The number of A and A monomer and dimer trajectories.

<p>The number of different conformations used for structural analysis acquired between and ns of each trajectory is given in parentheses.</p

The average SASA per amino acid in A dimers.

<p> <i>The thick black and red curves correspond to SASA for all-atom A</i><i> and A</i><i> dimers obtained by MD using the (A) SPCE and (B) TIP3P water model. The error bars are SEM values.</i></p

Probability distributions of SASA values and NT-CM values in MD-derived fully atomistic A and A monomers and dimers.

<p> <i>The SASA value was calculated as a sum of SASA values over all hydrophobic residues for each monomer and dimer conformation. Similarly, the NT-CM distance was calculated for each monomer and dimer conformation. The resulting histograms were normalized to obtain probability distributions, displayed as black curves for A</i><i> and red curves for A</i><i> monomers and dimers for each of the two water models. The error bars represent SEM values.</i></p

Salt bridge propensity in A and A dimers.

<p>The error bars correspond to SEM values.</p

Average turn, -strand, helical, and coil propensities within A and A dimers obtained by the all-atom MD approach with each of the two water models and the DMD approach.

<p>The error bars correspond to SEM values.</p

Free energy landscapes of A

<p><b> monomers and dimers with representative conformations. </b><i>The reaction coordinates are the SASA of all hydrophobic amino-acids (x-axis) and the NT-CM distance (y-axis). The PMF plots for (A,C) A</i><i> and (E,G) A</i><i> monomers were acquired by MD using the (A,E) SPCE and (C,G) TIP3P water models. The corresponding PMF plots for (B,D) A</i><i> and (F,H) A</i><i> dimers were acquired by MD using the (B,F) SPCE and (D,H) TIP3P water models. The color scheme to the right of each plot is given in units of k</i><i>T. The representative conformations of each conformational ensemble are displayed with the N-terminal amino acid D1 colored red and the C-terminal amino acid (V40/A42) colored green. The images were generated by VMD.</i></p

The average distance from the CM of each amino acid residue in A dimers.

<p> <i>The thick black and red curves correspond to the average distances from the CM of amino acids within A</i><i> and A</i><i> dimers, respectively, acquired by MD using (A) SPCE and (B) TIP3P water model. The thin black and red curves correspond to the average distances from the CM of amino acids within the corresponding DMD-derived A</i><i> and A</i><i> dimers, respectively. The error bars are SEM values.</i></p

Sampling efficiency and free energy landscapes of A dimers.

<p> <i>Dimer conformations of all acquired MD trajectories of (A,B) A</i><i> and (E,F) A</i><i>, respectively, projected onto two reaction coordinates, for the (A,E) SPCE and (B,F) TIP3P water models. Each trajectory is shown in one color and each point corresponds to one dimer conformation along the trajectory acquired at simulation times 20–50 ns. The open black circles correspond to the initial DMD-derived dimer conformations. The PMF plots for (C,D) A</i><i> and (G,H) A</i><i> dimers calculated from MD trajectories with the (C,G) SPCE and (D,H) TIP3P water model. The color scheme to the right of each plot is given in units of k</i><i>T. Images were created by the GNUPLOT software package.</i></p

Intrapeptide salt bridge formation between D1 and R5 in A and A dimers in SPCE water model.

<p> <i>The dimers are colored in green, D1 in red and R5 in blue. The distance between one oxygen of D1 side chain and one nitrogen of R5 side chain for each of the two peptides in a (A) A</i><i> and (B) A</i><i> dimer is shown as a function of simulation time. The D1-R5 salt bridges on each of the two peptides in a dimer are marked as 1 and 2.</i></p

Histograms of salt bridge propensities.

<p> <i>Total salt bridge propensities of the three positively charged amino acids: R5, K16, and K28 in A</i><i> and A</i><i> monomers and dimers are displayed as histograms for each of the two water models.</i></p