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Simple model for the simulation of peptide folding and aggregation with different sequences
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10.1063/1.4725883
/content/aip/journal/jcp/136/21/10.1063/1.4725883
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/21/10.1063/1.4725883

Figures

Image of FIG. 1.
FIG. 1.

Representation of some of the energetic contributions of our adapted hydrophobic interaction (green), compared to the original work by Brown and co-workers (blue).6 (a) Sequence-dependent long-range term for the hydrophobic–hydrophobic interactions. (b) Stiffness term associated to the torsional virtual angle between four consecutive α-carbons, compared to the turn-type interaction of the former work.6

Image of FIG. 2.
FIG. 2.

Schematic description of the relative arrangement of hydrophobic (blue) and hydrophilic (red) residues for (a) a helical fragment of sequence L 2 BL 2 B 2, and (b) a β-sheet where each chains' sequence is (LB)2 L.

Image of FIG. 3.
FIG. 3.

Cartoon representations of the most representative configurations found in our simulations of α-prone systems (left, structures (a), (b), and (c)) and β-prone systems (right, structures (d) and (e)). (a) Three-helix bundle. (b) β-sheet interacting with one helix. (c) Isolated α-helices (from helical sequence). (d) β-sandwich. (e) Isolated α-helices (from β-prone sequences).

Image of FIG. 4.
FIG. 4.

Thermodynamic and structural data of the helical-prone system for two different concentrations, a “diluted” (0.2 residue mol/L) and a “concentrated” one (2.0 residue mol/L). (a) Heat capacity curves versus temperature for the two concentrations. (b) Thermal evolution of the population of the different structures (helical bundles, β-type, independent helices, and unstructured configurations) found in the diluted system. (c) Thermal evolution of the population of the observed structures in the concentrated system.

Image of FIG. 5.
FIG. 5.

Thermodynamic and structural data of the β-prone system at a “diluted concentration” (0.2 residue mol/L) and a “concentrated” one (2.0 residue mol/L). (a) Heat capacity curves versus temperature. (b) Thermal evolution of the population of the different structures (β-sandwich, independent helices, and unstructured configurations) found in the diluted system. (c) Thermal evolution of the population of the observed structures in the concentrated system.

Image of FIG. 6.
FIG. 6.

Schematic structural phase diagram for multichain peptides according to our simulation model. (a) α-forming peptides. (b) β-prone peptides.

Tables

Generic image for table
Table I.

Optimal ranges for the three geometrical restrictions chosen in our model for backbone hydrogen bonds.

Generic image for table
Table II.

Values of the parameters for the sequence-dependent terms of E hp . The right hand side contains the values that σ int , S 1, and S 2 take depending on the kind of the interaction (note that the two latter quantities are adimensional).

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/content/aip/journal/jcp/136/21/10.1063/1.4725883
2012-06-07
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Simple model for the simulation of peptide folding and aggregation with different sequences
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/21/10.1063/1.4725883
10.1063/1.4725883
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