Additional file 1 of Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity
Creators: name: Pluhackova, Kristyna
name: Horner, Andreas
Publisher: name: figshare
Year: 2021
Subjects: subject: Biophysics
subject: Biochemistry
subject: Cell Biology
subject: Molecular Biology
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Cancer
subject: Computational Biology

description: Additional file 1 Tables S1-S6 and Figures S1-S25. Table S1 - Lipid tail names, shortcuts and stereochemistry. Table S2 - Molecular composition of each simulation system. Table S3 - List of performed simulations. Table S4 - Angle parameters for Martini3 tails including cyclopropane bead. Table S5 - Details on water permeability at AA resolution. Table S6 - Details on water permeability at CG resolution. Fig. S1 - Chemical structures of the lipid headgroups in E. coli polar extract membranes. Fig. S2 - Chemical structures of lipid tails included in this study. Fig. S3 - ChemDraw representations of lipid molecules in the Avanti model. Fig. S4 - Angle distributions from AA and CG simulations extracted from the Avanti model of the E. coli polar extract membrane simulations at 310 K. Fig. S5 - The time evolution of the average area per lipid of AA pure lipid bilayers. Fig. S6 - The time evolution of the average area per lipid of CG pure lipid bilayers. Fig. S7 - Area per lipid of each lipid type in pure lipid bilayers at all temperatures and their temperature dependence. Fig. S8 - Statistical analysis of error estimation of APL. Fig. S9 - Ratios of the curved area per lipid and the area per lipid estimated form the box size for all systems at all temperatures. Fig. S10 - Distribution of hydrophobic thickness of 171 transmembrane proteins localized in the inner membrane of E. coli obtained from the OPM database. Fig. S11 - Lipid diffusion in each simulated system for each lipid type including the corresponding activation energies. Fig. S12 - Interdigitation of membrane leaflets. Fig. S13 - Lipid mixing at low (277 K) and high (310 K) temperature visualized by coloring lipids according to their headgroups. Fig. S14 - Lipid tail mixing in individual leaflets at low (277K) and high (310K) temperature visualized by coloring different lipid tail types in different colors. Fig. S15 - Enrichment and depletion of neighboring lipids. Fig. S16 - CL clustering at different temperatures in all three membrane models at CG resolution. Fig. S17 - CL clustering at AA resolution at different temperatures for each lipid mixture. Fig. S18 - Membrane area compressibility of CG membranes. Fig. S19 - Order parameters along the lipid tails in CG simulations at different temperatures for all four membrane models and for the Avanti model including AQP1. Fig. S20 - AQP1 embedded in the E. coli PLE Avanti model at 310 K at AA and CG resolution Fig. S21 - P-P membrane thickness of E. coli PLE Avanti model in pure lipid systems and in 0.5 nm and 1 nm surroundings of AQP1 at different temperatures and at AA and CG resolutions. Fig. S22 - RMSD over time of C α atoms within helices of the AA tetramer documenting the stability of the protein’s quaternary structure in AA simulations. Fig. S23 - RMSD over time of C α atoms within helices of the AA monomer documenting the stability of the protein’s tertiary structure in AA simulations. Fig. S24 - Lipid binding times to CG AQP1 at different temperatures. Fig. S25 - Time evolutions of lipid enrichment in the first solvation layer around CG AQP1.