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Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
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10.1063/1.3383244
/content/aip/journal/jcp/132/16/10.1063/1.3383244
http://aip.metastore.ingenta.com/content/aip/journal/jcp/132/16/10.1063/1.3383244

Figures

Image of FIG. 1.
FIG. 1.

Specific heat as a function of temperature for the 50 residue polyQ monomer averaged over three time intervals: 50–100, 100–150, and 150–200 ns.

Image of FIG. 2.
FIG. 2.

Specific heat as a function of temperature for the 30, 40, and 50 residue polyglutamine monomers, averaged over the 150–200 ns time interval of a 200 ns, 16 temperature REMD simulation.

Image of FIG. 3.
FIG. 3.

Various structures observed for diPQ40: (a) Random structure used as initial configuration, (b) two -helices which are formed in diPQ30, (c) perfect 32 Å nanotube (constructed from a similar structure for diPQ35 by adding five residues to the tail of each chain), [(d)–(g)] various -sheets, (h) antiparallel twisted triangular -helix, (i) defective 32 Å nanotube, and (j) lowest-energy 22 Å nanotube. Structure (d) is found in the pathway of formation of six-stranded beta forms i.e., [(e)–(g)] and structures [(e)–(j)] are found as the center of the largest clusters.

Image of FIG. 4.
FIG. 4.

Specific heat of diPQ30 (top left), diPQ35 (top right), diPQ37 (bottom left), and diPQ40 (bottom right) dimers as a function of temperature. The center of the dominant cluster of the 50–120 ns time interval (before the formation of the 22 Å—diameter nanotube in diPQ40) is also represented in all cases for various temperatures from left to right.

Image of FIG. 5.
FIG. 5.

Energies at 0 temperature as a function of various chain lengths of the dimers. Red: Two independent helices; cyan: Triangular forms. blue: 32 Å nanotube; green: -sheets; and black: 22 Å nanotube.

Image of FIG. 6.
FIG. 6.

One of the possible pathways to the nanotube formation for diPQ40 compared to the folding of diPQ30 to the helices. All structures for the diPQ40 pathway, except the last two, are generated on a single trajectory in a REMD simulation, as it moves in the 270–350 K range. The last two structures are generated without bias, as explained in the text, from the preceding imperfect -helix.

Tables

Generic image for table
Table I.

Structural properties of the dominant ordered structures found in the simulations for the dimers of 30, 35, 37, and 40 glutamine residues. For comparison, all properties—the -strand and -helical contents, the number of hydrogen bonds, and the number of side-chain-side-chain contacts—are normalized by the number of residues. Letters above the structures for diPQ40 refers to the structures shown in Fig. 3.

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/content/aip/journal/jcp/132/16/10.1063/1.3383244
2010-04-26
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/132/16/10.1063/1.3383244
10.1063/1.3383244
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