Figure 1.
Illustration and Superposition of the Three States of DHFR
Red indicates occluded; green, open; and blue, closed. Five regions (loop10–23, helix 40–45, loop 64–71, loop116–121, and loop 142–149) near the active sites are highlighted.
Figure 2.
A Drawing of the Tertiary Structure of E. coli DHFR Taken from the Protein Data Bank and the Locations of the Proposed Folding Elements [5]
Four α-helices and eight β-strands are shown as ribbons. Proposed folding elements are light blue (1: Ser3~Ile14), green (2: Trp30~Leu36), red (3: Val40~Ser49), cyan (4: Arg57~Ser63), magenta (5: Glu80~Ala83), greenish-blue (6: Ile91~Leu104), orange (7: Ala107~Glu118), purple (8: His124~Phe125), and light purple (9: Val136~Ser138; and 10: Glu154~Ile155), respectively. The regions outside the folding elements form amino acid segments a–k (in yellow). The positions of the N- and C-termini are also indicated. Also see Table 1.
Table 1.
An Overview of the Performed Simulations
Figure 3.
(A) Comparison of the all-Cα atom RMSDs calculated from the MD trajectories for the folding element group, nonfolding element group, and the native DHFR at 300 °K during the 5-ns simulation (red: folding elements, green: nonfolding elements, blue: native DHFR).
(B) Comparison of the all-Cα atom RMSDs calculated from the MD trajectories for five folding element variants (a01, a02, a08, a08, and a10), five nonfolding element variants (b01, b04, b05, b08, and b09), and native DHFR at 300 °K during the 10-ns simulations (red: folding elements, green: nonfolding elements, blue: native DHFR).
(C) The comparison of RMSF for the folding element group, nonfolding element group, and the native DHFR averaged over 2.5- to 5.0-ns simulations (red: folding elements group, green: nonfolding elements group, blue: native DHFR). The blocks and numbers along the x-axis indicate the folding element region; see Figure 2 and Table 1 for reference.
Table 2.
Structural Variation of the MD Average Structures for the Native DHFR and Its Circular Permutation Variants
Figure 4.
Network-Bridging Effect of Ligand Binding
(A) Comparison of the closeness of native DHFR with and without cofactor binding. The blue line is the plot of the closeness of the apo form of DHFR, and the pink line is the closeness for the DHFR–cofactor complex.
(B) Clusters of docking solutions from patch-docking. The native cofactor is represented as colored spheres, and r1 and r2 are also located in the native binding site, but with different orientation. r3 is away from the binding site. Other docking solutions scattered around the DHFR surface in different regions.
(C) Average closeness change compared with DHFR after ligand binding into various surface patches; see Figure 3A.
Table 3.
The z-Scores of the Centrality for Key Residues
Figure 5.
Comparison of Network Centrality of the Crystal Structure (Blue Line) and MD Average Structure (Pink Line) for the Native DHFR
(A) Betweenness. (B) Closeness.
Figure 6.
The Change of Closeness for MD Average Structures for Folding and Nonfolding Groups
(A) z-Score of closeness for MD average wild-type DHFR structure (blue), averaged z-scores for the folding elements cutting group (pink), and averaged z-scores for the nonfolding elements cutting group (green).
(B) The changes of the z-scores of the two cutting groups compared with the z-score of closeness for the MD average wild-type DHFR structure.
(C) The differences of the z-scores of the folding element cutting group (a01, a02, a08, a08, and a10) and nonfolding element variants (b01, b04, b05, b08, and b09) averaged from 5-ns MD simulations and 10-ns simulations. The dynamics effects are in the functional loop regions.
Figure 7.
An Illustration of the Difference between Backbone-Connected Contact and Nonbonded Contact
The peptide backbone-linked connections are shown as solid arrows, and the nonbonded packing is shown as dashed arrows.