Biophysical Approaches for the Study of Membrane Structure Part B

1st Edition, Volume 701 - July 17, 2024
Imprint: Academic Press
Editors: Markus Deserno, Tobias Baumgart
Language: English
Hardback ISBN:
9 7 8 - 0 - 4 4 3 - 2 9 5 6 6 - 9
eBook ISBN:
9 7 8 - 0 - 4 4 3 - 2 9 5 6 7 - 6

Biophysical Approaches for the Study of Membrane Structure, Part B, Volume 701 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 B, Volume 701 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 challenges related to their creation, characterization, simulation, and theoretical description. Chapters in this new release include Characterization of domain formation in complex membranes: Analyzing the bending modulus from simulations of complex membranes, The density-threshold affinity: Calculating lipid binding affinities from unbiased Coarse-Grain Molecular Dynamics simulations, and much more.

Additional sections cover Uncertainty quantification for trans-membrane stresses and moments from simulation, Using molecular dynamics simulations to generate small-angle scattering curves and cryo-EM images of proteoliposomes, Binary Bilayer Simulations for Partitioning Within Membranes, Modeling Asymmetric Cell Membranes at All-atom Resolution, Multiscale remodeling of biomembranes and vesicles, Building complex membranes with Martini 3, Predicting lipid sorting in curved bilayer membranes, Simulating asymmetric membranes using P21 periodic boundary conditions, and many other interesting topics.

Cover image
Title page
Table of Contents
Series Page
Copyright
Contributors
Preface
Chapter One: Characterization of domain formation in complex membranes
Abstract
1 ARENA
2 DomHMM
3 Implementation
4 Alternatives
5 Outlook
6 Connections
Acknowledgement
References
Chapter Two: The density-threshold affinity: Calculating lipid binding affinities from unbiased coarse-grained molecular dynamics simulations
Chapter points
Abstract
1 Arena
2 Density-threshold affinity
3 Implementation
4 Performance
5 Alternatives
6 Outlook
7 Connections
References
Chapter Three: Quantifying uncertainty in trans-membrane stresses and moments in simulation
Abstract
Highlights
1 Arena
2 Accounting for spatiotemporal correlations
3 Implementation
4 Applications and usage
5 Connections
References
Chapter Four: Binary bilayer simulations for partitioning within membranes
Abstract
1 Arena
2 Binary bilayer system
3 Implementation
4 Preliminary symmetric bilayer simulations
5 Equilibration of individual bilayers
6 Assembly of the binary bilayer system
7 Performance
8 Alternatives
9 Outlook
10 Connections
Acknowledgements
References
Chapter Five: Modeling asymmetric cell membranes at all-atom resolution
Abstract
1 Introduction
2 Methods
3 Comparison between the methods
4 Conclusion
5 Connections
Acknowledgments
References
Chapter Six: Multiscale remodeling of biomembranes and vesicles
Abstract
1 Introduction
2 Shape remodeling of giant vesicles
3 Shape transformations of nanovesicles
4 Instabilities of lipid bilayers
5 Remodeling of vesicle topology
6 Summary and outlook
Acknowledgements
References
Chapter Seven: Building complex membranes with Martini 3
Abstract
1 Introduction
2 Symmetric mixtures
3 Asymmetric complex membranes
4 Complex membranes with proteins
5 Curved membranes
6 Final remarks
Acknowledgments
References
Chapter Eight: Predicting lipid sorting in curved membranes
Abstract
1 Introduction
2 The method
3 Outlook
References
Chapter Nine: Simulating asymmetric membranes using P21 periodic boundary conditions
Abstract
1 Introduction
2 P21 periodic boundary conditions
3 Implementation
4 Simple examples (lipid-only)
5 Area equilibration with peptides/proteins
6 Applications with in-plane restraints
7 Limitations
8 Alternatives
9 Summary and conclusions
10 Connections
Acknowledgments
References
Chapter Ten: Free energy calculations for membrane morphological transformations and insights to physical biology and oncology
Abstract
1 Mechanotransduction through membrane signalosomes
2 Computational methods
3 Applications in cellular biophysics
4 Insights to cancer biophysics and oncology
Acknowledgments
References
Chapter Eleven: Modeling the mechanochemical feedback for membrane-protein interactions using a continuum mesh model
Highlights
Abstract
1 Arena
2 Membrane dynamics in 3 dimensions using discrete differential geometry (Mem3DG)
3 Implementation
4 Performance
5 Alternatives
6 Outlook
7 Connections
References
Chapter Twelve: Lattice-based mesoscale simulations and mean-field theory of cell membrane adhesion
Abstract
1 Introduction
2 Lattice-based mesoscale model for membrane adhesion
3 Mean-field theory
4 Implementation of the mean-field theory: Phase diagram
5 Monte Carlo simulations
6 Implementation of the Monte Carlo simulation: Algorithm
7 Parameter tuning
8 Examples
9 Performance
10 Summary and outlook
11 Connections
Acknowledgements
References
Chapter Thirteen: Dynamic framework for large-scale modeling of membranes and peripheral proteins
Abstract
1 Introduction
2 Main
3 Future directions
References
Chapter Fourteen: Computing the influence of lipids and lipid complexes on membrane mechanics
Abstract
1 Methodology for extracting bilayer surface mechanics from simulations
2 Generalized spontaneous curvature and the SPEX method
3 Softening by complex lipid composition
4 Connections
Acknowledgments
References
Chapter Fifteen: Non-affine deformation analysis and 3D packing defects: A new way to probe membrane heterogeneity in molecular simulations
Abstract
1 Introduction
2 The non-affine deformation content (χ2) as a measure of local order
3 Results and insights
4 Hydrophobic defects as a measure of local lipid packing
5 Results and insights
6 Formalizing the connection between membrane order and packing via the NAD analysis and 3D packing defects
7 Summary and conclusions
8 Connections
References
Chapter Sixteen: Analyzing lipid distributions and curvature in molecular dynamics simulations of complex membranes
Abstract
1 Arena
2 Methods
3 Implementation and examples
4 Performance
5 Alternatives
6 Outlook
7 Connections
References

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

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

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