Adaptable Lipid Matrix Promotes Protein Protein Association in Membranes

Transcription

1 Supporting information Adaptable Lipid Matrix Promotes Protein Protein Association in Membranes Andrey S. Kuznetsov, Anton A. Polyansky,, Markus Fleck, Pavel E. Volynsky, and Roman G. Efremov *,, M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, , Russia Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, Vienna, AT-1030, Austria Higher School of Economics, Myasnitskaya Str., 20, Moscow, , Russia Figure S1. Potential of mean force (PMF) profiles for central part (residues 77 to 90) of peptides: GpA (black), PolyALA (red) and PolyLEU (blue). Total profiles (A) and contributions of protein-protein (B), protein-lipid (C), and protein-water interactions (D).

2 Figure S2. In-plane distributions of the average lipid density for three bilayer slices carved along the membrane normal for GpA peptide: the detailed view. Darker areas correspond to higher average lipid density. Each slice is 10 Å wide. They correspond to slice 2 (A), 3 (B) and 4 (C) on Figure 2. Colored numbers mark the average positions of Ca atoms of amino acids. Helical wheel diagram showing the relative positions of residues in GpA helix (D). Colors correspond to amino acid type: green small and polar, yellow aliphatic, orange aromatic, red negatively charged, blue positively charged.

3 Figure S3. In-plane distributions of the average lipid density for a number of the bilayer slices carved along the membrane normal for peptide dimers (GpA, PolyALA and PolyLEU) in the intermediate state (13 Å between helices). Darker areas correspond to higher density. Schematic representation of POPC molecule is shown on the left. Each slice is 10 Å wide. White pore corresponds to the inserted peptides. N-termini of the peptides are on the top, and C-termini correspond to the bottom slice.

4 Figure S4. In-plane distributions of the average lipid density for a number of the bilayer slices carved along the membrane normal for peptide dimers (GpA, PolyALA and PolyLEU) in the unbound state (22 Å between helices). All designations are the same as on the Figure S2.

5 Figure S5. Actual heterogeneity values depend on time-window used for averaging. Top panels correspond to absolute values of overall (left) and the middle slice (right) heterogeneities estimated respectively for pure POPC and the monomers inserted to the bilayer, their heterogeneity values relative to those in pure POPC are given in the second row of panels. Two bottom rows of panels depict heterogeneity values for tight (row 3) and spatially distant (row 4) dimers relative to those in pure POPC. Heterogeneity values are given in dimensionless arbitrary units.

6 Figure S6. Changes in heterogeneity values upon dimerization provide the dimer ranking relatively independent on time-window used for averaging. The values were calculated as the difference between heterogeneity parameters calculated for three independent replicas of systems with interhelical distance of 8 and 22 Å, respectively, and average over nine possible deltas. Figure S7. Correlation between relative (as compared with pure POPC) values of quasi-harmonic (QH) and dihedral conformational entropies of lipids calculated per molecule for each MD trajectory of the peptide-containing systems. Regression is shown with a dashed red line, regression parameters and Pearson correlation coefficient (R 2 ) are given at the top.

7 Figure S8. Changes in heterogeneity of lipid packing compared with pure POPC bilayer for GpA, PolyALA and PolyLEU peptide monomers (black) and dimers in oligomerized (red), intermediate (blue) and non-bound states (green). Values are calculated for the whole bilayer (A) and its central part (middle slice) (B). Lipid conformational entropy changes upon insertion of peptide monomers or dimers calculated using quasiharmonic approach for Cartesian coordinates (C) and using dihedral angles distributions (D). All the designations are the same as on panels A and B. The bars and error bars correspond to the means and standard deviations, respectively, obtained for three independent replicas of each system.