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Folding of a miniprotein with mixed fold
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10.1063/1.2753835
/content/aip/journal/jcp/127/3/10.1063/1.2753835
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/3/10.1063/1.2753835
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Figures

Image of FIG. 1.
FIG. 1.

Optimal overlap of a simulation structure from the minimum corresponding to the native structure and the experimental structure. Note that there are large fluctuations in both the turn and the strands of the hairpin, so that the native minimum turns out to be rather broad in the simulations [rendered with PYMOL (Ref. 21)].

Image of FIG. 2.
FIG. 2.

Specific heat curves for (a) FSD-EY with unmodified ECEPP/3 force field, (b) FSD-EY with ECEPP/3 and only the dihedral angle corrections, (c) FSD-EY with ECEPP and only the entropic correction term, and (d) FSD-EY with ECEPP and the full correction term as in Eq. (3). The curves were obtained using the multihistogram reweighting technique of Ferrenberg and Swendsen (Ref. 22).

Image of FIG. 3.
FIG. 3.

Helix content vs temperature for FSD-EY for (a) unmodified ECEPP/3 force field, (b) ECEPP/3 and only the dihedral angle corrections, (c) FSD-EY with ECEPP and only the entropic correction term, and (d) ECEPP/3 and the full correction term as in Eq. (3).

Image of FIG. 4.
FIG. 4.

Native population as a function of temperature for (a) FSD-EY under ECEPP/3 and only the dihedral angle corrections and (b) FSD-EY under the full correction term as in Eq. (3).

Image of FIG. 5.
FIG. 5.

One sequence of events which characterizes the folding process as observed in the simulations. The -terminal helix forms early and often consists of the entire sequence, as that state is the global minimum of energy for our potential. When the helix partially unfolds, however, some of the unfolded parts form hydrophobic contacts with the intact part of the helix. The system then gradually rearranges into a second minimum, corresponding to the experimentally observed native state.

Image of FIG. 6.
FIG. 6.

Free energy landscape for FSD-EY under the variant of the force field with maximum native population at , as a function of total energy and backbone RMSD . The contour lines are separated by . Observe that the free energy barriers are low, so that even if the native structure is a strong minimum, it has a low population. A wide variety of structures throughout this 2D projection are available at this temperature.

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/content/aip/journal/jcp/127/3/10.1063/1.2753835
2007-07-17
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Folding of a miniprotein with mixed fold
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/3/10.1063/1.2753835
10.1063/1.2753835
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