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Energy landscapes and global thermodynamics for alanine peptides
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10.1063/1.4813627
/content/aip/journal/jcp/139/12/10.1063/1.4813627
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4813627

Figures

Image of FIG. 1.
FIG. 1.

The alanine peptides studied in this work.

Image of FIG. 2.
FIG. 2.

Internal energy and heat capacity curves from MD PT (dashed line), MC PT (dotted line), and the harmonic superposition approximation (solid line) for alanine dipeptide.

Image of FIG. 3.
FIG. 3.

Internal energy and heat capacity curves from MD PT (dashed line), MC PT (dotted line), and the harmonic superposition approximation (solid line) for dialanine.

Image of FIG. 4.
FIG. 4.

Internal energy and heat capacity curves from MD PT (dashed line), MC PT (dotted line), and the harmonic superposition approximation (solid line) for tetra alanine.

Image of FIG. 5.
FIG. 5.

Convergence of the internal energy and heat capacity of tetra alanine using MD PT. The legend indicates the fraction of the total production data used.

Image of FIG. 6.
FIG. 6.

Convergence of the internal energy and heat capacity of tetra alanine using MC PT. The legend indicates the fraction of the total production data used.

Image of FIG. 7.
FIG. 7.

Global minimum conformations for the AMBER (in orange) and CHARMM (in blue) force fields aligned on backbone atoms. The RMSD of the backbone atoms is 0.078 Å, 0.75 Å, and 1.29 Å  for alanine diapeptide, dialanine, and tetra alanine, respectively.

Image of FIG. 8.
FIG. 8.

Disconnectivity graph for tetra alanine using the AMBER force field. Branches leading to the 27 minima with energies within 5 kcal/mol of the global minimum are coloured in red.

Image of FIG. 9.
FIG. 9.

Disconnectivity graph for tetra alanine using the CHARMM force field. The inset on the right shows the 77 minima within energies 5 kcal/mol of the global minimum. The global minimum funnel containing 43 minima is coloured in red. The global minimum conformation is at the bottom of the figure and a representative high energy minimum is shown at the top left.

Image of FIG. 10.
FIG. 10.

All 121 CHARMM minima (in blue, tube representation) that relax to the AMBER global minimum (all atom representation) when reoptimised for the AMBER force field for tetra alanine.

Image of FIG. 11.
FIG. 11.

Tetra alanine/CHARMM disconnectivity graph (Figure 9 ) redrawn to show only the 121 minima that relax to the AMBER global minimum.

Image of FIG. 12.
FIG. 12.

Convergence of the HSA internal energy and heat capacity of tetra alanine calculated for minima with energies below a given cutoff. The legend indicates the cutoff energy (in kcal/mol) followed by the number of minima included. For comparison, the MD parallel tempering results are shown as the dashed curves.

Image of FIG. 13.
FIG. 13.

Tetra alanine/AMBER disconnectivity graph including minima with a subset of C chiral centres in the D-form. All residues of minima in the black funnel (left most) are in the L-form; the N-terminal residue of the minima in the purple funnel is in the D-form, the rest being in the L-form; for the minima in the green funnel both N- and C-terminal residues are in the D-form; and for minima in the yellow funnel (right most) only the C-terminal residue is in the D-form. Graph created and plotted using PELE.

Tables

Generic image for table
Table I.

Slope (in /2) and vertical intercept (in kcal/mol) of linear fits to the internal energy curves.

Generic image for table
Table II.

Peak temperatures (Kelvin) in the heat capacity curves.

Generic image for table
Table III.

Statistics for the local energy minima used in computing thermodynamics via the harmonic superposition approach.

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/content/aip/journal/jcp/139/12/10.1063/1.4813627
2013-07-23
2014-04-20
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Energy landscapes and global thermodynamics for alanine peptides
http://aip.metastore.ingenta.com/content/aip/journal/jcp/139/12/10.1063/1.4813627
10.1063/1.4813627
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