Secondary structure of polyQ fragments of different lengths.

<p><b>A</b>. Q18. <b>B</b>. Q32. <b>C</b>. Q46. Colors indicate secondary structures of different types. Blue: parallel β structure; Sky blue: anti-parallel β structure; Dark green: 3-helix; Green: α-helix; Olive: pi-helix; Orange: turn; Red: bend; Black: loop. X-axis: residue index; Y-axis: percentage of frames in the 80 ns simulations. These results are the averaged ones over the six runs performed here.</p

Secondary structure of Q32 monomers at different time frames for each of the six independent MD runs performed.

<p>X-axis: frame index with each frame representing 100 ps of simulation; Y-axis: residue index indicating the secondary structure as depicted at the right panel.</p

Solvent-polyQ hydrogen bond count.

<p><b>A</b>. Total count. <b>B</b>. Count normalized by polyQ length. Shapes indicate hydrogen bonds of different types. The error bars represent the standard deviation of the average values calculated over the six independent MD runs performed in this study.</p

Comparison of AMBER CPU and GPU performance for simulations of polyQ monomers in explicit solvent with different number of repeats.

<p>Comparison of AMBER CPU and GPU performance for simulations of polyQ monomers in explicit solvent with different number of repeats.</p

Distance distribution of observed hydrogen bonds with more than 50% frequency.

<p>The normalized distance is calculated as (|acceptor residue index-donor residue index|+1)/(the number of repeat in polyQ). Red: Q18; Green: Q32; Blue: Q46.</p

Solvent accessible surface area.

<p><b>A</b>. Total SASA. <b>B</b>. Normalized SASA. Red: backbone SASA; Green: sidechain SASA; Blue: total SASA. The error bars represent the standard deviation of the average values calculated over the six independent MD runs performed in this study.</p

Distance distribution of observed solvent bridges lasting more than 100 frames in the simulation.

<p>The normalized distance is calculated as (|acceptor residue index-donor residue index|+1)/(number of repeat in polyQ). Red: Q18; Green: Q32; Blue: Q46.</p

Secondary structure of Q46 monomers at different time frames for each of the six independent MD runs performed.

<p>X-axis: frame index with each frame representing 100 ps of simulation; Y-axis: residue index indicating the secondary structure as depicted at the right panel.</p

Solvent-polyQ hydrogen bond count at the atomic level.

<p><b>A</b>. Total count. <b>B</b>. Count normalized by polyQ length. Shapes indicate hydrogen bonds of different donor and acceptor types. The error bars represent the standard deviation of the average values calculated over the six independent MD runs performed in this study.</p

Scaling laws for polyQ monomers in water.

<p>Dots represent the Rg values for each polyQ length averaged over the six MD run performed here. The error bars represent the standard deviation of the average values calculated over the six independent MD runs performed in this study.</p