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Protein mechanical unfolding: A model with binary variables
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10.1063/1.2776271
/content/aip/journal/jcp/127/14/10.1063/1.2776271
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/14/10.1063/1.2776271

Figures

Image of FIG. 1.
FIG. 1.

Cartoon of the model protein, with a force applied to one of the free ends. Dots denote amino acids and dashed lines denote contacts.

Image of FIG. 2.
FIG. 2.

Panel (a): Average order parameter as a function of the external force , for different molecules: 1TIT (full line), 1COA (dotted line), 1I6C (dashed line), and 1BBL (dashed-dotted line). The temperature value is taken to be . Panel (b): Root mean square length of the same molecules as a function of the external force , with .

Image of FIG. 3.
FIG. 3.

Phase diagram of 1TIT (full line), 1COA (dotted line), 1I6C (dashed line), and 1BBL (dashed-dotted line). For each molecule, the curves are defined by . The lower-left region of the phase diagram corresponds to folded molecules, and the upper-right region corresponds to unfolded molecules.

Image of FIG. 4.
FIG. 4.

Panel (a): Free energy landscape as a function of the molecular elongation , at , for different molecules: 1TIT (full line), 1COA (dotted line), 1I6C (dashed line), and 1BBL (dashed-dotted line). Panel (b): Tilted free energy landscapes , with .

Image of FIG. 5.
FIG. 5.

Mean unfolding time as a function of the force, at , for four different molecules: boxes, 1I6C; triangles, 1BBL; circles, 1COA; and inset, 1TIT.

Image of FIG. 6.
FIG. 6.

Histograms of the unfolding time for the 1TIT molecule in a force clamp, at with forces (main figure) and (inset). The lines in the main figure are fits of the data to a log-normal function (full line) and to the function (9) (line points). The line in the inset corresponds to a fit to a negative exponential function.

Image of FIG. 7.
FIG. 7.

Panel (a): Mean first passage time at for the 1I6C molecule and for different temperatures (in K), as obtained by direct computer simulations (points) and by Eq. (10) (lines). Panel (b): Free energy landscape as a function of the molecule length , at , for different values of the force (in pN). Inset: Free energy landscape at .

Image of FIG. 8.
FIG. 8.

Panel (a): Plot of the typical unbinding force of the 1TIT molecule as a function of the pulling velocity , for the three values of the temperature. The lines are fits to the data in the linear regime defined by Eq. (11). From such fits one can obtain the characteristic unfolding length . We find for , for , and for . Panel (b): The lines are fits of the data to Eq. (12).

Image of FIG. 9.
FIG. 9.

Distribution of unfolding force under dynamical loading for the 1TIT molecule for (a) and (b) , with . The dotted line is a fit to Eq. (13).

Image of FIG. 10.
FIG. 10.

Unfolding length as a function of , as obtained from fits of the unfolding force probability distribution to Eq. (13), with , for the (a) 1COA and (b) 1TIT molecules.

Image of FIG. 11.
FIG. 11.

Reconstructed free energy landscape of the PIN1 (a) and the 1BBL (b) for . The lines correspond to the exact result. The pulling rate is expressed in units of .

Tables

Generic image for table
Table I.

Width and height of the energy barrier separating the two minima of the free energy , with and , for the molecules considered here.

Generic image for table
Table II.

Unfolding length , as given from linear fits to Eq. (8), for the molecules considered in this paper.

Generic image for table
Table III.

Unfolding length , as given from linear fits to Eq. (11), for the molecules considered in this paper.

Generic image for table
Table IV.

Unfolding length , barrier height , and characteristic exponent , as given from fits of the unfolding data with dynamic loading technique to Eq. (12).

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/content/aip/journal/jcp/127/14/10.1063/1.2776271
2007-10-12
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Protein mechanical unfolding: A model with binary variables
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/14/10.1063/1.2776271
10.1063/1.2776271
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