Energy Landscape of Pentapeptides in a Higher-Order Conformational Subspace

Figure 2

The disconnectivity graphs of the potential energy surfaces in the principal conformational space of pentapeptide segments (a), thermodynamic propensities (at 298 K) superposed on the potential energy slice corresponding to the dominant energy valley (b), superposition of respective sequences on these slices (c) (in green), and Ramachandran plots of dominant energy valleys (d) for the penta-alanine (1), pentaglycine (2), and Val.Asn.Thr.Phe.Val (3) sequences. The disconnectivity graphs (a) are offset relative to the respective global minima; minima are labelled with their secondary structure classification based on position on the Ramachandran plot (per residue: H indicates helix and E an extended sheet while n indicates nonavailable secondary structure classification). Minima corresponding to the two valleys with the highest propensities are coloured in green and orange. Inset: the distribution within energy intervals of the disconnectivity plots. The thermodynamic propensities (b) are superposed on the potential energy slice closest to the minimum of the highest propensity energy valley (shown in green). The predominant secondary structure classification of each energy valley is indicated. The density of the five pairs of the structures within the predominant energy valleys is superposed on the Ramachandran plots of the raw dataset (d) in respective colours while the density contours of raw data are shown in black.