Figure 7

Models used for generation of linker peptide between A1 and A2 domains, A) The A1 and A2 domains with missing linker peptide and the distance between the core residues Glu332 (A1 domain) and Pro379 (A2 domain) is shown. B) The top ten structures of the proposed linker peptide derived from clustering the last 30 ns of 100 ns MD trajectory are presented. Converged structures of isolated sequences C) Arg336-Met355 and D) Asn369-Lys380 in the linker peptide (based on 50 ns of MD simulations each) to demonstrate the reproducibility of the helical nature of the sequences is shown. E) The RMS deviations in the backbone (Cα) atoms during the simulations of the linker peptide model with reference to the starting structure are shown.