User Stories:ROP four-helix bundle

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The A31P mutant of ROP forms a helix–turn–helix motif that homodimerizes to form a four-helix bundle. The asymmetric unit contains two copies of the helix–turn–helix motif (Glykos & Kokkinidis, 2003; Fig. 4b). The structure was originally solved with a 26-residue polyalanine single helix as the model and an extremely computationally intensive 23- dimensional Monte-Carlo search implemented in the program Queen of Spades (Glykos & Kokkinidis, 2001). The command script for the solution of the ROP four-helix bundle using the ‘automated MR’ mode of Phaser is shown in Appendix A2. The r.m.s. deviation for ROP is given as 1.0 Å ,since the sequence identity of the polyalanine helix is not a valid estimation of the r.m.s. deviation between the polyalanine helix and the backbone atoms of the ROP structure. The r.m.s. deviation value of 1.0 Å is a reasonable guess. Phaser produces eight solutions after a tree search with hundreds of branches, especially in the search for the second of the four helices. The eight solutions are nearly identical, differing only in the registration of the model to the structure helices (i.e. the Cα residues slip up or down the helix). All eight solutions generate a complete structure after model building with ARP/wARP (Perrakis et al., 2001). Although many potential solutions are stored in the intermediate stages of the search, the search itself is not computationally intensive.