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Proteins in a shear flow
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10.1063/1.2795725
/content/aip/journal/jcp/127/15/10.1063/1.2795725
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2795725
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Reduced diffusion coefficient as a function of a hydrodynamic radius of an amino acid. The horizontal line marks the experimental value .

Image of FIG. 2.
FIG. 2.

(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.

Image of FIG. 3.
FIG. 3.

(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.

Image of FIG. 4.
FIG. 4.

(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.

Image of FIG. 5.
FIG. 5.

Same as in the lower panel of Fig. 4 but for .

Image of FIG. 6.
FIG. 6.

Histogram of RMSD for the helix (48 residues) in a shear flow at .

Image of FIG. 7.
FIG. 7.

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.

Image of FIG. 8.
FIG. 8.

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.

Image of FIG. 9.
FIG. 9.

(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).

Image of FIG. 10.
FIG. 10.

Same as in Fig. 9 but for

Image of FIG. 11.
FIG. 11.

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 .

Image of FIG. 12.
FIG. 12.

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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/content/aip/journal/jcp/127/15/10.1063/1.2795725
2007-10-18
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Proteins in a shear flow
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2795725
10.1063/1.2795725
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