Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling - PubMed (original) (raw)

Understanding the role of amphipathic helices in N-BAR domain driven membrane remodeling

Haosheng Cui et al. Biophys J. 2013.

Abstract

Endophilin N-BAR (N-terminal helix and Bin/amphiphysin/Rvs) domain tubulates and vesiculates lipid membranes in vitro via its crescent-shaped dimer and four amphipathic helices that penetrate into membranes as wedges. Like F-BAR domains, endophilin N-BAR also forms a scaffold on membrane tubes. Unlike F-BARs, endophilin N-BARs have N-terminal H0 amphipathic helices that are proposed to interact with other N-BARs in oligomer lattices. Recent cryo-electron microscopy reconstructions shed light on the organization of the N-BAR lattice coats on a nanometer scale. However, because of the resolution of the reconstructions, the precise positioning of the amphipathic helices is still ambiguous. In this work, we applied a coarse-grained model to study various membrane remodeling scenarios induced by endophilin N-BARs. We found that H0 helices of N-BARs prefer to align in an antiparallel manner at two ends of the protein to form a stable lattice. The deletion of H0 helices causes disruption of the lattice. In addition, we analyzed the persistence lengths of the protein-coated tubes and found that the stiffness of endophilin N-BAR-coated tubules qualitatively agrees with previous experimental work studying N-BAR-coated tubules. Large-scale simulations on membrane liposomes revealed a systematic relation between H0 helix density and local membrane curvature fluctuations. The data also suggest that the H0 helix is required for BARs to form organized structures on the liposome, further illustrating its important function.

Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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Figures

Figure 1

Figure 1

CG model of endophilin N-BARs is shown in panel a. The BAR domain main arch CG sites are colored in green, H0 helices are colored in blue, and the insert helices in white. The sites are assigned based on essential dynamics coarse-graining calculations. Panels b to d show top views of zigzag N-BAR, triad N-BAR, and BAR domain, respectively. Panels e and f show the zigzag model and the triad model fitted into the cryo-EM map, respectively.

Figure 2

Figure 2

CG simulation snapshots of membrane tubes coated by zigzag N-BARs and triad N-BARs. Panels a and b show the initial and final configurations of zigzag simulation and panels c and d show the initial and final configurations of the triad system. The lattice structure remains more organized in the zigzag system.

Figure 3

Figure 3

Order of the N-BAR protein coats. Panel a illustrates the local orientation order parameter, defined by the cosine of the orientational difference between two BARs. Panel b shows a snapshot of the protein lattice, colored from blue to red as the order parameter decreases. Panel c plots the order parameters of the zigzag N-BAR system and the triad N-BAR system as functions of time. The lattice of the triad system is significantly disrupted at the end of the simulation.

Figure 4

Figure 4

Simulation snapshots of BAR domain-coated membrane are shown; panel a is the initial configuration and panel b is the final state of the simulation. Panel c shows the local orientational order parameters calculated for multiple trajectories in the N-BAR system and BAR system. The N-BAR system stays much more organized after the simulation compared to the BAR system with H0 helices deleted.

Figure 5

Figure 5

Persistence length calculations. Panel a shows an example of the regression used to compute the persistence length for one membrane tube at one time frame; error bars show the standard deviations of the value of angle correlation for segments that have the same contour lengths. Panel b plots the persistence length for one tube over the simulation as a function of simulation time, demonstrating that the persistence length converges after 50 million CG MD time steps. Panels c and d show representative experimental EM images of endophilin N-BAR-coated tubes.

Figure 6

Figure 6

Representative snapshots of the N-BAR system (left) and the BAR-coated liposome systems (right) after 5 million CG MD timestep simulations. The proteins are colored by a packing order parameter that is explained in the main text. Circles in the left panel highlight the region where proteins gather into structures that have similar orientations. This kind of clustering is missing in the BAR domain system in the right panel. The data are consistent with the hypothesis that BAR domains require H0 helices to form arrays and strings on the liposome.

Figure 7

Figure 7

EM image showing aligned arrays of endophilin N-BARs on a liposome surface in an area that is not yet tubulated.

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