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Figure 3 | BMC Bioinformatics

Figure 3

From: Alignment of protein structures in the presence of domain motions

Figure 3

Alignment of two structures of GroEL from Thermus Thermophilus(1we3) and Escherichia Coli(1oel). (a) Superposition of the two structures on the first rigid body identified by RAPIDO (in blue, 1we3 is in darker colors while 1oel is in lighter colors). (b) Flexible superposition based on the rigid bodies identified by RAPIDO. Scissor symbols indicate the points in which the 1oel was divided in order to separately superpose the regions identified as rigid bodies (1st rigid body: 220 atoms, RMSD 0.81 Å; 2nd rigid body: 178 atoms, RMSD 0.93 Å; 3rd rigid body: 71 atoms, RMSD 1.04 Å; 4th rigid body: 20 atoms, RMSD 0.68 Å). (c) Flexible superposition generated by FlexProt (1st fragment: 122 atoms, RMSD 2.62 Å; 2nd fragment: 21 atoms, RMSD 3.02 Å; 3rd fragment: 193 atoms, RMSD 2.95 Å; 4th fragment: 177 atoms, RMSD 2.95 Å). (d) Flexible superposition generated by FATCAT (1st fragment: 186 atoms, RMSD 3.17 Å; 2nd fragment: 179 atoms, RMSD 0.96 Å; 3rd fragment: 153 atoms, RMSD 3.17 Å). (e) Mapping of the conserved domains identified by different methods onto the primary sequence. Residue numbers of domain boundaries in the E. Coli structure (1oel) as determined by RAPIDO are indicated; small flexible insertions within the domains have been left out for clarity.

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