The minor groove environment.

<p>A) Electrostatic potential inside the minor groove. The potential has been rescaled such that the minima in the studied region was set to 0 to facilitate the comparison with the computed PMF. B) The minor groove width was computed using the software Curves [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#pcbi.1003980.ref051" target="_blank">51</a>]. Grey shadows correspond to one standard deviation. For examples of different structures see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#pcbi.1003980.s005" target="_blank">S5 Fig.</a>.</p

Methyl-guanidinium sliding along the minor groove.

<p>A) 1D-PMFs of one turn along the helical path at different radii from the DNA’s axis. Grey shadow correspond to one standard deviation (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#sec004" target="_blank">Methods</a> section). B) Minimum free energy path obtained by assuming that, at every angular position, the ligand will localize the radii of minimum free energy. The PMF has been color coded to show the radius using the same color scheme as A).</p

Binding free-energy landscape of methyl-guanidinium in the minor groove.

<p>A) PMF was computed for one complete turn (2<i>π</i>) along the minor groove in the helical coordinates system (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#pcbi.1003980.s001" target="_blank">S1 Fig.</a>). Notice that in this coordinate system there is no angular periodicity. The PMF wasprojected to the 2D plane, such that the z-axis is perpendicular to the page. Orange crosses correspond to the average position of the DNA’s backbone phosphates of the studied turn (i.e. 10.5 base pairs). The red cross correspond to the methyl-guanidinium initial center of mass position. B) 1D-PMFs of removing the methyl guanidinium from the minor groove at 4 different angular positions (red letters in boxes) as shown in A. Grey shadow correspond to one standard deviation.</p

Binding free-energy landscape for Na⁺ in the minor groove: The PMF was computed for one complete turn (2<i>π</i>) along the minor groove in the helical coordinates system (see S1 Fig.).

<p>The PMF was projected to the 2D plane, such that the <i>ξ</i>-axis is perpendicular to the page (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#sec004" target="_blank"><i>Methods</i></a> sections and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#pcbi.1003980.s001" target="_blank">S1 Fig.</a>) and the obtained free-energies are those of a “ribbon” passing through the middle of the minor groove’s sampled volume. In this representation the DNA’s axis is at the center of the plot. Note that in this coordinate system there is no angular periodicity.</p

Schematic representation of the helical coordinates system.

<p>A) The helical coordinate system establishes the position of the ligand center of mass with respect to the DNA’s axis. The DNA axis was aligned to the z-axis. The helical coordinate system is defined in terms of coordinates (<i>ρ</i>, <i>ϕ</i>, <i>ξ</i>) (in yellow). Coordinates (<i>r</i>, <i>θ</i>, <i>z</i>) (in red) correspond to a cylindrical coordinate system. <i>p</i> is the pitch of the helix and <i>α</i> the pitch angle. B) The components of a vector <b>V</b> in a surface of constant <i>ρ</i> in both helical (yellow) and cylindrical coordinates (red). C) Snapshot of the initial DNA methyl-guanidinium complex.</p

Radial distribution functions (<i>g</i>_{<i>OW</i>−<i>cation</i>}) of water oxygens around the methyl-guanidinium cation.

<p>A) <i>g</i>_{<i>OW</i>−<i>cation</i>} computed at different radii from the DNA’s axis. B) Average number of water oxygen atoms 〈N〉 in the first hydration of the methyl-guanidium cation at different radius from the DNA’s axis.</p

Na⁺ sliding along the minor groove.

<p>A) 1D-PMFs of one turn along the helical path at different radii from the DNA’s axis. Grey shadow correspond to one standard deviation computed using the Bootstrap method (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003980#sec004" target="_blank">Methods</a> section). B) Radial distribution functions (<i>g</i>_{<i>OW</i>−<i>Na</i>⁺}) of water oxygen around the Na⁺ cations. The red line corresponds to the bulk <i>g</i>_{<i>OW</i>−<i>Na</i>⁺} and the blue line was determined considering only the Na⁺s that localized to the minor groove. Inset: snapshot from the simulations showing the localization of a hydrated Na⁺ to the minor groove.</p

A single trajectory snapshot of a 3 × 3 × 3 <i>μ</i>m³ actomyosin system simulation at R_α:a = 0.1 and R_m:a = 0.02 after 500 s of network evolution.

<p>Actin filament cylinders are colored by their angle with respect to the x-y plane.</p

MSD analysis of actin filaments in simulation.

<p>(A) MSD over time for various values of <i>χ</i>. Error bars represent the standard error of the MSD, for each set of trajectories, are smaller than the data points. (B) Diffusion exponent <i>ν</i> acquired from a log-log linear fit of (A). Error bars represent the standard linear regression error in <i>ν</i>.</p

Actomyosin network R_g,f/R_g,i over time for various R_α:a with fixed R_m:a = 0.01.

<p>We see that above a threshold <i>α</i>-actinin concentration, contraction is observed, and the time of bundle formation for these contractile structure formations decreases with increasing <i>α</i>-actinin concentration. Standard deviations of the <i>R</i>_g,f/<i>R</i>_g,i values over all trajectories are shaded.</p