Additional file 3: of Variation in the ribosome interacting loop of the Sec61α from Giardia lamblia

Tertiary structure of GlSec61α obtained by homology modeling based on 2WWB (a & b) and 3J7Q (c & d), followed by molecular dynamic simulation for 30 ns, with (b & d) or without (a & c) docked RNA. Other details are same as those described in Fig. 1b. The corresponding RMSD graphs are shown below each structure. The templates used for modeling (2WWB and 3J7Q) had several other protein/peptide chains and RNA fragments, all of which exerted a constraint on the protein conformation. Thus, although the homology modeled structures resembled that conformation of the template, the above-mentioned constraints were absent in our simulations as only a fragment of the RNA was used for docking. As a result, during simulation, the structures relaxed in the first few nanoseconds and this resulted in a rise of the RMSD before subsequent stabilization. Hence observed increase of RMSD does not reflect any destabilization. (PPTX 1691 kb)