.15.2 An Introduction to the Families of Molecular Motors

4.15.3 Single-Molecule Properties of the Molecular Motors

4.15.4 From Single Motor Function to In Vivo Transport: The Issues

4.15.5 Summary

REFERENCES

4.16 Mechanical Forces in Mitosis

Glossary

4.16.1 Introduction

4.16.2 Metaphase Spindle Organization and Dynamics

4.16.3 Molecular Origin of Forces

4.16.4 Mapping Forces within Spindles

4.16.5 Spindle Length Regulation

4.16.6 Mechanics of the Kinetochore–Microtubule Interface

Acknowledgements

REFERENCES

Kinesin

4.17 Kinesin Structure and Biochemistry

Glossary

4.17.1 Introduction

4.17.2 Processive KinN Kinesins

4.17.3 Nonmotile Kinesin-10 NOD

4.17.4 Perspectives

Acknowledgments

REFERENCES

4.18 Kinesin Single-Molecule Mechanics

Glossary

4.18.1 Introduction

4.18.2 Structure

4.18.3 Kinesin Motility

4.18.4 Mechanochemical Cycle

4.18.5 Conclusion and Future Directions

REFERENCES

Dynein

4.19 Cytoplasmic Dynein: Its ATPase Cycle and ATPase-dependent Structural Changes

Glossary

4.19.1 Cytoplasmic Dynein is a Mechanochemical Enzyme Belonging to the AAA+Superfamily

4.19.2 The Modular Structure of the Dynein Heavy Chain

4.19.3 The Minimal Motor Domain of Cytoplasmic Dynein

4.19.4 The AAA Ring as the ATPase Module

4.19.5 The Linker as the Powerstroke Module

4.19.6 The Stalk as the Switching Module for MT Attachment/Detachment

4.19.7 The Mechanochemical Properties of the Motor Domain

4.19.8 Future Perspectives

REFERENCES

4.20 Axonemal Motility

Glossary

4.20.1 Introduction

4.20.2 The Axoneme

4.20.3 Axonemal Dyneins

4.20.4 Conclusion

Acknowledgments

REFERENCES

Nucleic Acid Motors

4.21 The Ribosome

Glossary

4.21.1 Introduction

4.21.2 Ribosome Composition and Structure

4.21.3 The Translation Cycle

4.21.4 Biophysical Approaches to Elucidating the Mechanisms of Individual Steps of the Translation Cycle

4.21.5 The Overall Rhythm of Protein Synthesis

4.21.6 Is the Ribosome a Biomolecular Brownian Motor?

4.21.7 Overall Summary

4.21.8 A Note on Translation Videos

REFERENCES

4.22 Viral DNA Packaging Motors

Glossary

4.22.1 Packaging in the Double-Stranded DNA Bacteriophages

4.22.2 What are the Components and Organization of the Packaging Complex?

4.22.3 How is Packaging Initiated?

4.22.4 How is the DNA Translocated?

4.22.5 What are the Organization and Physics of the Genome during and after Packaging?

4.22.6 How is Packaging Terminated?

4.22.7 Conclusions and Future Directions

REFERENCES

Volume 5 Membranes

Volume Introduction

5.1 Biophysics of Membranes

REFERENCES

Lipid Bilayers

5.2 Lipid Bilayer Structure

Glossary

5.2.1 General Concepts

5.2.2 Lipids and Water (Hydrophobicity)

5.2.3 Structural Parameters (Geometry)

5.2.4 Molecular Fluctuations within Bilayers

5.2.5 Structural Deformations

5.2.6 Bilayer Undulations

5.2.7 Appendix: X-Ray and Neutron Scattering of Lipid Bilayers

REFERENCES

5.3 Membrane Domains and Their Relevance to the Organization of Biological Membranes

Glossary

5.3.1 Historical Perspectives of Membrane Domains

5.3.2 Lateral Organization of Lipid Bilayers: Model Systems and Experimental Techniques

5.3.3 Direct Visualization of Lipid Domains

5.3.4 Specialized Biological Membranes: Pulmonary Surfactant and Skin Lipids

5.3.5 Membrane Domains in Biological Membranes and Their Relation to the ‘Raft’ Hypothesis

5.3.6 Challenges and Future Perspectives

Acknowledgments

REFERENCES

5.4 Atomic Force Microscopy and Fluorescence Microscopy of Lipid Bilayers

Glossary

5.4.1 Fluorescence and Atomic Force Microscopy

5.4.2 Imaging Lipid Phase Behavior

5.4.3 Imaging Supported Lipid Bilayer Formation

5.4.4 Imaging Curvature Effects in Lipid Bilayers

5.4.5 Measurements of Lipid Forces by AFM

REFERENCES

5.5 Detergent Interactions with Lipid Bilayers and Membrane Proteins

5.5.1 Scope and Introduction

5.5.2 Self-Association

5.5.3 Stages and Phases of a Lipid/Detergent System, an Overview

5.5.4 Membrane Partitioning (Stage I)

5.5.5 Sublytic Membrane Perturbation (Stage I)

5.5.6 Solubilization of Membranes via Bilayer/Micelle Coexistence (Stage II)

5.5.7 Lipid–Detergent Micelles (Stage III)

5.5.8 Detergents in Membrane Protein Studies

Acknowledgments

REFERENCES

Membrane Proteins

5.6 Atomic Force Microscopy and Electron Microscopy of Membrane Proteins

Glossary

5.6.1 Introduction

5.6.2 Electron-crystallography

5.6.3 Atomic Force Microscopy

5.6.4 Single Molecule Force Spectroscopy

5.6.5 Perspectives

Acknowledgments

REFERENCES

5.7 Solution NMR Spectroscopy of Integral Membrane Proteins

Glossary

5.7.1 Introduction

5.7.2 Preparation of Membrane Protein Samples for Solution NMR Studies

5.7.3 Solution NMR Techniques for Integral Membrane Proteins

5.7.4 Solution NMR Studies of Integral Membrane Proteins

5.7.5 Discussion and Outlook

REFERENCES

5.8 Structure and Folding of Outer Membrane Proteins

5.8.1 Introduction

5.8.2 Outer Membrane Protein Structures

5.8.3 Outer Membrane Protein Folding

Acknowledgments

REFERENCES

5.9 Pore-Forming Toxins

5.9.1 Introduction

5.9.2 General Mode of Action of Pore Forming Toxins

5.9.3 Structural Classification of Pore-Forming Toxins

5.9.4 Methodological Approaches to Understanding Pore-Forming Toxins

5.9.5 Pore-Forming Proteins as Tools in Cell Biology, Immunology, and Bioengineering

REFERENCES

Protein Interactions With Membranes

5.10 Interactions of Antimicrobial Peptides with Lipid Bilayers

Glossary

5.10.1 Introduction

5.10.2 Types of Antimicrobial Peptides

5.10.3 How Sequence Determines Structure and Activity

5.10.4 Kinetics of Membrane Disruption

5.10.5 Thermodynamics and Kinetics of Binding to Membranes

5.10.6 Membrane Elasticity and Peptide Activity

5.10.7 Membrane Disruption by Antimicrobial Peptides

5.10.8 Conclusion

Acknowledgment

REFERENCES

5.11 Membrane Recruitment of Signaling Domains

Glossary

5.11.1 Introduction

5.11.2 Phospholipid Bilayers and Membrane Binding Domains

5.11.3 Mechanisms of Membrane Recruitment

5.11.4 In Vitro and In Silico Analyses of Membrane Recruitment

5.11.5 Cell-Based Analyses of Membrane Recruitment

REFERENCES

5.12 Membrane Protein–Lipid Match and Mismatch

5.12.1 Introduction

5.12.2 The Principle of Hydrophobic Matching and Its Relation to Trans-Bilayer Structure

5.12.3 Lipid-Protein Interactions in Membranes by Hydrophobic Matching

5.12.4 Experimental Evidence for Hydrophobic Matching being in Control of Protein Function

5.12.5 Membrane Organization by Hydrophobic Matching

Acknowledgments

REFERENCES

5.13 Supported Membranes – Structure and Interactions

5.13.1 Introduction – Membranes as Assemblies of Lipids and Proteins

5.13.2 Biogenesis of Membrane Proteins

5.13.3 Fabrication of Biomembrane Models: Supported Membranes

5.13.4 Supported Membranes: Functionalization with Proteins

5.13.5 Lateral Diffusion in Two-Dimensional Membranes: Continuum Approach

5.13.6 Lateral Diffusion in Two-Dimensional Membranes: Free Volume Approach

5.13.7 Lateral Diffusion of Proteins in Supported Membranes

5.13.8 Contact Between Supported Membranes and Solid Substrates

5.13.9 Polymer Interlayers at Membrane-Substrate Contacts

5.13.10 Modulation of Membrane-Substrate Contacts with Polymers

5.13.11 Native Membranes on Polymer Supports

Acknowledgments

REFERENCES

Membrane Fusion

5.14 The Biophysics of Membrane Fusion

5.14.1 How Can We Study Membrane Fusion?

5.14.2 Do Membranes Spontaneously Fuse?

5.14.3 Is the Interior of The Fusion Pore Made of Protein or Lipid?

5.14.4 Why Is Synaptic Vesicle Fusion So Fast?

5.14.5 Why Is PtdIns-4,5-P2 Needed for Exocytotic Fusion?

5.14.6 Biophysical Approaches to Understanding Viral Fusion Machines

5.14.7 Questions Arising from Structural Studies of SNARE Proteins

5.14.8 Single Molecule Studies of Membrane Fusion

5.14.9 What Can Membrane Fission Tell Us About Membrane Fusion?

5.14.10 Perspective

Acknowledgments

REFERENCES

5.15 Mechanisms of Enveloped Virus Entry by Membrane Fusion

Glossary

5.15.1 Introduction

5.15.2 Structure and Classification of Viral Envelope Glycoproteins

5.15.3 Regulation and Control of the Fusion Reaction

5.15.4 Diverse Viral Proteins Evolved to Mediate Membrane Merger through the Same Principal Mechanism

5.15.5 Detection and Quantification of Viral Fusion

5.15.6 Functional Characterization of Viral Fusion Intermediates: Filling the Blanks

5.15.7 Roles of the Transmembrane Domain and Cytoplasmic Tail

5.15.8 Stoichiometry and Cooperativity of Viral Fusion

5.15.9 Viral Entry Pathways and Host Cell Factors

5.15.10 Conclusion

Acknowledgments

REFERENCES

Membrane Dynamics

5.16 Computer Simulation of Membrane Dynamics

5.16.1 Introduction

5.16.2 Methods

5.16.3 Example Applications

5.16.4 Outlook

Acknowledgments

REFERENCES

5.17 Single Molecule Measurements in Membranes

Glossary

5.17.1 Introduction

5.17.2 Single Molecule Detection in General

5.17.3 Single Molecule Detection in Biomembranes

5.17.4 Model and Biomembrane Systems

5.17.5 Labels for Single Molecule Studies in Membranes

5.17.6 Biomembranes Studied at the Single Molecule Level

5.17.7 Conclusion

Acknowledgments

REFERENCES

Volume 6 Channels

6.1 Channel Proteins – An Introduction

Glossary

REFERENCES

6.2 Structure-Function Correlates of Glutamate-Gated Ion Channels

6.2.1 Structure of Glutamate-Gated Ion Channels

6.2.2 Glutamate Receptor Activation and Modulation

6.2.3 Glutamate Receptor Gating

6.2.4 Glutamate Receptor Permeation

Acknowledgments

REFERENCES

6.3 Gating Dynamics of the Potassium Channel Pore

Glossary

6.3.1 Introduction

6.3.2 Diverse and Ubiquitous K Channels

6.3.3 The Structure of Ion Channels

6.3.4 Gating Kinetics

6.3.5 Energetics of Pore Gating

6.3.6 Single Molecule Dynamics

6.3.7 Structural Dynamics of Gating at the Single Molecule Level

6.3.8 Structural Dynamics of the KcsA Channel

6.3.9 Intramolecular Wave Propagation

6.3.10 Conclusion

REFERENCES

6.4 Biophysics of TRP Channels

6.4.1 Introduction

6.4.2 Structural Features of TRP Channels

6.4.3 Voltage and Ca2+ Dependence of TRP Channels

6.4.4 Activation and Regulation Mechanisms of TRP Channels

6.4.5 TRP and Lipids

6.4.6 Physiological Implications

6.4.7 TRP Integrative Function

6.4.8 Concluding Remarks

REFERENCES

6.5 Mechanosensory Transduction

6.5.1 Introduction

6.5.2 Mechanotransduction in Microbial Cells

6.5.3 Mechanosensory Transduction in Plants

6.5.4 Diversity of MS Channels and Receptors in Animal Cells

6.5.5 Mechanosensitivity in the Nervous System: Physiological and Pathological Significance of MS Channels

6.5.6 Mechanosensation in Cochlea

6.5.7 Mechanoreception in Peripheral Tissue

6.5.8 Conclusions and Outlook

REFERENCES

6.6 Structures and Mechanisms in Chloride Channels

6.6.1 Introduction

6.6.2 Structures and Mechanisms of CLC Channels/Transporters

6.6.3 Structures and Mechanisms of CFTR Chloride Channels

Acknowledgments

REFERENCES

6.7 Biophysics of Ceramide Channels

Glossary

6.7.1 Introduction to Ceramide and Its Role in Apoptosis

6.7.2 Ceramide Channel Formation in Phospholipid Membranes

6.7.3 Ceramide Channel Formation in Mitochondrial Membranes

6.7.4 Molecular Structure of the Ceramide Channel

6.7.5 Results from Molecular Dynamic Simulations

6.7.6 Regulation by Anti-Apoptotic Proteins

6.7.7 Perspective and New Questions

Acknowledgment

REFERENCES

6.8 Voltage Gated Proton Channels

6.8.1 Research History of Voltage-Gated Proton Channel

6.8.2 Basics of Proton Transfer in Biological Environment and Lessons from Several Proton-Transporting Proteins

6.8.3 Properties of Native Hv Channels

6.8.4 Molecular Structure of Voltage-Gated Proton Channels

6.8.5 Mechanisms of Hv Channel Proton Permeation and Gating

6.8.6 Hv Channel Activities in Physiological Contexts

REFERENCES

6.9 STIM1-ORAI1 Store-Operated Calcium Channels

6.9.1 STIM1-ORAI1 Store-Operated Calcium Current

6.9.2 CRAC Current

6.9.3 Recombinant STIM1 and ORAI1

6.9.4 ORAI1 – The Plasma Membrane Calcium Channel

6.9.5 STIM1 – The ER Calcium Sensor

6.9.6 STIM1 and ORAI1 – Channel Gating

6.9.7 Conclusion

Acknowledgment

REFERENCES

6.10 Structure–Function Correlates in Plant Ion Channels

Glossary

6.10.1 Introduction

6.10.2 Topology of K+ Channels

6.10.3 Selectivity Filter of K+ Channels and the HKT K+ Transporter

6.10.4 Channel or Transporter: What Determines Protein Function?

6.10.5 Integration of K+ Channels into the Membrane

6.10.6 Gating of Plant K+ Channels

6.10.7 Assembly of Plant K+ Channels: Diversity through Heteromerization

6.10.8 Outlook

REFERENCES

Volume 7 Cell Biophysics

7.1 Introduction

7.2 Biophysics of Cell-Matrix Adhesion

Glossary

7.2.1 Cell Adhesion in Multicellular Organisms

7.2.2 Cell-ECM Adhesion Through Focal Adhesions

7.2.3 Response of Cells to Mechanical Forces Through Focal Adhesions

7.2.4 Integrin Family and Affinity Regulation

7.2.5 Measuring Force Regulation of Integrin/Ligand Dissociation

7.2.6 Lifetime–Force Relationship of FNIII7–10/α5β1-Fc Interaction

7.2.7 Biological Relevance of Integrin/Ligand Catch Bonds

7.2.8 Closing Remarks

REFERENCES

7.3 Biophysics of Selectin-Mediated Cell Adhesion

Glossary

7.3.1 Introduction

7.3.2 Two-dimensional (2-D) Receptor–Ligand Binding Kinetics

7.3.3 Selectin–Ligand Dissociation: Slip Bond Kinetic Parameters

7.3.4 Selectin–Ligand Bonds Exhibit Catch Bond Behavior

7.3.5 Selectin-Mediated Cell Adhesion in Shear Flow

7.3.6 Conclusion

Acknowledgments

REFERENCES

7.4 Biophysics of Cadherin-Mediated Cell–Cell Adhesion

Glossary

7.4.1 Introduction

7.4.2 Cadherin Junction as a Dynamic Mechanical Integrator

7.4.3 Molecular Interactions at Cadherin Junctions

7.4.4 Generation of Forces at Cadherin Junctions

7.4.5 Conclusions

Acknowledgements

REFERENCES

7.5 Understanding How Dividing Cells Change Shape

Glossary

7.5.1 Introduction

7.5.2 Physical Parameters

7.5.3 The Mechanical Parts List

7.5.4 Mechanical Features of the Cortical Cytoskeletal Network

7.5.5 Dissecting Mechanics Across Variable Timescales and Length Scales

7.5.6 Mechanical Properties of Cytokinesis: Active vs. Passive

7.5.7 Mechanical Interplay Between Myosin II and Actin Crosslinkers

7.5.8 Role of Cell Surface Interactions

7.5.9 Mechanosensing and Mechanical Feedback

7.5.10 Biochemical-Mechanical Feedback Loops

7.5.11 Cleavage Furrow Ingression Through Three Mechanical Transitions

7.5.12 Cylinder-Thinning Model

7.5.13 Contractile Rings: The Schizosaccharomyces pombe Case

7.5.14 Comparisons Between Systems

7.5.15 Conclusion

Acknowledgments

REFERENCES

7.6 Biophysics of Bacterial Cell Growth and Division

7.6.1 Introduction

7.6.2 Bacterial Cell Wall and the Physics of Morphogenesis

7.6.3 Physical Properties of FtsZ and Formation of the Z-ring

7.6.4 Z-ring Force Generation Mechanisms

7.6.5 Conclusions and Perspectives

Acknowledgments

REFERENCES

7.7 Biophysics of Three-Dimensional Cell Motility

Glossary

7.7.1 Introduction

7.7.2 Extracellular Matrix

7.7.3 Components of Cell Motility

7.7.4 Other Mechanisms of Cell Motility in Three Dimensions

7.7.5 Computational Models of Cells Moving in Three Dimensions

7.7.6 Conclusions

REFERENCES

7.8 Biophysics of Molecular Cell Mechanics

Glossary

7.8.1 Introduction and Motivation

7.8.2 Basic Concepts of Molecular and Cellular Mechanics

7.8.3 Particle Tracking Microrheology

7.8.4 Microrheology of Live Cells

Acknowledgments

REFERENCES

7.9 Biophysics of Nuclear Organization and Dynamics

Glossary

7.9.1 Introduction and Motivation

7.9.2 Nuclear Envelope

7.9.3 Lamina Nucleoskeleton

7.9.4 Nucleoplasm and Genome

7.9.5 Conclusions and Future Challenges

Acknowledgment

REFERENCES

7.10 Cell-Extracellular Matrix Mechanobiology in Cancer

Glossary

7.10.1 Introduction

7.10.2 Cellular Mechanotransdution: Background and Overview

7.10.3 Mechanobiology of Tumor Initiation

7.10.4 Mechanobiology of Angiogenesis

7.10.5 Mechanobiology of Tumor Invasion and Metastasis

7.10.6 Case Study: Mechanobiology of Glioblastoma Multiforme

7.10.7 Mechanobiological Signaling Pathways as Therapeutic Targets in Cancer

7.10.8 Conclusions and Future Directions

Acknowledgments

REFERENCES

7.11 Biomechanics of Cell Motility

7.11.1 Introduction

7.11.2 Cellular Movements in Fluid

7.11.3 Gliding and Crawling on a Surface

7.11.4 Conclusions

Acknowledgments

REFERENCES

7.12 Biophysics of Cell Developmental Processes: A Lasercutter's Perspective

Glossary

7.12.1 Laser-Based Targeted Elimination of Subcellular Structures and Entire Cells

7.12.2 Laser Ablation for Active Cell and Tissue Mechanics

7.12.3 Conclusion

REFERENCES

7.13 Bacterial Organization in Space and Time

Glossary

7.13.1 Introduction

7.13.2 Organization Principles

7.13.3 The Bacterial Cytoskeleton

7.13.4 Positioning The Z-Ring

7.13.5 Polar Protein Localization

7.13.6 Chromosome segregation and protein distributions

7.13.7 Temporal Organization

7.13.8 Concluding remarks

REFERENCES

Volume 8 Bioenergetics

8.1 Ion Electrochemical Gradients, Roles and Measurements

8.1.1 Introduction to Electrochemical Gradients

8.1.2 Mechanisms of Generating Electrochemical Gradients

8.1.3 Roles of Electrochemical Gradients

8.1.4 Measuring Electrochemical Gradients

REFERENCES

8.2 Structure-Function Relationships in P-Type ATPases

Glossary

8.2.1 Introduction

8.2.2 SERCA1a Domain Structures

8.2.3 Towards a Structural Description of the SERCA1a Transport Cycle

8.2.4 Regulatory Aspects of the Pumping Mechanism

8.2.5 Structure of Other P-Type Atpases

REFERENCES

8.3 Rotational Catalysis by F1-ATPase

Glossary

8.3.1 Introduction

8.3.2 Rotation of F1

8.3.3 Chemo-Mechanical Coupling

8.3.4 Energetics of Coupling

8.3.5 Structural Basis of Rotation

Acknowledgments

REFERENCES

8.4 The Rotary Bacterial Flagellar Motor

8.4.1 Introduction

8.4.2 Propeller and Universal Joint

8.4.3 Energy Transduction

8.4.4 Mechanism of Torque Generation

8.4.5 Control of Motor Rotation

8.4.6 Outlook

REFERENCES

8.5 Electron Transfer Chains: Structures, Mechanisms and Energy Coupling

Glossary

8.5.1 Introduction

8.5.2 Common Types of Electron Transfer Prosthetic Groups

8.5.3 Respiratory Connectors: Quinones, Cytochromes c, and Blue Copper Proteins

8.5.4 The Mitochondrial Electron Transfer Chain

8.5.5 Bacterial Electron Transfer Systems

Acknowledgement

REFERENCES

8.6 Light Capture in Photosynthesis

8.6.1 Introduction

8.6.2 Chromophore Pigments

8.6.3 Overview of the Mechanisms for Energy Transfer among Pigments

8.6.4 Methods of Measurement of Energy Transfer between Pigments

8.6.5 Structures and Energy Transfer Properties of Antenna Pigment-Protein Complexes

8.6.6 Synthetic Macromolecular Systems That Mimic Photosynthetic Light Harvesting

Acknowledgments

REFERENCES

8.7 The Structure-Function Relationships of Photosynthetic Reaction Centers

8.7.1 Introduction

8.7.2 Overview of Photosynthetic RCs

8.7.3 Structure and Mechanism of the RC of Purple Photosynthetic Bacteria

8.7.4 The RCs of Oxygenic Photosynthesis

8.7.5 Structure and Function of the Photosystem II RC of Oxygenic Photosynthesis

8.7.6 Structure and Function of the Photosystem I RC of Oxygenic Photosynthesis

8.7.7 Type I RCs of Green Sulfur Bacteria and Heliobacteria

8.7.8 Conclusions

REFERENCES

8.8 Molecular Aspects of the Translocation Process by ABC Proteins

Glossary

8.8.1 Introduction

8.8.2 Generic Aspects of Transbilayer Translocation Processes

8.8.3 Substrate Binding by ABC Proteins

8.8.4 Energy Transduction in ABC Transporters

8.8.5 Coupling Energy Production and Substrate Binding in ABC Transporters

8.8.6 Conclusion

REFERENCES

8.9 Structural and Mechanistic Aspects of Mitochondrial Transport Proteins

8.9.1 Introduction

8.9.2 Physiological Role of Mitochondrial Transport Proteins

8.9.3 Structure of the Mitochondrial Carriers

8.9.4 Substrate and Proton Binding Sites of Mitochondrial Transport Proteins

8.9.5 Mitochondrial Transport Proteins Function as Monomers

8.9.6 Proposed Transport Mechanism of Mitochondrial Transport Proteins

8.9.7 Properties of Mitochondrial Nucleotide Transport Proteins

8.9.8 Properties of Mitochondrial Keto Acid Transport Proteins

8.9.9 Properties of Mitochondrial Amino Acid Transport Proteins

8.9.10 Properties of Mitochondrial Inorganic Ion Transport Proteins

8.9.11 Properties of Mitochondrial Uncoupling Proteins and Orthologs

8.9.12 Properties of Mitochondrial Cofactor Transport Proteins

8.9.13 Mitochondrial Transport Proteins with Unknown Specificity

8.9.14 Perspectives

REFERENCES

8.10 Light Capture and Energy Transduction in Bacterial Rhodopsins and Related Proteins

8.10.1 Introduction

8.10.2 Structure and Structural Changes

8.10.3 The Chromophore and Absorption of Light

8.10.4 Pre-Proton Transfer Intermediates

8.10.5 Deprotonation of the Retinal Schiff Base and Proton Release

8.10.6 The Protonation Switch

8.10.7 Reprotonation of the Schiff Base, Retinal Reisomerization, and Proton Uptake

8.10.8 Large-Scale Conformational Changes

8.10.9 Mechanistic Schemes Based on Structural Results

8.10.10 Ion Specificity

8.10.11 Overall Energetics of the Pump

REFERENCES

8.11 Transporters and Co-transporters in Theory and Practice

Glossary

8.11.1 Introduction to the General Theory of Transporters

8.11.2 Enzyme versus Transport Kinetics

8.11.3 Cotransport Models

8.11.4 Serotonin Transporters

8.11.5 DATs

8.11.6 Chloride Channels and Transporters

8.11.7 Summary

Acknowledgment

REFERENCES

8.12 Membrane Proteins for Secondary Active Transport and their Molecular Mechanisms

8.12.1 Introduction

8.12.2 Bioenergetics of Membrane Transport

8.12.3 Classification of Transporters by their Amino Acid Sequences

8.12.4 Secondary Active Membrane Transport Proteins

8.12.5 The Major Facilitator Superfamily (MFS) is Related by Similarities of Amino Acid Sequences

8.12.6 The LeuT Superfamily Related by Similarity of Three-Dimensional Structures

8.12.7 The Mhp1 Protein and its Molecular Mechanism

8.12.8 The Na+/H+ Antiport Transport Protein

8.12.9 Reprise of the Alternating Access Concept of Transport

8.12.10 Concluding Remarks

Acknowledgments

REFERENCES

Volume 9 Simulation and Modelling

Volume Introduction

9.1 Theoretical Biophysics: A Cornerstone of Understanding in Modern Biology and Biomedicine

In Silico Approaches to Structures and Function of Cell Components and Their Aggregates

9.2 Coarse-Grained Methods: Theory

9.2.1 Introduction

9.2.2 Spatial Coarse Graining

9.2.3 Temporal Coarse Graining

REFERENCES

9.3 In Silico Coarse-Grained Approaches to Structural Dynamics and Function of Proteins and their Assemblies

9.3.1 Introduction: Protein Dynamics, Allostery and Function

9.3.2 Elastic Network Models: Theory and Methods

9.3.3 Applications to Allosteric Systems and Supramolecular Machines

9.3.4 Beyond Structural Dynamics: Extensions and Future Directions

Acknowledgment

REFERENCES

9.4 Coarse Grained Methods: Applications to Membranes

9.4.1 What Can We Learn from Coarse Grained Models of Lipid Bilayers?

9.4.2 How to Coarse Grain a Lipid Bilayer?

9.4.3 Learning from Examples

9.4.4 Prospects for Coarse Grained Lipid Models

Acknowledgments

REFERENCES

9.5 Dynamics of Very Large Systems: The Ribosome

Glossary

9.5.1 The Ribosome Synthesizes Proteins in all Organisms

9.5.2 The Ribosome is a Ribonucleoprotein Complex

9.5.3 Transfer RNA Molecules are Used by the Ribosome to Translate the Genetic Code

9.5.4 Protein Synthesis Occurs in Three Stages: Initiation, Elongation, and Termination

9.5.5 The Ribosome is Dynamic in Nature

9.5.6 Computational Studies of the Ribosome

9.5.7 Implications for the Free Energy Landscape of the Ribosome and Translation Energetics

REFERENCES

9.6 New Technologies for Molecular Dynamics Simulations

Glossary

9.6.1 Introduction

9.6.2 Scope

9.6.3 Anatomy of an MD Simulation

9.6.4 Speed

9.6.5 Force Field Accuracy

9.6.6 Analysis of Very Long Trajectories

9.6.7 Applications of Very Long MD Simulations

9.6.8 Conclusion

Acknowledgment

REFERENCES

Simulations of Molecular Mechanisms

9.7 Molecular Modeling and Simulations of Transporter Proteins – The Transmembrane Allosteric Machinery

Glossary

9.7.1 Background and Introduction

9.7.2 Structure-Function Information Deduced from the Sequence and Structural Alignments

9.7.3 Elements in Building Models and Simulation Systems

9.7.4 Molecular Simulations in the Mechanistic Studies

9.7.5 The Leading Role of Modeling and Simulations in Advancing Mechanistic Understanding of NSS Transport

9.7.6 Concluding Remarks

REFERENCES

9.8 Gene Protein Coupled Receptors

Glossary

9.8.1 Structure and Dynamics of GPCR Monomers

9.8.2 Structure and Dynamics of GPCR Dimers/Oligomers

Acknowledgments

REFERENCES

9.9 Quantum Mechanical Methods for Enzyme Modeling: Accurate Computation of Kinetic Isotope Effects

9.9.1 Introduction

9.9.2 Method

9.9.3 Illustrative Examples

9.9.4 Conclusion

Acknowledgments

REFERENCES

9.10 MNDO-PSDCI and the Analysis of the Photophysical Properties of Visual Chromophores and Retinal Proteins

Glossary

9.10.1 Introduction

9.10.2 Methods of Studying Electronically Excited States

9.10.3 Application of MNDO-PSDCI to Isolated Biological Molecules

9.10.4 Applications of MNDO-PSDCI to Protein-Bound Chromophores

9.10.5 Conclusions

REFERENCES

In Silico Approaches to Structure and Function of Cell Components and Their Assemblies

9.11 Molecular Electrostatics and Solvent Effects

Glossary

9.11.1 Introduction

9.11.2 Intracellular Water

9.11.3 Atomistic Representations of Water and Solutes

9.11.4 Continuum Description of Water Electrostatic Effects

9.11.5 Modeling of Hydrophobic and Hydrophilic Forces

9.11.6 pH-Dependent Electrostatic Properties in Proteins

9.11.7 Perspectives for the Future

Acknowledgments

REFERENCES

9.12 Interactions of the Cell Membrane with Integral Proteins

Glossary

9.12.1 Evidence for Role of Lipid Environment for Membrane Protein Function

9.12.2 Key Elements of Lipid-Protein Interactions

9.12.3 Framework for Quantitative Description of Lipid-Protein Interactions

9.12.4 Illustrative Applications

9.12.5 Concluding Remarks

Acknowledgments

REFERENCES

Modeling of Interaction Networks in the Cell

9.13 Theory and Mathematical Methods

9.13.1 Introduction

9.13.2 Chemical Reactions and Mass-Action Kinetics

9.13.3 Approximation by Separation of Timescales

9.13.4 Laplacian Dynamics and the Matrix-Tree Theorem

9.13.5 Chemical Reaction Network Theory

9.13.6 Algebraic Approaches

9.13.7 Conclusion

REFERENCES

Mathematical Modeling of Complex Biological Systems

9.14 From Genes and Molecules to Organs and Organisms: Heart

9.14.1 Introduction

9.14.2 The Cardiac Ventricular Action Potential

9.14.3 Propagation of the Cardiac Action Potential

9.14.4 The Electric Field of the Heart

Acknowledgments

REFERENCES

9.15 Biophysical Representation of Kidney Function

9.15.1 Kidney Structure and Function

9.15.2 Glomerular Function

9.15.3 Epithelial Function

9.15.4 Conclusion

Acknowledgment

REFERENCES

9.16 Systems Immunology: A Primer for Biophysicists

9.16.1 Introduction

9.16.2 Overview of Systems Immunology

9.16.3 Modeling T-Cell Activation Quantitatively

9.16.4 T-Cell Proliferation and Differentiation

9.16.5 Conclusion

REFERENCES

Index