Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks
Figure 3
Different modes of stabilization of central β barrel in TIM Barrel families.
(a) The cartoon shows the residues involved in the conserved cluster of interactions (f–PEN–30(1.0)) in the C1A family. The residues that are involved in these conserved interactions are highlighted in spheres with blue for basic and red for acidic residues (the representative protein being d1p1xa_). (b) The entropy based conservation indices (EC) (obtained from family specific MSSAs (see Methods section)) for residues involved in long range β/β interactions in f–PEN–15(0.8) are given. (c) The cartoon shows the residues involved in low–energy contiguous β barrel interactions formed by the side–chains of residues from adjacent β strands in DC (c.1.2.3) family. The residues that are involved in these conserved interactions are highlighted in spheres with white for hydrophobic and green for polar residues (the representative protein being d1x1za1). Few polar/charged residues (blue) forms vdW interactions with other residues inside the barrel. (d) The ECs for the residues involved in contiguous hydrophobic stabilization of the β barrel (obtained from f–ljPEN–7(1.0)) are given. The TIM barrels in (a) and (d) are depicted at an orientation similar to Figure 1a.