Extended Data Figure 9: Modeling of binding of IFITM3 to PIP2 and PIP3.

The hierarchical scheme of MD simulations (a-c) to delineate the structural and dynamical basis of PIP2 and PIP3 binding to IFITM3 (yellow). a, Coarse grained simulations of IFITM3 in composite cell membrane. The side views of the lipid bilayer are shown. The lipid raft markers are shown in color with GM1 (pink), cholesterol (green) and sphingomyelin (blue). The gray surface represents all the other lipids. b, The simulation cell extracted from the coarse grained simulation as the starting structure for all-atom MD simulations. The IFITM3 protein is shown in yellow and the PIP2 and PIP3 are shown in green and red stick representations. c, Close up view of one of the predicted binding poses of PIP2 and PIP3 in the most populated conformation of IFITM3. The dashed lines shown are the PIP2 or PIP3 contacts with the basic residues in IFITM3 (top). The amino acid sequence of IFITM3 in the stretch of residues between TM1 and TM2 from 57 to 128 modeled in this work is shown. The conserved intracellular loop (CIL) region is boxed and basic amino acids are highlighted with blue. The average interaction energy of PIP2 or PIP3 with the two basic batches measured in all-atom MD simulations is indicated (see Supplementary Table S6). d, e, The average interaction energy of PIP2 (green) or PIP3 (red) with the IFITM3 (residues 57–128) was measured in all-atom MD simulations. The 1-residue contact indicates the conformation of PIP2 or PIP3 binding with only one basic residue in the basic amino patch KSRDRK of IFITM3. The 2-residue contact refer to the binding conformation of PIP2 or PIP3 that show contacts with two basic residues. Shown are representative plots from at least 4 independent experiments (mean ± s.d.). P-values were determined by two-tailed t-test (d). Populations showing one or two-residue contacts of PIP2 (green) or PIP3 (red) to IFITM3 were quantitated from all-atom MD simulations. The population density was assessed by the normalization of number of events with the total number of frames. Shown are representative plots from 3 independent experiments (mean ± s.d.). Statistical significance was determined by two-tailed t-test (e).