Reduced diffusion coefficient as a function of a hydrodynamic radius of an amino acid. The horizontal line marks the experimental value .
(Color) Example of cycle of the motion of a tethered protein in shear flow: integrin at . The anchoring point (C terminus) is marked by a circle.
(Color) Example of cycle of the motion of a free protein in shear flow: integrin at . For tracing purposes, half of the chain is colored red, and another half is colored green.
(Color) Integrin tethered by the C terminus. (Upper) Examples of the time evolution of the RMSD from the native structure in unfolding of integrin in a uniform flow for various flow rates. The plateaus correspond to successive stationary conformations (intermediates) marked by the letters (A)–(E). The snapshots of conformations A, B, D, and E are shown on the right. (Lower) The histogram of RMSD for the integrin in a shear flow at . The respective values of RMSD corresponding to the intermediates seen in the upper panel are marked.
Same as in the lower panel of Fig. 4 but for .
Histogram of RMSD for the helix (48 residues) in a shear flow at .
Relative extension of the integrin molecule as a function of the Weissenberg number for a chain tethered by the C terminus (filled triangles), N terminus (empty triangles), and a free chain (squares). The average end-to-end distance of the molecule is normalized by the maximum extension length , where is the number of amino acids.
Power spectral density (psd) of the protein orientation angle for integrin tethered by the N terminus in a shear flow at . Frequencies are scaled by the protein folding time and the psd is normalized with its maximum value.
(Color online) Angle between the end-to-end direction of the protein and the direction of the flow (upper panel) and RMSD for integrin tethered by the C terminus in a shear flow at (lower panel).
Same as in Fig. 9 but for
Peak frequencies and derived from the power spectrum densities of orientation angle as a function of the Weissenberg number for integrin tethered by the C terminus (empty squares) and the N terminus (filled squares). The solid line corresponds to the relation .
Relative extension of ubiquitin anchored by the N terminus as a function of the Weissenberg number for the model without hydrodynamic interactions (filled triangles), and with hydrodynamic interactions for (open triangles) and (squares).
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