Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins
TL;DR: The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.
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Abstract: Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.
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Citations
Mesoscale modeling in biophysics: Applications to formin
Derek Bryant
- 01 Jan 2016
TL;DR: An emerging mod-eling method is defined, which is called mesoscale modeling, and a model of formin-mediated actin polymerization is developed in the context of this method, which includes monomer capture and delivery by FH1, which sterically interacts with actin along its entire length.
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Quantification of Curvature Sensing Behavior of Curvature-Inducing Proteins on Model Wavy Substrates
TL;DR: The Widom insertion technique is used to compute the free energy landscape for an inhomogeneous system with spatially varying density and the results obtained show excellent agreement with experimental studies that demonstrate the association between membrane curvature and local protein density.
4
Molecular Simulations of Protein-Induced Membrane Remodeling
Ryan Bradley
- 01 Jan 2016
TL;DR: This dissertation presents a series of molecular models which, when combined with continuum models and both in vitro and in vivo experiments, describe the molecular basis for membrane morphology changes, and investigates the mechanisms by which proteins assemble on a bilayer undergoing thermal fluctuations.
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Forceful patterning: theoretical principles of mechanochemical pattern formation
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TL;DR: The theoretical principles underlying different types of mechanochemical pattern formation across spatial scales and levels of biological organization are reviewed.
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Modeling Membrane-Protein Interactions
Haleh Alimohamadi,Padmini Rangamani +1 more
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TL;DR: Some of the commonly used continuum elastic membrane models that have been developed for this purpose and their applications are reviewed and some fundamental challenges that future theoretical methods need to overcome are addressed in order to push the boundaries of current model applications.
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