Biophysical Approaches for the Study of Membrane Structure Part B.

This book, part of the 'Methods in Enzymology' series, focuses on biophysical approaches to study membrane structures. Edited by Markus Deserno and Tobias Baumgart, it delves into theoretical and simulation methods to understand complex membrane dynamics. The text covers topics such as lip...

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Bibliographic Details
Main Author:	Deserno, Markusu
Corporate Author:	ScienceDirect (Online service)
Other Authors:	Baumgart, Tobias
Format:	eBook
Language:	English
Published:	San Diego : Elsevier Science & Technology, 2024.
Edition:	1st ed.
Series:	Issn Series.
Subjects:	Membranes (Biology) Cell membranes. Membranes (Biologia) Membranes cel·lulars. Ultraestructura (Biologia) Electronic books. Llibres electrònics.
Online Access:	Connect to the full text of this electronic book

Table of Contents:

Front Cover
Series Page
Methods in Enzymology
Copyright
Contents
Contributors
Preface
Chapter One: Characterization of domain formation in complex membranesCharacterization of domain formation in complex membranes
1 ARENA
1.1 Physical situation
1.2 Challenges
1.3 Typical solutions
1.4 Common issues
2 DomHMM
2.1 Big idea
2.2 Main tools
2.3 Scope
3 Implementation
3.1 Technical implementation
3.1.1 Trajectory preparation
3.1.2 Leaflet identification
3.1.3 Area per lipid
3.1.4 SCC order parameters
3.1.5 Gaussian mixture model
3.1.6 Gaussian-based Hidden Markov Model
3.1.7 Getis-Ord statistic
3.1.8 Hierarchical clustering
3.2 Examples
3.2.1 System preparation
3.2.2 Structural properties
3.2.3 Gaussian mixture model
3.2.4 Gaussian-based hidden Markov models
3.2.5 Getis-Ord statistic
3.2.6 Hierarchical clustering
3.3 Parameter tuning
3.4 What can go wrong?
3.5 Advantages
3.6 Limitations
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
1 Arena
1.1 Physical situation
1.2 Challenges
1.3 Typical solution(s)
1.4 Common issues
2 Density-threshold affinity
2.1 Big idea
2.2 Theory
2.2.1 Any bead criterion
2.2.2 Many beads criterion
2.2.3 Excess beads criterion, the density-threshold affinity
2.3 Main tools
2.4 Scope
3 Implementation
3.1 Protocol
3.2 Preparatory steps
3.2.1 Running an appropriate CG-MD simulation
3.2.2 Preparing a simulation for analysis
3.2.3 Defining an appropriate binding site
3.3 Discussion of major protocol components
3.3.1 Constructing the Psite,nY histogram.
3.2 Determination of lateral dimensions
3.3 Generation of binary bilayer system
4 Preliminary symmetric bilayer simulations
5 Equilibration of individual bilayers
6 Assembly of the binary bilayer system
6.1 Preparation for equilibration and production simulations
6.2 Verification of lateral packing in BBS
6.3 Examples
6.4 Parameter tuning
6.5 What can go wrong?
7 Performance
7.1 Advantages
7.2 Limitations
8 Alternatives
9 Outlook
10 Connections
Acknowledgements
References
Chapter Five: Modeling asymmetric cell membranes at all-atom resolution
1 Introduction
1.1 Physiological functions
1.2 Molecular dynamics simulations
2 Methods
2.1 Simple methods for building asymmetric membranes
2.1.1 Equal number of lipids
2.1.2 Area per lipid
2.1.3 Surface area per lipid
2.1.4 0-DS
2.2 Complex methods for building asymmetric membranes
2.2.1 Simulations with P21 PBCs (P21)
2.3 Induced asymmetry with Monte Carlo
3 Comparison between the methods
4 Conclusion
5 Connections
Acknowledgments
References
Chapter Six: Multiscale remodeling of biomembranes and vesicles
1 Introduction
2 Shape remodeling of giant vesicles
2.1 Polymorphism of giant vesicles
2.1.1 Two-sphere shapes with out-buds
2.1.2 Two-sphere shapes with in-buds
2.2 Curvature elasticity
2.2.1 Spontaneous curvature model
2.2.2 Shape functional for giant vesicles
2.2.3 Shape parameters and morphology diagrams
2.2.4 Effective mean curvature of closed membrane necks
2.2.5 Positive and negative membrane necks
2.2.6 Local properties of closed membrane necks
2.3 Controlled shape remodeling of giant vesicles
2.3.1 Low density of membrane bound GFP
2.3.2 Shape parameters and morphology diagram
2.3.3 Control experiments with other fluorophores.
2.4 Two-sphere shapes and condensate droplets
2.4.1 Condensate droplets from aqueous phase separation
2.4.2 Geometry of vesicle-droplet systems
2.4.3 Morphological responses of vesicle membranes
2.4.4 Complete engulfment of condensate droplets
2.5 Multispherical shapes of giant vesicles
2.5.1 Positive multispheres for positive spontaneous curvature
2.5.2 Morphology diagrams for positive multispheres
2.5.3 Negative multispheres for negative spontaneous curvature
3 Shape transformations of nanovesicles
3.1 Volume parameter for nanovesicles
3.2 Leaflet tensions and stress asymmetry
3.2.1 Assembly of planar bilayers and nanovesicles
3.2.2 Positive and negative leaflet tensions
3.2.3 Computation of leaflet tensions
3.2.4 Dependence of leaflet tensions on lipid numbers
3.2.5 Two-dimensional leaflet tension space
3.2.6 Voronoi tessellation and volume per lipid
3.2.7 Stress asymmetry of vesicle bilayers
4 Instabilities of lipid bilayers
4.1 Stability regime of vesicle bilayers
4.2 Stress-induced flip-flops of lipids
4.3 Stress-induced structural instabilities
5 Remodeling of vesicle topology
5.1 Topology of closed vesicle membranes
5.1.1 Euler characteristic
5.1.2 Topological genus
5.2 Topological transformations of vesicles
5.2.1 Local topology changes by fission and fusion
5.2.2 Fission geometries for two-sphere vesicles
5.2.3 Fusion geometries for spherical vesicles
5.3 Free energy landscapes for fission and fusion
5.3.1 Free energy landscape for fission
5.3.2 Free energy barrier for neck fission
5.3.3 Free energy landscape for fusion
5.4 Neck fission and division of giant vesicles
5.5 Neck fission and division of nanovesicles
5.6 Droplet endocytosis by nanovesicles
5.6.1 Adhesion of condensate droplets to nanovesicles.
5.6.2 Partial versus complete engulfment
5.6.3 Two-step process of endocytosis
5.6.4 Two pathways for complete engulfment
5.6.5 Axisymmetric droplet engulfment and endocytosis
5.6.6 Tight-lipped membrane neck and blocked fission
5.6.7 Positive and negative line tension of contact line
5.7 Fusion of nanovesicles
5.8 Membrane architecture of endoplasmic reticulum
5.8.1 Multiscale architecture of ER membrane
5.8.2 Bicontinuous structure and topological genus
5.8.3 Tensile forces and junction dynamics
6 Summary and outlook
Acknowledgements
Appendix A Computation of bilayer tension
A.1 Anisotropic pressure tensor for planar bilayers
A.2 Anisotropic pressure tensor for spherical nanovesicles
Appendix B Computation of leaflet tensions
B.1 CHAIN protocol for computation of rmid
B.2 VORON protocol for computation of rmid
References
Chapter Seven: Building complex membranes with Martini 3
1 Introduction
2 Symmetric mixtures
2.1 System setup using insane
2.2 Simulation parameters
2.3 Fetching Martini 3 topology files for lipids
2.4 Maintaining relatively flat bilayers
3 Asymmetric complex membranes
3.1 Setting up symmetric membranes with each leaflet's composition
3.2 Calculating the difference in number of lipids between the leaflets of an asymmetrical membrane
3.3 Building an asymmetric membrane composed of leaflets with equal surface areas
3.4 Setting up the cholesterol ratio in an asymmetric membrane
3.5 Convergence, analysis, and common pitfalls
4 Complex membranes with proteins
4.1 Setting up a protein-membrane simulation system
4.2 Analysis of a protein-membrane simulation system
5 Curved membranes
5.1 Determine membrane thickness from a flat reference simulation
5.2 Setting up a curved membrane with TS2CG.