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Identification of key residues for protein conformational transition using elastic network model
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10.1063/1.3651480
/content/aip/journal/jcp/135/17/10.1063/1.3651480
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/17/10.1063/1.3651480
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Diagram of thermodynamic cycle.

Image of FIG. 2.
FIG. 2.

Results for Hsp 70 NBD. (a) Structural alignment of the closed (gray) with the open (colored) conformations. In the open structure, the four subdomains of Hsp 70 NBD are shown as different colors: IA (green), IB (purple), IIA (cyan) and IIB (yellow). (b) The locations of the central residues for the 15 residual clusters with relative high ΔΔG values (see panel (c)). These central residues are marked by their cluster number and shown as space filled circles. (c) ΔΔG values in response to residual perturbations. Number 1–15 denotes clusters of residues with high ΔΔG values centered at Thr13, Tyr41, Ala60, Phe92, Val105, Val119, Tyr149, Glu175, Gly202, Asp234, Arg258, Tyr288, Leu305, Ser340, and Asp366, respectively. (d) The intrinsic fluctuations of residues in the open structure of Hsp70 NBD. The 15 clusters of residues with high ΔΔG values were marked by the empty circles and the numbers 1–15.

Image of FIG. 3.
FIG. 3.

Results for pol β. (a) Structural alignment of the closed (gray) with the open (colored) conformations. In the open structure, the four subdomains of pol β are shown as different colors: 8 kD domain (purple), fingers (green), palm (cyan) and thumb (yellow). (b) The locations of the central residues for the 10 residual clusters with relative high ΔΔG values (see panel (c)). These central residues are marked by their cluster number and shown as space filled circles. (c) ΔΔG values in response to residual perturbations. Number 1–10 denotes clusters of residues with high ΔΔG values centered at Asn28, Tyr39, Arg102, Phe146, Ser180, Leu228, Gly237, Arg254, Ile277, and Glu335, respectively. (d) The intrinsic fluctuations of residues in the open structure of pol β. The 10 clusters of residues with high values were marked by the empty circles and the numbers 1–10.

Image of FIG. 4.
FIG. 4.

Fluctuation profiles of the slowest modes for the studied proteins. (a) and (b) display the fluctuation profiles in the first and the second slowest modes for Hsp 70 NBD, and (c) and (d) show the corresponding profiles for pol β, respectively. The global hinge sites at the crossover between anticorrelated domains are highlighted by filled triangles. The key functional residue clusters identified by our method are marked with open circles in the figure.

Image of FIG. 5.
FIG. 5.

Fluctuation profiles of the high frequency modes for the studied proteins. (a) and (b) display the mode shape as the average of the 18 fastest modes for Hsp 70 NBD and 8 fastes modes for pol β, respectively. The key functional residue clusters identified by our method are marked with open circles in the figure

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/content/aip/journal/jcp/135/17/10.1063/1.3651480
2011-11-01
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Identification of key residues for protein conformational transition using elastic network model
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/17/10.1063/1.3651480
10.1063/1.3651480
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