Biophysical Approaches for the Study of Membrane Structure Part A

1st Edition, Volume 700 - July 4, 2024
Editors: Tobias Baumgart, Anna Maria Pyle, David Christianson, Markus Deserno
Language: English
Hardback ISBN:
9 7 8 - 0 - 4 4 3 - 2 9 3 0 4 - 7
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 9 3 0 5 - 4

Biophysical Approaches for the Study of Membrane Structure, Part A, Volume 700 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown… Read more

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Biophysical Approaches for the Study of Membrane Structure, Part A, Volume 700 explores lipid membrane asymmetry and lateral heterogeneity. A burst of recent research has shown that bilayers whose leaflets differ in their physical properties—such as composition, phase state, or lateral stress—exhibit many fascinating new characteristics, but also pose a host of new challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Evaluation of functional transbilayer coupling in live cells by controlled lipid exchange and imaging FCS, Effects of lateral and hydrostatic pressure on membrane structure and properties, and much more.

Other sections cover Using the yeast vacuole as a system to test the lipid drivers of membrane heterogeneity in living cells, Direct quantification of cellular membrane lipids using ratiometric fluorescence sensors, The spectral phasor approach to resolving membrane order with environmentally sensitive dyes, The use of hemifusion to create asymmetric giant unilamellar vesicles: Insights on induced order domains, Advanced microscopy methods to study membrane pores, Use of cryo-EM to study membrane phase separation, and much more.

Cover image
Title page
Table of Contents
Series Page
Copyright
Contributors
Preface
Chapter One: Evaluation of functional transbilayer coupling in live cells by controlled lipid exchange and imaging fluorescence correlation spectroscopy
Abstract
1 Arena
2 Before you begin
3 Key resources table
4 Equipment
5 Step-by-step method details
6 Expected outcomes
7 Advantages
8 Limitations and possible improvements
9 Optimization and troubleshooting
10 Safety considerations and standards
11 Connections
Acknowledgements
References
Chapter Two: Fluorescence imaging of lamellipodin-mediated biomolecular condensates on solid supported lipid bilayer membranes
Abstract
1 Physical situation
2 Challenges
3 Typical solution(s)
4 The big idea
5 Materials and equipment
6 Method details
7 Expected outcomes
8 Quantification and statistical analysis
9 Advantages
10 Limitations
11 Optimization and troubleshooting
12 Safety considerations and standards
13 Alternative methods/procedures
14 Connections
References
Chapter Three: The effect of hydrostatic pressure on lipid membrane lateral structure
Abstract
1 Arena
2 High pressure small angle x-ray scattering and microscopy
3 Before you begin
4 Example experiment: Triggering lateral phase separation in ternary model membranes
5 Materials and equipment
6 Step-by-step method details
7 Analysis
8 Outcomes and analysis
9 Advantages
10 Safety considerations and standards
11 Connections
References
Chapter Four: Using the yeast vacuole as a system to test the lipidic drivers of membrane heterogeneity in living cells
Abstract
1 Arena
2 Method 1: Imaging of yeast vacuole domains
3 Method 2: Biochemical isolation of yeast vacuoles
4 Method 3: µ-lipophagy or lipid droplet flux assay for vacuole domain function
5 Connections
References
Chapter Five: The spectral phasor approach to resolving membrane order with environmentally sensitive dyes
Abstract
1 Introduction
2 Preparing giant unilamellar vesicles for hyperspectral imaging measurements
3 Measuring hyperspectral images of giant unilamellar vesicles
4 Using phasor analysis for hyperspectral imaging
5 Summary and conclusions
6 Connections
References
Chapter Six: The use of hemifusion to create asymmetric giant unilamellar vesicles: Insights on induced order domains
Abstract
1 Arena
2 Challenges
3 Typical solutions
4 Common issues
5 Method to prepare asymmetric giant unilamellar vesicles using hemifusion
6 Expected outcomes
7 Quantification and statistical analysis
8 Advantages
9 Limitations
10 Optimization and troubleshooting
11 Safety considerations
12 Alternative methods/procedures
Acknowledgement
References
Chapter Seven: Super-resolution microscopy methods to study membrane pores in situ
1 Physical situation
2 Before you begin
3 Materials and equipment
4 Dual-color STED microscopy of BAK and BAX
5 STORM microscopy of BAK-induced pores in apoptotic mitochondria in situ
6 Expected outcomes
7 Quantification and statistical analysis
8 Advantages
9 Limitations
10 Optimization and troubleshooting
11 Optimization and troubleshooting of STED microscopy
12 Connections
References
Chapter Eight: Phase separation in model lipid membranes investigated with cryogenic electron microscopy
Abstract
1 ARENA
2 Cryo-EM imaging of liposomes
3 Before you begin
4 Key resources table
5 Materials and equipment
6 Step-by-step method details
7 Expected outcomes
8 Quantification and statistical analysis
9 Advantages
10 Limitations
Acknowledgements
References
Chapter Nine: Using lipid binding proteins and advanced microscopy to study lipid domains
Abstract
Abbreviations
1 Introduction
2 Visualizing distribution of SM-rich and/or Chol-rich lipid domains in the presence of HIV-1 Gag by FLIM-FRET
3 Labeling intracellular SM-rich domains
4 Summary
Acknowledgements
References
Chapter Ten: Structural characterization of lateral phase separation in polymer–lipid hybrid membranes
Highlights
Abstract
1 Introduction to intramembrane heterogeneity in polymer–lipid hybrid membranes
2 Application of atomic force microscopy in analyzing hybrid polymer–lipid membranes
3 Characterization of hybrid polymer–lipid membranes using X-ray scattering techniques
4 Investigation of hybrid polymer–lipid membranes through cryo-electron microscopy
References
Chapter Eleven: Applications of phase-separating multi-bilayers in protein-membrane domain interactions
Abstract
1 Arena
2 Spin‐Coated Multi-bilayers
3 Before You Begin
4 Materials and Equipment
5 Alternatives
6 Step‐By‐Step Method Details
7 Notes
8 Expected Outcomes and Analysis
9 Optimization and Troubleshooting
References
Chapter Twelve: Studying lipid flip-flop in asymmetric liposomes using 1H NMR and TR-SANS
Abstract
1 Introduction
2 Asymmetric vesicle preparation by cyclodextrin-mediated lipid exchange
3 Lipid flip-flop analysis using solution 1H NMR
4 Lipid flip-flop analysis of asymmetric liposomes using TR-SANS
5 Conclusions and connections
Acknowledgements
References
Chapter Thirteen: Thickness determination of hydroperoxidized lipid bilayers from medium-resolution cryo-TEM images
Abstract
1 Arena
2 Membrane profile improvement by selective radial alignement
3 Before you begin
4 Materials and equipment
5 Step-by-step method details
6 Expected outcomes
7 Conclusions and connections
References
Chapter Fourteen: Structure of symmetric and asymmetric lipid membranes from joint SAXS/SANS
Abstract
1 Arena
2 Small angle scattering
3 Before you begin
4 Materials and sample preparation procedures
5 Expected outcomes
6 Quantification and data analysis
7 Advantages and limitations
8 Safety considerations and standards
9 Alternative methods/procedures
10 Connections
References
Chapter Fifteen: Quantification of membrane geometry and protein sorting on cell membrane protrusions using fluorescence microscopy
Abstract
1 Arena
2 “The method”
3 Before you begin
4 Key resources table
5 Materials and equipment
6 Step-by-step method details
7 Expected outcomes
8 Quantification and statistical analysis
9 Safety considerations and standards
10 Potential connections
Acknowledgments
References
Chapter Sixteen: A live cell imaging-based assay for tracking particle uptake by clathrin-mediated endocytosis
Abstract
1 Arena
2 Method for high throughput tracking of individual particles during cellular uptake via clathrin-mediated endocytosis
3 Before you begin
4 Key resources table
5 Equipment
6 Step-by-step method details
7 Expected outcomes
8 Quantification and statistical analysis
9 Advantages
10 Limitations
11 Optimization and troubleshooting
12 Safety considerations and standards
13 Connections
References
Chapter Seventeen: Pore-spanning membranes as a tool to investigate lateral lipid membrane heterogeneity
Abstract
1 Introduction
2 General aspects of phase-separated pore-spanning membranes
3 Preparation of phase-separated pore-spanning membranes
4 Quantification and statistical analysis
5 Summary and conclusions
References
Chapter Eighteen: MαCD-based plasma membrane outer leaflet lipid exchange in mammalian cells to study insulin receptor activity
Abstract
1 Arena
2 MαCD mediated lipid exchange method
3 Before you begin
4 Key resources table
5 Materials and equipment
6 Step by step method details
7 Expected outcomes
8 Quantification and statistical analysis
9 Advantages
10 Limitations
11 Optimization and troubleshooting
12 Alternative methods/procedures
13 Connections
References

Tobias Baumgart

Tobias Baumgart is a professor in the Chemistry Department of the University of Pennsylvania. An experimental biophysical chemist at heart, he focuses on understanding how both lipids and proteins, as well as the continuum mechanics of bilayer assemblies determine membrane function. Baumgart obtained his Ph.D. from the Max Planck Institute for Polymer Research (MPI-P) and the Johannes Gutenberg University in Mainz, Germany, in 2001. He was a postdoctoral research associate with Watt Webb, Gerald Feigenson, and Barbara Baird at Cornell University in Ithaca, before becoming an Assistant Professor in 2005, and a full professor in 2017. He was on the Biophysical Journal’s Editorial Board between 2013 and 2019. He is a recipient of the Alfred P. Sloan and NSF CAREER awards, as well as the Dennis M. DeTurck and Charles Ludwig awards for distinguished teaching. Edit

Affiliations and expertise

Professor, Chemistry Department, University of Pennsylvania, USA

David Christianson

After completing studies for the A.B., A.M., and Ph.D. degrees in chemistry at Harvard University, David W. Christianson joined the faculty of the University of Pennsylvania, where he is currently the Roy and Diana Vagelos Professor in Chemistry and Chemical Biology. At Penn, Christianson’s research focuses on the structural and chemical biology of the zinc-dependent histone deacetylases as well as enzymes of terpene biosynthesis. His research accomplishments have been recognized by several awards, including the Pfizer Award in Enzyme Chemistry and the Repligen Award in Chemistry of Biological Processes from the American Chemical Society, a Guggenheim Fellowship, and the Elizabeth S. and Richard M. Cashin Fellowship from the Radcliffe Institute for Advanced Study at Harvard University. Christianson is also a dedicated classroom teacher, and his accomplishments in this regard have been recognized by the Lindback Award for Distinguished Teaching at Penn and a Rhodes Trust Inspirational Educator Award from Oxford University. Christianson has also held visiting professorships in the Department of Biochemistry at Cambridge University and the Department of Chemistry and Chemical Biology at Harvard University. Christianson has served with Prof. Anna Pyle as Co-Editor-in-Chief of Methods in Enzymology since 2015.

Affiliations and expertise

University of Pennsylvania, USA

Markus Deserno

Markus Deserno is a professor in the Department of Physics at Carnegie Mellon University, where he works in the field of theoretical and computational biophysics. He focuses on lipid membranes and proteins, using a wide spectrum of techniques that range from coarse-grained molecular dynamics simulations up to differential geometry, continuum elasticity, and statistical field theory. Deserno received his Ph.D. from the Max Planck Institute for Polymer Research (MPI-P) in Mainz, Germany, in 2000. After graduation, he held a postdoctoral research position in the Department of Chemistry and Biochemistry at UCLA, followed by a group leader position back at the MPI-P. In 2007 he joined the Department of Physics at Carnegie Mellon University, where he got tenured in 2011 and became Full Professor in 2016. Between 2014 and 2020 Deserno served on the Editorial Board of the Biophysical Journal. He is an elected Fellow of the American Physical Society and received the Thomas E. Thompson Award of the Biophysical Society. Edit

Affiliations and expertise

Professor, Department of Physics, Carnegie Mellon University, USA

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Biophysical Approaches for the Study of Membrane Structure Part A

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Tobias Baumgart

David Christianson

Markus Deserno