1887
banner image
No data available.
Please log in to see this content.
You have no subscription access to this content.
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.
Pathways of mechanical unfolding of : Low force intermediates
Rent:
Rent this article for
USD
10.1063/1.3464476
/content/aip/journal/jcp/133/6/10.1063/1.3464476
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/6/10.1063/1.3464476

Figures

Image of FIG. 1.
FIG. 1.

Sketch of the native structure of (Protein Data Bank ID 1ttf) with -strands labeled A–G in sequence order. Figure generated by PyMOL.

Image of FIG. 2.
FIG. 2.

Free energy landscape at temperature and for forces (red line), (green line), and (blue line). .

Image of FIG. 3.
FIG. 3.

Mean unfolding time as a function of the force applied to the molecule (average over 100 different trajectories). The red line is a fit to Arrhenius’ law in the range of forces from 25 to 60 pN. In this range we find from the fit . The green line is a fit from 60 to 115 pN, .

Image of FIG. 4.
FIG. 4.

Unfolding pathways scheme of pulled by a constant force. Transitions denoted by red arrows have been observed only at low forces (40, 36, and 28 pN). Oblique red arrows represent refolding transitions.

Image of FIG. 5.
FIG. 5.

Typical MC trajectories: end-to-end length (red line) and a few order parameters as functions of time, with a . Green line: fraction of native contacts, whole . Blue line: fraction of native contacts between strands G and F. Purple line: fraction of native contacts between strands A and B. Cyan line: fraction of native contacts between strands C and F.

Image of FIG. 6.
FIG. 6.

Mixed AG-GF trajectory: MC time evolution of the end-to-end length (red line) and of some order parameters with a constant force of 28 pN. Colors as in Fig. 5

Image of FIG. 7.
FIG. 7.

Histograms of the intermediate life times for AG pathway (red line) and GF pathway (green line) at force . Data obtained from 3600 different trajectories. The lines are exponential fits.

Image of FIG. 8.
FIG. 8.

Histograms of the unfolding times at force . Data obtained from 5000 different trajectories and the bin size of the histogram is 1. The fit is to a lognormal distribution.

Image of FIG. 9.
FIG. 9.

Unfolding pathways scheme of pulled at constant velocity. Intermediate states in the full square boxes have a rupture force remarkably higher than those in dashed boxes.

Image of FIG. 10.
FIG. 10.

MC time evolution of the end-to-end length (red line) and of a few order parameters with a constant velocity of . Green line: weighted fraction of native contacts, whole . Blue line: weighted fraction of native contacts between strands G and F. Purple line: weighted fraction of native contacts between strands A and B. Cyan line: weighted fraction of native contacts between strands C and F.

Image of FIG. 11.
FIG. 11.

MC time evolution of end-to-end length (red line), force (yellow line), and of some order parameters with a constant velocity of for a mixed AG-GF trajectory. Green line: weighted fraction of native contacts, whole . Blue line: weighted fraction of native contacts between strands G and F. Purple line: weighted fraction of native contacts between strands A and B. Cyan line: weighted fraction of native contacts between strands C and F. Bins of 2000 MC steps have been used to reduce fluctuations in the plot.

Image of FIG. 12.
FIG. 12.

Distributions of the rupture forces of the native state at pulling velocity . Data obtained from 500 different trajectories; bin size of the histogram is 2. The fit is to Eq. (9).

Tables

Generic image for table
Table I.

Unfolding time , waiting phase life time , AG intermediate life time , and GF intermediate life time at different constant forces. Values are in MC steps and are approximated averages on 100 different trajectories at each force.

Generic image for table
Table II.

Relative frequencies of unfolding pathways at constant force. 100 trajectories for each value of the force.

Generic image for table
Table III.

Relative frequencies of unfolding pathways. 100 trajectories for each value of the velocity.

Generic image for table
Table IV.

Average rupture forces.

Loading

Article metrics loading...

/content/aip/journal/jcp/133/6/10.1063/1.3464476
2010-08-12
2014-04-20
Loading

Full text loading...

This is a required field
Please enter a valid email address
752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Pathways of mechanical unfolding of FnIII10: Low force intermediates
http://aip.metastore.ingenta.com/content/aip/journal/jcp/133/6/10.1063/1.3464476
10.1063/1.3464476
SEARCH_EXPAND_ITEM