Force-Extension curve of the (Ala) chain (<i>grey dots</i>).

<p>The average is shown in <i>blue</i>, and the fitting result of the worm-like-chain model is shown in <i>red</i>. A minimized root mean square residual error of 0.1 nN was obtained by nonlinear least square fitting.</p

How Fast Does a Signal Propagate through Proteins?

<div><p>As the molecular basis of signal propagation in the cell, proteins are regulated by perturbations, such as mechanical forces or ligand binding. The question arises how fast such a signal propagates through the protein molecular scaffold. As a first step, we have investigated numerically the dynamics of force propagation through a single (Ala) protein following a sudden increase in the stretching forces applied to its end termini. The force propagates along the backbone into the center of the chain on the picosecond scale. Both conformational and tension dynamics are found in good agreement with a coarse-grained theory of force propagation through semiflexible polymers. The speed of force propagation of 50Å ps⁻¹ derived from these simulations is likely to determine an upper speed limit of mechanical signal transfer in allosteric proteins or molecular machines.</p></div

Tension propagation from MD simulations and comparison to dynamic bead-spring and semiflexible chain models.

<p>(a) Tension evolution as predicted by a bead-spring model (colored curves) fitted to the tension in Ala as obtained from MD simulations (colored diamonds). Coloring red, yellow, green yellow, blue and purple show residue pairs 1–2, 4–5, 7–8, 10–11, 15–16 and 20–21, respectively. A manually reduced friction coefficient was used to map the WLC model and numerical results. We note that here forces were averaged over 100 fs time periods for clarity. (b) Tension evolution from the dynamic WLC model (colored curve) fitted to the tension in Ala as obtained from MD simulations (colored diamonds). Coloring and averaging as in (a). (c) Boundary layer size relative to the contour length obtained from MD simulations shown in <i>blue</i>. Numeric solution to the dynamic WLC model prediction in <i>green</i> and growth law in <i>black</i>. (d) Extension shown as <i>black dots</i> compared to two growth laws, in <i>blue</i> and in <i>red</i>.</p

Force propagation along a polypeptide in water.

<p>(a) After first equilibrating an (Ala) polypeptide under a relatively low stretching force of applied to both termini of the polypeptide, we then suddenly increase the stretching force by a factor of 10 to . As the polymer is straightened, backbone tension propagates from the two termini into the center of the chain. (b) Structure used in the MD simulation. The (Ala) polypeptide is surrounded by explicit solvent molecules. A constant force, or is applied to the terminal C- atoms, and the end-to-end distance of the peptide is measured.</p