Molecular Dynamics of the UPF proteins from H. sapiens and U. maydis.

A) Graphic representation of the RMS calculated for the superposed structures of hUPF1 and umUPF1. A structural alignment was generated for the hUPF1 crystal 2IYK and the model generated for umUPF1. Each amino acid of the umUPF1 protein is colored accordingly to its RMS backbone deviation from the corresponding residue in hUPF1. The scale goes from dark blue for good superposition to red where superposition is poor (Swissmodel). B) Radius of gyration (Rg). Black line corresponds to U. maydis and red line for H. sapiens during the simulation of 10ns at 300K. C) RMSD plot. Root mean square deviation of backbone atoms shown as a function of time for the structure reported for hUPF1 (red, PDB ID: 2iyk) and the modeled structure for umUPF1 (black) during the simulation of 10ns at 300K. D) RMSF plot. Root mean square fluctuations of carbon alpha residues were calculated over time during 10ns simulation at 300K for both hUPF1 (red) and umUPF1 (black).