Figure 1. Probability map to form side-chain–side-chain contacts between pairs of residues i and j separated by more than 1 amino acid residue along the sequence, j − i > 1, inferred for Aβ 10-35 from our constant temperature molecular dynamics simulations. The map is shown at simulation times t = 0 (NMR ensemble) and 0.5 ns in (a) and at 1.0 ns and 2.0 ns in (b). The data are shown for the simulations using the PME electrostatics method.

Figure 2. Residue-specific secondary structure assignments for Aβ 10-35, determined in the present work using DSSP algorithm.⁴⁰ Seven different elements of secondary structure were employed which are denoted as “α-Helix” for α-helix, “3-Helix” for 3₁₀-helix, “Beta-S” for β-sheet, “Beta-B” for β-bridge, “Bend” for bends, “Turns” for β-turns and “Coil” for all other conformations.

Figure 3. Hydrogen bond probabilities for Aβ 10-35 inferred from our REMD simulations. For viewing convenience, the data are broken into backbone–backbone (B-B), side-chain–backbone (SD-B) and side-chain–side-chain (SD-SD) categories. Most populated bonds are seen for the side-chain of D23 interacting with amide hydrogen atoms of adjacent residues. A similar network of hydrogen bonds is also predicted for the side-chain of E11.

Figure 4. Map of side-chain–side-chain contacts of Aβ 10-35, computed in our replica-exchange simulations. For comparison, the map of the NMR-derived ensemble⁶ is also shown.

Figure 5. Residue-specific SASA of side-chains in Aβ 10-35 computed in the present REMD simulations. In (a), SASA terms of side-chain atoms of all 26 residues are compared to the values of the NMR-derived structures and those appropriate for fully extended peptide conformations. In (b), absolute and relative SASA values are plotted for each residue of Aβ 10-35. Hydrophobic residues appear to share a similar extent of solvent exposure as all other residues.

Figure 6. Comparison of the upper bounds determined experimentally for 30 long-range NOE constraints⁶ with the < 1 / r⁶ >^− 1/6 averages of the corresponding inter-proton distances observed in our replica-exchange simulations. The corresponding distances of the experimentally derived models are also shown.

Figure 7. Random mean-square deviation (RMSD) over C^α atoms averaged over 75 independent trajectories started from 15 different NMR models of A β 10-35.⁶ The results of simulations employing PME approach⁷¹ and RF method,⁷⁰ coupled with OPLS⁵⁹ molecular force field and TIP3P water model⁶⁰ are shown. Also, simulations using GROMOS96⁷² and Simple Point Charge water model⁷³ are presented. Additionally, the results of OPLS-based simulations in which H13 and H14 are considered charged are shown.