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Effects of surface interactions on peptide aggregate morphology
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10.1063/1.3624929
/content/aip/journal/jcp/135/8/10.1063/1.3624929
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/8/10.1063/1.3624929
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

The elements of the model used are depicted: the peptide, the surface, and the repulsive ceiling potential. The peptide model consists of two backbone interaction centers per residue (X and Y), hydrophobic side chains (H), polar side chains (P), cationic (C), and anionic (A) side chains with charges +e and −e, respectively, and end caps (E).

Image of FIG. 2.
FIG. 2.

Phase plots showing dominant aggregate morphologies observed in equilibrium within simulated temperature ranges for each parameter set {ε, K χ}. Part (a) is with K χ = 1kcal/mol and (b) is with K χ = 2kcal/mol. Regions outside of the lines are not sampled in our simulations. The data at the bottom of each panel are from a previous study (Ref. 61) with no surface (i.e., in the bulk) and are shown for comparison. The following abbreviations are used: (L1) single layers on surface, (L2) double layers on surface, (L1/Am) single layers with attached amorphous aggregates, (B1) binding phase: a coexistence state of amorphous aggregates in the bulk and single- or multi-layered aggregates on the surface, frequently with large amorphous aggregates attached to them, (B2) alternate binding phase: a coexistence state of peptides scattered individually or part of small aggregates in the bulk and single-layered aggregates on the surface, (Am) amorphous aggregates in bulk, (Fi) fibrillar structures in bulk, and (Be) β-barrel structures in bulk. Visualizations of these states are shown in Fig. 3 and supplementary material (Ref. 62).

Image of FIG. 3.
FIG. 3.

A visualization of the most common equilibrium phases observed in our simulations. The following abbreviations are used: (L1) single layers on surface, (L2) double layers on surface, (L1/Am) single layers with attached amorphous aggregates, (B1) binding phase: a coexistence state of amorphous aggregates in the bulk and single- or multi-layered aggregates on the surface, frequently with large amorphous aggregates attached to them, (B2) alternate binding phase: a coexistence state of peptides scattered individually or part of small aggregates in the bulk and single-layered aggregates on the surface, and (Am) amorphous aggregates in bulk. The binding phase states B1 and B2 differ by the presence of amorphous aggregates observed and the existence of multi-layered aggregates in type B1 but not type B2. Larger images of these structures, and other structures observed, may be found in the supplementary material (Ref. 62).

Image of FIG. 4.
FIG. 4.

(a) Transition of the average height order parameter, z av. Units of ε and K χ are kcal/mol, suppressed in the plots for neatness. The point type gives the value of ε and the line type gives the value of K χ. (b) The heat capacity for two simulations with the weak surface attraction (ε = 0.30kcal/mol). Only two sets of parameters are compared for clarity. (c) The transition is shown in various order parameters (described in Sec. II E) normalized to their maximum value in the range of temperatures simulated. This simulation is for ε = 0.55kcal/mol and K χ = 1kcal/mol, but all other values of the parameters showed similar behavior.

Image of FIG. 5.
FIG. 5.

A summary of the binding transition temperatures for all parameter sets. Part (a) is for K χ = 1kcal/mol and part (b) is for K χ = 2kcal/mol. Both plots have the same scale. The “low,” “mid,” and “high” transition temperatures are judged from the bottom, middle, and top, respectively, of the regions of steepest slope in Fig. 4(a). These give an idea of the range over which the most rapid transition is taking place. The “free energy” transition is judged from plots of the free energy, see Fig. 7. The “half” transition temperature occurs when the average height is z av = 12.5 Å, precisely halfway to its maximum averaged value.

Image of FIG. 6.
FIG. 6.

The binding transition temperatures for varying surface attraction. This plot combines data from Figs. 5(a) and 5(b), assuming that increasing K χ from 1 to 2kcal/mol is equivalent to raising ε by 0.08kcal/mol.

Image of FIG. 7.
FIG. 7.

Plot of the free energy across the transition. Units of ε and K χ are kcal/mol, suppressed in the plots for neatness. The parameters used are (a) ε = 0.42kcal/mol and K χ = 2kcal/mol and (b) ε = 0.55kcal/mol and K χ = 2kcal/mol.

Image of FIG. 8.
FIG. 8.

Transition of the average height order parameter, with data for the model with full peptide-peptide interactions (“int”) and a simplified model with peptide-peptide interactions removed (“no int”). Units of K χ are kcal/mol, suppressed in the plot for neatness. These simulations have a surface attraction of ε = 0.55kcal/mol.

Image of FIG. 9.
FIG. 9.

Plots of the transition in the peptide mean height order parameter, z av. Units of ε and εLJ are kcal/mol, suppressed in the plots for neatness. Part (a) fits simulation results (data points, also in Fig. 4(a)) for K χ = 1kcal/mol with the zeroth order approximation of a peptide-surface interaction (solid or dashed curves): a Lennard-Jones surface density interacting with a peptide interaction center. The zeroth order fits choose a value of εLJ such that they cross at the halfway point of the transition (see Sec. ???). Part (b) fits the equivalent zeroth order approximation to simplified results of noninteracting peptide simulations (where all peptide-peptide interactions are removed).

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/content/aip/journal/jcp/135/8/10.1063/1.3624929
2011-08-24
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Effects of surface interactions on peptide aggregate morphology
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/8/10.1063/1.3624929
10.1063/1.3624929
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