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Dipole-induced self-assembly of helical -peptides
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10.1063/1.2928700
/content/aip/journal/jcp/129/1/10.1063/1.2928700
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/1/10.1063/1.2928700

Figures

Image of FIG. 1.
FIG. 1.

One of the -peptides considered in this work is the ten-residue . On the top is the chemical structure of the peptide. It forms a 14-helix and has been reported to exhibit a liquid crystalline phase (Ref. 12). On the bottom is a representation of the peptide with the backbone in black, the cyclic residues in green, the -homolysine residues in blue, and the -homotyrosine residue in red.

Image of FIG. 2.
FIG. 2.

Some of the possible helices for -peptides. The helix is named by the number of atoms between the hydrogen bond. For example, a 14-helix has 14 atoms between and .

Image of FIG. 3.
FIG. 3.

The reaction coordinates used in this paper. The backbone is shown as sticks, and the spheres represent the atoms used to define the reaction coordinates. is defined as the separation between the nitrogen on the N-terminus (orange) and the carbonyl carbon of the C-terminus (yellow). is defined as the distance between the carbons of the fifth residue (purple) for each residue.

Image of FIG. 4.
FIG. 4.

PMF [ top] and number of H-14 hydrogen bonds (bottom) of a single molecule of -peptide 5 in implicit water as a function of distance from EXEDOS simulations. This peptide shows a clear minimum near corresponding to a 14-helix. For the number of bonds, we are excluding those hydrogen bonds to N- and C-terminal residues.

Image of FIG. 5.
FIG. 5.

PMF [ top] and directional cosine ( bottom) between two molecules of -peptide 5. The solid lines represent the atomistic results, and the dashed lines the coarse-grained model.

Image of FIG. 6.
FIG. 6.

Representative configuration of two molecules of -peptide 5 oriented in a head-to-tail, end-to-end orientation (left) and a side-by-side orientation (right). The end-to-end orientation is the optimal arrangement calculated from EXEDOS simulations between two peptides. The c.m. of these two peptides are separated by approximately . Coloring is similar to Fig. 1.

Image of FIG. 7.
FIG. 7.

PMF and the entropic and energetic contributions for two molecules of -peptide 5 in an implicit solvent. The energetic contribution is quite similar for the end-to-end and side-by-side orientations, but the entropic penalty is greater for the side-by-side arrangement of the two peptides than for the end-to-end arrangement.

Image of FIG. 8.
FIG. 8.

Contributions to the potential energy between two molecules of -peptide 5 as a function of separation. Shown here is the total energy, the Lennard–Jones energy, and the electrostatic energy. The electrostatic potential is the dominant contribution to the overall potential.

Image of FIG. 9.
FIG. 9.

The stability of two molecules of -peptide 5 as a function of separation is shown by monitoring the average number of hydrogen bonds of each peptide during EXEDOS simulations.

Image of FIG. 10.
FIG. 10.

Coarse-grained representation of the -peptide: two-point-dipole interaction site for electrostatics and two beads for hydrodynamics.

Image of FIG. 11.
FIG. 11.

c.m. MSD (top) and average cluster size (bottom) as a function of the time for different concentrations and .

Image of FIG. 12.
FIG. 12.

c.m. MSD (top) and average cluster size (bottom) as a function of the time for different concentrations and .

Image of FIG. 13.
FIG. 13.

Radial distribution function as a function of the distance for different concentrations. Solid lines are for the and dashed lines are for .

Image of FIG. 14.
FIG. 14.

Probability of two peptide 5 in a specific orientation at 0.8, 1.25, and at a concentration of and .

Image of FIG. 15.
FIG. 15.

Cluster moment of inertia , , and as a function of time for 10 and and .

Tables

Generic image for table
Table I.

Calculated dipole moments of various -peptides. A CHARMM-like force field was used with molecular dynamics simulations in an implicit solvent to generate multiple configurations over which to average the dipole moment. These values correspond to a temperature of .

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/content/aip/journal/jcp/129/1/10.1063/1.2928700
2008-07-02
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Dipole-induced self-assembly of helical β-peptides
http://aip.metastore.ingenta.com/content/aip/journal/jcp/129/1/10.1063/1.2928700
10.1063/1.2928700
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