Figure 1.
Histogram of the pairwise sequence identities for amongst 1,742 non-redundant CheW sequences.
The pairwise identity between the sequences i and j was calculated for
and
. All
values were binned in 1% bins and displayed in the histogram format.
Figure 2.
Mapping of sequence and structural similarity into the CheW structure.
A. Sequence similarity between E. coli CheW and T. maritima CheW (BLOSUM60) mapped to E. coli NMR structure. B. To measure structure similarity we measure the RMSD per residue between the selected homology model and the NMR structure of E. coli (left) and T. maritima (right).
Figure 3.
Comparison of the RMSDs between 20 homology models and 20 NMR structures.
Prior to the RMSD calculation of each pair, the structures were aligned, taking into consideration the backbone atoms of the residues that can be aligned without gap in the protein cheW from E. coli and T. maritima pairwise alignment. The selected residues for E. coli are: 7 to 72, 74 to 120, 123 to 151, and 154 to 161, while for T. maritima, all residues were included except 151. The RMSD values calculated for the same set of residues used in the alignment were calculated using the measure RMSD function of VMD.
Figure 4.
RMSD matrices comparing the similarity of each point of the homology-modeled trajectories with each point of the NMR trajectories for the α/β consensus regions. The top two matrices are for the MD simulations, and the bottom two are for the LBMC simulations. The small green dots in each graph indicate the lowest RMSD values.
Table 1.
RMSD values (Å) for MD simulation trajectories, from Figure 4.
Table 2.
RMSD values (Å) for LBMC simulation trajectories, from Figure 4.
Figure 5.
Structural Superimposition of Similar Models.
Superimposition of the most similar structure in the NMR trajectory (red) with the most similar structure in the homology-modeled trajectory (blue) for (A): E. coli MD simulation (RMSD = 0.8 Å), (B) E. coli LBMC simulation (RMSD = 1.0 Å), (C) T. maritima MD simulation (RMSD = 1.5 Å), and (D) T. maritima LBMC simulation (RMSD = 1.1 Å). The ribbon segments colored in green indicate the residues that are proposed to participate in protein-protein interactions (c.f. Supplementary Information: Table S1 in File S1).
Figure 6.
Histograms of the RMSD values comparing the NMR ensembles and MD/LBMC simulated trajectories.
Blue: RMSD values of the 20 homology models versus each other; Green: RMSD values of the 20 NMR structures versus each other; Red: RMSD values of the 20 homology models versus 20 NMR structures; Purple: RMSD values of every structure of the homology model simulation versus every structure of the NMR simulation, using LBMC; Cyan: RMSD values of every structure of the homology model simulation versus every structure of the NMR simulation, using MD. The vertical black line indicates the starting RMSD value between the homology model and the NMR structures simulated by MD or LBMC.