TCB Publications - Abstract

Ying Yin, Anton Arkhipov, and Klaus Schulten. Multi-scale simulations of membrane sculpting by N-BAR domains. In Philip Biggin and Mark Sansom, editors, Molecular Simulations and Biomembranes: From Biophysics to Function, chapter 6, pp. 146-176. Royal Society of Chemistry, 2010.

YIN2010 Cells contain membranes of various shapes, often formed with the help of cellular proteins. In particular, proteins of the BAR domain superfamily participate in various membrane sculpting processes, bending membranes through the concerted action of multiple BAR domains arranged in lattices. Despite extensive experimental studies, information on the dynamics of membrane bending and an explanation of the lattices’ role are still lacking. Computational studies can furnish such information. Here we summarize recent work on the dynamics of membrane bending by N-BAR domains, a well-studied member of the BAR domain superfamily, at four levels of resolution: described by all-atom molecular dynamics, residue-based coarse graining (resolving single amino acids and lipid molecules), shape-based coarse graining (resolving overall protein and membrane shapes), and a continuum elastic membrane model. Simulations showed how the membrane curvature generated depends on the arrangement of N-BAR domains on the membrane surface. The lattice arrangements found to be optimal for producing high membrane curvature are composed of protein rows separated by $\sim$5 nm, stability of the rows being maintained through electrostatic interactions between N-BAR domains. Formation of entire membrane tubes by lattices of N-BAR domains over time scales of $\sim$200 $\mu$s was observed in coarse-grained simulations; an all-atom simulation of a 2.3 million atom system covering 0.3$\mu$s complemented the coarse-grained simulations.

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