Extended Data Fig. 7: CG MD simulations.
From: Cryo-EM architecture of a near-native stretch-sensitive membrane microdomain
a, Total occupancy per lipid for all lipids in each CG MD system. Total occupancy was averaged across the 3 replicas, error bars are s b, Comparison of DOPC occupancy and cholesterol occupancy in the +PI(4,5)P2/+sterol system for AH region residues <5 Å from DOPC and/or sterol headgroup, revealing the specificity of the sterol occupancy over the DOPC occupancy at the bulky side chains of the AH. c, PI(4,5)P2 occupancy reported for all residues <5 Å from PI(4,5)P2 headgroups. d, DOPS lipid occupancy for residues <5 Å from DOPS headgroup with >5% occupancy in CG MD simulations. e, Comparison of PI(4,5)P2 occupancy and DOPS occupancy in the +PI(4,5)P2/+sterol system for residues <5 Å from PI(4,5)P2 and/or DOPS headgroup. In b–e, values represent averages of per-residue occupancy computed along three replicas of 10 μs each, error bars are SEM. f, Lipid diffusion coefficients from CG simulations with PO- lipids. The values reported are the 1D axial diffusion of lipids in the outer leaflet of the tubes, with (green) and without (cyan) the Pil1 coat. Diffusion coefficients were computed from 5 replicas of 2 μs. Box plots elements are defined as follows: Centre line is the median, box limits are 25% to 75% lower and upper quartiles, whiskers extend from the box to the minimum and maximum data points lying within 1.5x interquartile range (IQR), and green triangle indicates the mean value. g, Total occupancy per lipid for all lipids in each CG MD system using PO- lipids instead of DO- lipids. * indicates sterol-binding residues and # indicates charged predicted lipid-binding-pocket residues. Total occupancy was averaged across the 3 replicas, error bars are SEM.
