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Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study
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10.1063/1.2796165
/content/aip/journal/jcp/127/16/10.1063/1.2796165
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/16/10.1063/1.2796165

Figures

Image of FIG. 1.
FIG. 1.

Root mean square deviation of different structural fragments of ubiquitin at —from (A) to (G) we have RMSD values obtained in the simulation of ubiquitin—(A) , (B) , (C) , (D) , (E) , (F) -helix, and (G) helix.

Image of FIG. 2.
FIG. 2.

Correlation matrix of ubiquitin obtained at averaged over total simulation time. Cross-correlation matrix or covariance of atoms of ubiquitin calculated from explicit water simulation, value of correlation between the atoms decreases from black to white, and different ranges of the values are indicated in the adjacent column. The secondary structures are marked along the two axes.

Image of FIG. 3.
FIG. 3.

Root mean square deviation of three important structural fragments of melittin as a function of simulation time.

Image of FIG. 4.
FIG. 4.

Correlation matrix of melittin obtained at averaged over total simulation time. Cross-correlation matrix or covariance of atoms of melittin calculated from explicit water simulation, value of correlation between the atoms decreases from black to white, and different ranges of the values are indicated in the adjacent column. The secondary structures are marked along the two axes.

Image of FIG. 5.
FIG. 5.

Potential energy landscape of ubiquitin (three state)—three-dimensional (3D) representation. At the bottom of the 3D diagram, motion of the Ubiquitin molecule in one of the three trajectories is projected as a function of RMSD and .

Image of FIG. 6.
FIG. 6.

Potential energy landscape of melittin (multistate)—three-dimensional representation.

Tables

Generic image for table
Table I.

Survival times of the H bonds that are between different secondary structural fragments of ubiquitin. (SC denotes side chain.)

Generic image for table
Table II.

Survival times of the H bonds that are not only between different secondary structural fragments of ubiquitin. (SC denotes side chain.)

Generic image for table
Table III.

Survival times of the H bonds of melittin.

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/content/aip/journal/jcp/127/16/10.1063/1.2796165
2007-10-29
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Application of principal component analysis in protein unfolding: An all-atom molecular dynamics simulation study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/16/10.1063/1.2796165
10.1063/1.2796165
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