(a) X-ray structure of ubiquitin (PDB accession code 1UBI).

Abstract

<p>The lower view is rotated 90 around the horizontal axis with respect to the upper view. Helices are colored red, and beta strands green. Note that the beta strands 1 and 5 are closest to the N- and C- termini respectively, and thus the interaction between them is the primary determinant of the protein's mechanical stability against stretching from the termini. (b) The network representing the inter-residue forces for ubiquitin, averaged over 100 ns of molecular dynamics simulations, superimposed on the 3D structure of the protein. The color and width of cylinders connecting residue pairs correspond to the direction and magnitude of the mean inter-residue force: blue for repulsive force, red for attractive force, and the maximum width corresponding to a force magnitude of pN. (c) A circle graph representation of the prestress network in (b). Numbers around the circumference are residue indices. Colored arcs correspond to secondary structure: alpha helix (red), beta strand (green), hydrogen-bonded loop (purple) and 3–10 helix (cyan).</p