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Density functional theory study of the conformational space of an infinitely long polypeptide chain
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10.1063/1.3207815
/content/aip/journal/jcp/131/8/10.1063/1.3207815
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/8/10.1063/1.3207815

Figures

Image of FIG. 1.
FIG. 1.

(a) Torsional angles typically used for describing backbone conformations. (b) Alternative description of the backbone conformation in terms of a rotation and a translation along the local chain axis . (c) Polyalanine inside the employed supercell. Dotted lines denote hydrogen bonds.

Image of FIG. 2.
FIG. 2.

Calculated potential energy surface (PES) of an infinite polyalanine chain as a function of the rotation and the translation along the chain axis. (a) PES connected to structures in which . (b) PES connected to structures in which or . Labels indicate the conformation connected to each minimum.

Image of FIG. 3.
FIG. 3.

(a) Minimum energy pathway projected on . Solid line, projection corresponding to PES A. Dotted line, projection corresponding to PES B. (b) values from residues in the set A averaged over intervals, with (dots). values along the minimum energy pathway of the PES in Fig. 2(a) (solid line). Dashed line indicates the transition between the helical and extended regions.

Image of FIG. 4.
FIG. 4.

Distribution of (, ) values obtained from an extended set of protein structures derived by x-ray crystallography. (a) Values from the set A of residues plotted over PES A. (b) Values from the set B of residues plotted over PES B. Dashed lines enclose sparsely populated regions in which DFT-PBE predicts that conformations should not be observed. These regions are populated by less than 0.5% of the analyzed residues.

Tables

Generic image for table
Table I.

(, ) parameters connected to the minima of the potential energy surface shown in Fig. 2.

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/content/aip/journal/jcp/131/8/10.1063/1.3207815
2009-08-28
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Density functional theory study of the conformational space of an infinitely long polypeptide chain
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/8/10.1063/1.3207815
10.1063/1.3207815
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