Biomembranomics Structure Techniques and Applications 1st Edition by Hongda Wang ISBN ‎ 9814968617 978-9814968614

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ISBN 10: ‎ 9814968617
ISBN 13:  978-9814968614
Author: Hongda Wang

The membrane is an intricately structured entity that performs numerous vital biological functions, including materials transport, signal transduction, energy transfer, and enzymatic reactions. Abnormal expression and distribution of certain membrane proteins are even associated with genetic disorders, neurodegenerative diseases, and malignant tumors. Despite the widely acknowledged significance of membranes, comprehensive and systematic research on membranes akin to genomics, proteomics, and metabolomics is still lacking. Furthermore, the broad concept of biomembranes is not confined to the plasma membrane alone; it also includes organelle membranes and membranes of endocytosis or exocytosis vesicles, which are also derived from the biomembrane system.

This book introduces the concept of “omics” to membranes and proposes the term ‘biomembranomics.’ It compiles the latest advancements in structural analysis techniques for biomembranes, including single-molecule manipulation techniques, single-molecule fluorescence techniques, super-resolution fluorescence imaging, cryo-electron microscopy, mass spectrometry, molecular dynamics simulation, and hyphenated instrumental techniques. The book presents both classic and cutting-edge protocols in text and illustrative forms, serving as a valuable and applicable reference material. It provides a profound understanding of biomembrane organization at single-molecule level, paving new avenues for unveiling the relationship between membrane structure and function. Therefore, this book is essential reading for researchers across all related fields.

Biomembranomics Structure Techniques and Applications 1st Table of contents:

Chapter 1 Biomembranomics: New Concept

1.1 Introduction

1.2 Composition of Membranes

1.2.1 Lipids

1.2.2 Membrane Proteins

1.3 Membrane Compartmentalization and Dynamics

1.3.1 Lipid Rafts-Dynamic Domains

1.3.2 Approaches to Resolve Membrane Dynamics

1.3.3 Organizers of Membrane Compartmentalization

1.4 Mechanobiology of the Cell Membrane

1.4.1 Membrane Tension

1.4.2 Methods to Access Membrane Mechanics

1.5 Membrane Functions and Diseases

1.5.1 Membrane Proteins as Biomarkers and Drug Targets

1.5.2 Membrane-Lipid Therapy

1.5.3 Membrane Rafts in Diseases

1.6 Why Should Biomembranomics Be Proposed?

1.6.1 Significance of Biomembranomics

1.6.2 Progresses and Limitations of Membrane Research

1.6.3 Combination of Methods and Interdisciplinary Collaborations

1.7 Conclusion

References

Chapter 2 Mass Spectrometry for Studying Ensemble Biomembranomics

2.1 Introduction

2.2 Membrane Proteomics

2.2.1 Development of Shotgun Proteomics

2.2.2 Practical Examples of Membrane Proteomics

2.3 Membrane Glycoproteomics

2.4 Membrane Lipidomics

2.5 Interactions between Membrane Molecules

2.6 Protocols for Mass-Spectrometry-Based Biomembranomics Study

2.6.1 Protocols for Membrane Proteomics Study

2.6.2 Protocols for Membrane Glycoproteomics Study

2.6.3 Protocols for Membrane Lipidomics Study

2.6.4 Experimental Details of Membrane Interactomics by nMS

References

Chapter 3 Mapping Membrane by High-Resolution Atomic Force Microscopy

3.1 Introduction

3.2 Principles of AFM and Its Related Technologies

3.2.1 Basics of AFM

3.2.2 AFM Imaging Mode

3.2.3 Principle of Topography and Recognition (TREC) Imaging

3.3 Imaging the Cell Membrane

3.3.1 Imaging the Lipid/Lipid Bilayer

3.3.2 Imaging Membrane Proteins

3.4 Study on Erythrocyte Membrane by AFM

3.4.1 Ectoplasmic Side of Erythrocyte Membranes

3.4.2 Cytoplasmic Side of Erythrocyte Membranes

3.4.3 A New Model of the Erythrocyte Membrane Structure

3.5 Nucleated Mammalian Cell Membrane Research Using AFM

3.6 AFM Study of Lipid Rafts and Related Membrane Proteins

3.6.1 Discovery and Verification of Lipid Rafts

3.6.2 Microdomains of Membrane Proteins

3.6.3 Organelle Membranes

3.7 Protocols for AFM Experiment

3.7.1 Making APTES-Mica

3.7.2 Modification of AFM Tip

3.7.3 AFM Recognition Imaging with Modified Tips

3.7.4 Preparation of Red Blood Cell Membranes

3.7.5 Preparation of the Nucleated Mammalian Cell Membranes

3.8 Conclusion and Prospects

References

Chapter 4 Super-Resolution Imaging for Mapping Membrane Proteins and Carbohydrates

4.1 Principles of Super-Resolution Fluorescence Imaging Technology

4.1.1 Structured Illumination Microscopy

4.1.2 Stimulated Emission Depletion Microscopy

4.1.3 Single-Molecule Localization Microscopy

4.2 Key Factors in the Imaging Quality of SMLM

4.2.1 Types of Fluorescent Probes

4.2.2 Precise Localization

4.2.3 Structural Resolution

4.2.4 Steric Effect of Labeling

4.3 Super-Resolution Imaging of Membrane Molecules Using Different Probes

4.3.1 Revealing the Organization of Membrane Proteins by Antibody-Probe Labeling

4.3.2 Small Bio-probes for Imaging Membrane Structure

4.3.3 Small Chemical Probes for Revealing the Relationship between Membrane Protein Structure and Function

4.4 Protocols for STORM Experiment

4.4.1 Preparation of Fluorescent Probes

4.4.2 Sample Preparation

4.4.3 STORM Imaging

4.4.4 Image Reconstruction

4.4.5 Measurement of the Imaging Resolution

4.4.6 Cluster Analysis

4.4.7 Dual-Color Colocalization Analysis

4.5 Conclusion

References

Chapter 5 Fluorescence Microscopy for Studying Plasma Membrane and Intracellular Membranes

5.1 Introduction

5.2 Overview of Fluorescence Imaging System

5.2.1 Fluorescence Imaging Methods

5.2.2 Fluorescent Labeling Techniques

5.3 Applications of Fluorescence Imaging in Studying Dynamic Organelle Interactions

5.3.1 Ongoing Knowledge of Organelle–Organelle Interplay Network

5.3.2 Orderly Membrane Trafficking among Organelles

5.3.3 Membrane Protein Dense Distribution Determines the Orderly Organelle Interactions

5.4 Protocols for Performing Fluorescence Imaging

5.4.1 Transient Transfection of Mammalian Cells with Fluorescent Protein Expression Vectors

5.4.2 Immuno-fluorescence

5.4.3 Live-Cell Labeling Probes

5.4.4 Imaging System

References

Chapter 6 Single-Molecule Fluorescence for Studying the Membrane Protein Dynamics and Interactions

6.1 Introduction

6.2 Fundamental Principles

6.2.1 smFRET

6.2.2 Fcs

6.2.3 Tirfm

6.2.4 Smlm

6.2.5 Deep-Learning-Assisted SMF Techniques

6.3 Fluorophore Selection and Labeling

6.3.1 Fluorescent Proteins

6.3.2 Organic Dyes

6.3.3 Nanoparticles

6.4 In Vitro Studies of Membrane Proteins

6.5 In Situ Studies of Membrane Proteins

6.5.1 Diffusion Dynamics

6.5.2 Conformational Dynamics

6.5.3 Signaling Transduction

6.5.4 Membrane Organization

6.6 Protocols for SMF Analysis of Membrane Proteins

6.6.1 Cell Culture

6.6.2 Fluorescence Labeling

6.6.3 Fluorescence Microscopy Setup

6.6.4 Data Processing and Analysis

References

Chapter 7 Cryo-Transmission Electron Microscopy for Studying Cell Membranes

7.1 Introduction

7.2 Cryo-Electron Microscopy

7.2.1 Cryo-EM Imaging Modes

7.3 Applications of Cryo-EM in Cell Membranes and Membrane Proteins

7.3.1 Applications of SPA in Cell Membranes and Membrane Proteins

7.3.2 Applications of Cryo-ET in Cell Membranes and Membrane Proteins

7.4 Protocols for Cryo-EM Experiment

7.4.1 Protocols for SPA Experiment

7.4.2 Protocols for Cryo-ET Experiment

References

Chapter 8 Cryo-Scanning Electron Microscope for Studying Plasma Membranes

8.1 Introduction

8.2 Scanning Electron Microscopy

8.2.1 Imaging Principle of SEM

8.2.2 Surface Topography Contrast of SEM

8.2.3 Sample Requirements for SEM

8.2.4 Basic Parameters of SEM

8.3 Cryo-Scanning Electron Microscopy

8.3.1 Basic Construction of Cryo-SEM

8.3.2 Sample Preparation for Cryo-SEM

8.3.3 Applications of Cryo-SEM in Cell Biology

8.4 Observation of Human Red Blood Cell Membrane through Cryo-SEM

8.4.1 Cryo-SEM Imaging of Erythrocyte Membrane

8.4.2 Cryo-SEM Coupled with AFM for Imaging

8.4.3 Tagging of Specific Proteins on Erythrocyte Membrane through Gold Nanoparticle

8.5 Protocols for Cryo-SEM Imaging of hRBC Membrane

8.5.1 Preparation of hRBC Membrane on Silicon Wafer

8.5.2 Au-PEG1000-Antibody Conjugated with Erythrocyte Membrane Protein

8.5.3 Frozen Sample Preparation

8.5.4 Selection of Electron Microscope Parameters

8.6 Conclusion

References

Chapter 9 Infrared Spectroscopy Studying Plasma Membrane

9.1 Introduction

9.2 Principles

9.2.1 Molecular Vibrations

9.2.2 Infrared Absorption

9.2.3 What Infrared Absorption Tells

9.2.4 Infrared Spectrometers

9.2.5 Surface-Enhanced Infrared Absorption Spectroscopy

9.3 Applications in Plasma Membrane Studies

9.3.1 Physicochemical Characterization of Lipid Membranes

9.3.2 Structure and Functions of Interfacial Water of Membranes

9.3.3 Structure and Function Study of Membrane- Related Proteins

9.3.4 Interfacial Interaction at Membrane/Water Interface

9.3.5 Living Cell Membrane

9.4 Protocols

9.4.1 Constructing ATR-SEIRA Spectroelectrochemistry

9.4.2 Constructing Living Cell ATR-SEIRA Spectroscopy

Acknowledgments

References

Chapter 10 Application of Single-Molecule Force Spectroscopy in Membrane Receptors Dynamics and Signal Transduction

10.1 Introduction

10.2 Single-Molecule Force Spectroscopy

10.2.1 Biomembrane Force Probe

10.2.2 Magnetic Tweezers

10.2.3 Atomic Force Microscopy and Optical Tweezers

10.3 Mechanical Force

10.3.1 Mechanical Force in Cell Adhesion

10.3.2 Mechanical Force in Immune Defense

10.3.3 Mechanical Force in Viral Invasion

10.3.4 Force Fluctuations

10.4 Spatial Confinement of Cell Plasma Membrane

10.5 Biophysical Regulation in Transmembrane Signaling

10.6 Protocols

10.6.1 Single-Molecule Biomembrane Force Probe

10.7 Conclusion

References

Chapter 11 Studying Membrane Dynamics Using Force Spectroscopy Based on Atomic Force Microscopy

11.1 Introduction

11.1.1 Single-Molecule Force Spectroscopy

11.1.2 Force Tracing

11.2 Applications of Force Spectroscopy

1.2.1 Membrane Dynamics

11.2.2 Single-Molecule Interaction and Transporting on Membrane

11.2.3 Endocytosis of Nanoparticles

11.2.4 Virus-Like Particles Invading Cells

11.2.5 Nanodrug Delivery

11.3 Protocols

11.3.1 Spring Constant and Sensitivity Calibration of AFM Tip Cantilever

11.3.2 Functionalization of AFM Tip

11.3.3 Preparing Samples on Supporting Surfaces

11.3.4 Recording Force Curves: Force–Distance Curve and Force–Time Curve

11.3.5 Data Analysis: FD Curve and FT Curve (Force, Time, Displacement, and Speed)

11.4 Conclusion

References

Chapter 12 Computer Simulations to Explore Membrane Organization and Transport

12.1 Introduction

12.2 Technical Principle

12.2.2 Force Fields

2.12.2 Molecular Dynamic Simulation

12.3 Applications of Computer Simulations

12.3.1 Unbiased Molecular Dynamic Simulation Case Study

12.3.2 Enhanced Sampling Molecular Dynamic Simulation Case Study

2.3.3 Large-Scale Molecular Dynamics Simulation Case Study

12.4 Protocols

12.4.1 Swiss-Model

12.4.2 Charmm-Gui

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