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Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
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10.1063/1.3702195
/content/aip/journal/jcp/136/14/10.1063/1.3702195
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/14/10.1063/1.3702195

Figures

Image of FIG. 1.
FIG. 1.

The initial structure of Aβ17-42 protofibril used for molecular dynamics simulations and the final structure of Aβ17-42 protofibril obtained from the molecular dynamics simulations. For clarity, the peptides are represented by the NewCartoon model with different colors. The snapshots are plotted with the visual molecular dynamics (VMD) software (http://www.ks.uiuc.edu/Research/vmd/).

Image of FIG. 2.
FIG. 2.

Root mean square deviation (RMSD) from the initial structure for the heavy atoms as a function of simulation time.

Image of FIG. 3.
FIG. 3.

Binding free energy contribution of each residue of monomers (B, C, and D) in Aβ17-42 protofibril.

Image of FIG. 4.
FIG. 4.

The nonpolar contribution of each residue of monomer C in Aβ17-42 protofibril (a), and the nonpolar energies decomposed into the contributions of the main chain and the side chains of the peptide (b).

Image of FIG. 5.
FIG. 5.

The electrostatic contribution of each residue of monomer C in Aβ17-42 protofibril (a), and the electrostatic energies decomposed into the contributions of the main chain and the side chains of the peptide (b).

Tables

Generic image for table
Table I.

Binding free energy components of Aβ17-42 protofibril.

Generic image for table
Table II.

Binding free energy contribution of peptide fragments of Aβ17-42 monomer C.a

Generic image for table
Table III.

Hydrogen bonds occupancies.a,b

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/content/aip/journal/jcp/136/14/10.1063/1.3702195
2012-04-12
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Exploring the inter-molecular interactions in amyloid-β protofibril with molecular dynamics simulations and molecular mechanics Poisson-Boltzmann surface area free energy calculations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/14/10.1063/1.3702195
10.1063/1.3702195
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