Replica Exchange Molecular Dynamics Study of Dimerization in Prion ...
Supplementary Information
Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization Neharika G. Chamachi and Suman Chakrabarty* Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
Corresponding Author *[email protected]
S1
Figure S1. Comparison of secondary structure formation propensity between GROMOS 54a7 and Amber99SB-ILDN force fields for monomeric Prion using REMD simulations at T=300K, 350K and 400K.
S2
Figure S2. Spontaneous dimer formation in a regular MD trajectory at 300K: (i) surface-to-surface minimum distance (black line) and (ii) COM-COM distance between the monomers. The inset shows the data for full 400ns trajectory to confirm that the dimer remains stable during rest of the trajectory.
S3
Figure S3. Time evolution of the total hydrophobic SASA (H-SASA) during the dimerization process: The decrease in H-SASA signifies that the dimer interface helps burying the solvent exposed hydrophobic regions, which leads to stabilization of the dimer state. The inset shows the data for full 400ns trajectory to confirm that the dimer remains stable during rest of the trajectory.
S4
Figure S4. Projection on the (PC1, PC3) plane for (a) monomer and dimer trajectories: (b) Prion 1 and (c) Prion 2 at T=300K. We do not see any appearance of additional unique cluster upon inclusion of PC3. Thus, we restrict ourselves to the (PC1, PC2) projection in the main text.
S5
Figure S5. Projection on the (PC1, PC2) plane for dimer trajectory at T=300K: The huge number of unique clusters highlights the extensive conformational heterogeneity possible in the dimer system. A few representative snapshots for a few of the clusters have been shown here.
S6
Replica Exchange Molecular Dynamics Study of Dimerization in Prion Protein: Multiple Modes of Interaction and Stabilization Neharika G. Chamachi and Suman Chakrabarty* Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
Corresponding Author *[email protected]
S1
Figure S1. Comparison of secondary structure formation propensity between GROMOS 54a7 and Amber99SB-ILDN force fields for monomeric Prion using REMD simulations at T=300K, 350K and 400K.
S2
Figure S2. Spontaneous dimer formation in a regular MD trajectory at 300K: (i) surface-to-surface minimum distance (black line) and (ii) COM-COM distance between the monomers. The inset shows the data for full 400ns trajectory to confirm that the dimer remains stable during rest of the trajectory.
S3
Figure S3. Time evolution of the total hydrophobic SASA (H-SASA) during the dimerization process: The decrease in H-SASA signifies that the dimer interface helps burying the solvent exposed hydrophobic regions, which leads to stabilization of the dimer state. The inset shows the data for full 400ns trajectory to confirm that the dimer remains stable during rest of the trajectory.
S4
Figure S4. Projection on the (PC1, PC3) plane for (a) monomer and dimer trajectories: (b) Prion 1 and (c) Prion 2 at T=300K. We do not see any appearance of additional unique cluster upon inclusion of PC3. Thus, we restrict ourselves to the (PC1, PC2) projection in the main text.
S5
Figure S5. Projection on the (PC1, PC2) plane for dimer trajectory at T=300K: The huge number of unique clusters highlights the extensive conformational heterogeneity possible in the dimer system. A few representative snapshots for a few of the clusters have been shown here.
S6
