Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations

Abstract

The Escherichia coli chaperonin GroEL, which helps proteins to fold, consists of two heptameric rings stacked back-to-back. During the reaction cycle GroEL undergoes a series of allosteric transitions triggered by ligand (substrate protein, ATP, and the cochaperonin GroES) binding. Based on an elastic network model of the bullet-shaped double-ring chaperonin GroEL-(ADP)(7)-GroES structure (R''T state), we perform a normal mode analysis to explore the energetically favorable collective motions encoded in the R''T structure. By comparing each normal mode with the observed conformational changes in the R''T --> TR'' transition, a single dominant normal mode provides a simple description of this highly intricate allosteric transition. A detailed analysis of this relatively high-frequency mode describes the structural and dynamic changes that underlie the positive intra-ring and negative inter-ring cooperativity. The dynamics embedded in the dominant mode entails highly concerted structural motions with approximate preservation of sevenfold symmetry within each ring and negatively correlated ones between the two rings. The dominant normal mode (in comparison with the other modes) is robust to parametric perturbations caused by sequence variations, which validates its functional importance. Response of the dominant mode to local changes that mimic mutations using the structural perturbation method technique leads to a wiring diagram that identifies a network of key residues that regulate the allosteric transitions. Many of these residues are located in intersubunit interfaces, and may therefore play a critical role in transmitting allosteric signals between subunits.

FIGURE 1

Dependence of B-factors fitting and the maximal overlap on R_c. The cross-correlation coefficient between the calculated B-factors based on the ENM and the crystallographic B-values is shown by the top line. The bottom line shows the maximal overlap between each mode and the observed R″T → TR″ conformational changes in GroEL, which is defined as Interestingly, for both quantities, R_c = 10 Å is the optimal value.

FIGURE 2

Mode-dependent variations of key factors in the allosteric transitions in GroEL. The top panel shows the overlap with the observed R″T → TR″ transition for the lowest 50 modes. The middle panel gives the robustness score based on the eigenvalue (f_δE) for the lowest 50 modes. The bottom panel displays the robustness score based on the eigenvector (f_δv) for the lowest 50 modes. Nonzero mode number starts from 1. Low values of the dimensionless robustness scores mean high robustness (see Methods for details). The coincidence of the modes that are important to the allosteric transition (with high overlap values) and the modes that are most robust (with low values of the robustness scores) is shown by the arrows (including modes 3, 8, 17, 18).

FIGURE 3

Amplitude of the eigenvector of mode 18 (green for trans-ring, red for cis-ring) and the observed trans-cis-swapping transition (blue) as a function of residue position. Displacement amplitudes at seven subunits of trans- and cis-rings are overlaid in the same panel. The locations of the domains are: A domain (191–376), E domain (6–133, 409–548), I domain (134–190, 377–408). The superposition of the amplitudes for the seven subunits is indicative of the concerted nature of the allosteric transitions (see a similar plot in Yang 2006 (42)).

FIGURE 4

Structural displacements (from blue to red) as predicted by mode 18. (a) This shows the side view (perpendicular to the central axis) for one trans-ring subunit (chain H). (b) The side view for cis-ring subunit of chain A is shown using the ribbon diagram. (c) Structural representation of the double-ring complex is displayed. The boxes enclose a single subunit from cis- and trans-ring as shown in panels a and b. The arrows give the two viewing directions for panels d and e. (d) The structure shows the top view (along the central axis) for the apical domains of cis-ring. The clockwise rotation of the A domains are indicated. (e) We show a bottom view for the apical domains of trans-ring with explicit counterclockwise rotation of the A domains.

FIGURE 5

Some key residues in the allostery wiring diagram for GroEL determined using the SPM are overlaid in the structure. Residues with high-δω for mode 18 (spheres in red and orange) involved in intersubunit contacts in trans-ring subunits (green) and cis-ring subunits (blue) are explicitly shown. For clarity, only three subunits from each ring are shown.