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