Figure 3
From: Integrating protein structural dynamics and evolutionary analysis with Bio3D
Cross-species normal modes analysis of DHFR. (A) Sequence conservation of the collected DHFR species. (B) Aligned fluctuation profiles for selected species of DHFR. Shaded blue regions depict areas discussed in the text showing different fluctuation patterns between specific species. The region shaded in light red depict the Met20 loop in E. coli DHFR and the corresponding loop in the remaining species. The location of major secondary structure elements in E. coli DHFR are also shown in the plot margins with β strands in gray and α helices in black. (C) A visual comparison of mode fluctuations between DHFR from E. coli and H. sapiens. Fluctuation magnitude is represented by thin to thick tube colored blue (low fluctuations), white (moderate fluctuations) to red (large fluctuations). See Additional file 3 for full details and corresponding code for this analysis.