Two modes of membrane binding by H-Ras were observed in previous simulations [17].

<p>(a) An approximately perpendicular orientation of the catalytic domain with respect to the membrane plane. This conformation, which we refer to as conf1, was frequently sampled during GDP-H-ras simulations <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071018#pone.0071018-Gorfe1" target="_blank">[17]</a>. (b) Semi-parallel orientation of the catalytic domain with respect to the membrane plane, which we refer to here as conf2. These two conformations were used as starting structures for the current simulations. Helices 4 and 5, as well as the bound nucleotide, are labeled. The canonical switches SI and SII are at the bottom of the image surrounding the nucleotide. Also shown in space-filling representation are side chains of the HVR along with Arg128 and Arg135 on helix 4, as well as the three lipid modifications (two palmitoyls at positions 181 and 184 and a farnesyl at position 186).</p

Lateral diffusion coefficient (D) of molecules in the bilayer (×10⁻⁸ cm²/s).

<p>Lateral diffusion coefficient (D) of molecules in the bilayer (×10⁻⁸ cm²/s).</p

Summary of the simulations.

<p>Summary of the simulations.</p

Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation

The mechanism of curvature generation in membranes has been studied for decades due to its important role in many cellular functions. However, it is not clear if, or how, aggregates of lipid-anchored proteins might affect the geometry and elastic property of membranes. As an initial step toward addressing this issue, we performed structural, geometrical, and stress field analyses of coarse-grained molecular dynamics trajectories of a domain-forming bilayer in which an aggregate of lipidated proteins was asymmetrically bound. The results suggest a general mechanism whereby asymmetric incorporation of lipid-modified protein aggregates curve multidomain membranes primarily by expanding the surface area of the monolayer in which the lipid anchor is inserted

Aggregation of Lipid-Anchored Full-Length H-Ras in Lipid Bilayers: Simulations with the MARTINI Force Field

<div><p>Lipid-anchored Ras oncoproteins assemble into transient, nano-sized substructures on the plasma membrane. These substructures, called nanoclusters, were proposed to be crucial for high-fidelity signal transmission in cells. However, the molecular basis of Ras nanoclustering is poorly understood. In this work, we used coarse-grained (CG) molecular dynamics simulations to investigate the molecular mechanism by which full-length H-ras proteins form nanoclusters in a model membrane. We chose two different conformations of H-ras that were proposed to represent the active and inactive state of the protein, and a domain-forming model bilayer made up of di16:0-PC (DPPC), di18:2-PC (DLiPC) and cholesterol. We found that, irrespective of the initial conformation, Ras molecules assembled into a single large aggregate. However, the two binding modes, which are characterized by the different orientation of the G-domain with respect to the membrane, differ in dynamics and organization during and after aggregation. Some of these differences involve regions of Ras that are important for effector/modulator binding, which may partly explain observed differences in the ability of active and inactive H-ras nanoclusters to recruit effectors. The simulations also revealed some limitations in the CG force field to study protein assembly in solution, which we discuss in the context of proposed potential avenues of improvement.</p></div

Snapshots and aggregation profiles derived from simulations B1 and B2.

<p>Top view of initial (a) and final configurations of conf1 (b), and conf2 (c), in a 5:3:2 DPPC:DLiPC:CHOL ternary bilayer. The 32 H-ras proteins are colored in yellow, DPPC in red, DLiPC and CHOL in blue and white. (d) The number of total clusters during the simulations.</p

Contour maps of P for the snapshots sampled from the 24–25 µs window, with key regions highlighted as in Figure 3 (upper half: conf.1, lower half: conf2).

<p>The corresponding ΔSASA distributions are displayed next to the contour maps. Residues with ΔSASA>0.75 nm² are highlighted in red. Average SASA was calculated on 4ns-spearated frames and averaged over the last and first 1 µs windows. Major secondary structure are indicated schematically with helices in red and strands in blue in (c).</p

Mean square displacements of conf1 (a) and conf2 (b) during the indicated time windows.

<p>The lateral diffusion coefficient was calculated from a linear fit to the MSD curve in the time interval highlighted by bold lines.</p

Snapshots illustrating inter-protein interactions in Ras aggregates derived from simulations with Ras in conf1 (left) and conf2 (right).

<p>Shown are side (a & b) and top views of conf1 and conf2 aggregates. The color scheme for the lipid molecules is the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071018#pone-0071018-g001" target="_blank">Figure 1</a> (except for DPPC, which is in now tan). Proteins are shown in different colors.</p

The National Spatial Strategy: Lessons for implementing a National Planning Framework

The Irish Government is in the process of developing a National Planning Framework (NPF). This will replace the National Spatial Strategy for Ireland 2002-2020 (NSS). The NSS is generally considered to have been unsuccessful, mainly due to a lack of implementation driven by shortcomings in governance. This paper explores these shortcomings, and suggests ways to prevent similar difficulties with the NPF. The paper concludes that the political process needs to be at the heart of the preparation and adoption of the NPF. There is the danger that the NPF will fail if the political environment remains embedded in traditional approaches to planning across the state