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Figure 4 Topologies constructed by SolarTC 2. (a) No backbone (simply connected topology produced by LMST), (b) 2-connected backbone, (c) simply connected backbone, and (d) disconnected backbone.

In an effort to contribute to the understanding of the conformational features of NUPR1 and to provide clues on amino acid interactions in disordered states of proteins, we measured the pKa values of all its acidic groups (aspartic and glutamic residues, and backbone C terminus) by using NMR spectroscopy at low (100 mM) and high (500 mM) NaCl concentration.

Open image in new window Fig. 1 Structures of a a spirostane backbone, b an isospirostane backbone, c a furostane backbone, d a pregnane backbone, e a cholestane backone, a glucopyranosyl moiety (Glcp), a galactopyranosyl moiety (Galp), a rhamnopyranosyl moiety (Rhap), a frutofuranosyl moiety (Furf) and an arabinopyranosyl moiety.

The similarity in geometry of the docked pose to the original was assessed in terms of RMSD of the position of the backbone C and N atoms of two poses, calculated using MOE [37].

We have shown that although the reactive groups are different for amino acids, this difference is encapsulated in the backbone C β atoms.

Although the reactive groups are different for amino acids, we show that this difference is encapsulated in the backbone C β atoms.

Backbone C-alpha bonds trajectories were obtained using g_covar and g_anaeig of gromacs utilities.

Secondary backbone C-chemical shifts of PLK4-PB3 (dark blue) and PLK4-PB3 as part of the PLK4-PB3/STIL CC complex (light blue) and their differences (black), plotted against the amino acid residue number of PLK4-PB3.

Bisphosphonates have a common P C P backbone, where C is carbon and P represents a phosphonate group.

Consistent with this view, comparisons of C-helix "in" (active) and C-helix "out" (inactive) conformations indicates loss of capping interaction between p.R776105PKA side-chain and C-helix backbone upon C-helix movement (Fig. 6B).

The hydrogen bonds between the backbone NH (C'O) groups and the C'O (NH) groups on each side of them are disallowed.