Molecular representations and length scales of ClpY and p97. (a) Side view of ClpY (green) with two subunits removed for clarity. The central pore loops are highlighted in blue and the substrate protein is represented using orange for the SsrA degradation tag, and magenta for the helical bundle protein (HBP). The SP C-terminus bead is shown in red and the N-terminus bead in blue. The directionality of allostery is indicated by the arrows where black (red) corresponds to (counter)clockwise motions. (b) Side view of p97 with two subunits removed for clarity. The D1 domain is highlighted in yellow, the D2 domain in green, and the N domain in orange. (c) Top view of ClpY indicating the change in azimuthal angles between the open (blue) and closed (cyan) conformations of the pore (d) Side view of three subunits of ClpY indicating the axial displacement of individual loop residues during allosteric motions.
Translocase activity of ClpY and p97. Average substrate protein contour length translocated as a function of time in (a) CW (black), CCW (red), and R (green) allosteric cycles of ClpY and (b) CW (black) and CCW (red) allosteric cycles of p97. The unit of time is the duration of one allosteric cycle (Γ).
Substrate protein interaction with ClpY in consecutive allosteric steps. Probability density map of interaction energy between the SP and active subunits in CW (column 1), CCW (column 2), and R (column 3) intra-ring subunit motions for allosteric steps one and two (row 1), steps two and three (row 2), and steps three and four (row 3).
Translocase activity of ClpY via directional processing. The HBP chain length translocated through the ClpY pore is shown as a function of time for individual simulation trajectories (indicated by blue, green, or red curves) in (a) clockwise, (b) counterclockwise, and (c) random simulations. Transitions correspond to translocation of the SsrA degradation tag and part of the C-terminus helix of HBP.
Kinetics of SP unfolding in allosteric cycles of ClpY. Probability distribution of the fraction of native contacts Q N in CW (black), CCW (red), and R (green) allostery at (a) t = 0.5 Γ and (b) t = 5.0 Γ.
Asymmetric chiral handling of the SP by ClpY and p97. The probability distribution of torque in ClpY for CW (black), CCW (red), and R (green) allostery for allosteric steps (a) one and two, (b) two and three, and (c) three and four. The probability distribution of torque in p97 for CW (black) and CCW (red) allostery for allosteric steps (d) one and two, (e) two and three, and (f) three and four.
Reaction kinetics and conformational states of substrate protein during unfolding and translocation mediated by p97. The probability density map of the fraction of native contacts (Q N ) versus the radius of gyration (R g ) of HBP is shown in allosteric cycles of p97, in (a) clockwise and (b) counterclockwise motions.
Cross-correlation of the probability of SP binding (E ⩽ −8 kcal/mol) to active loops in consecutive allosteric steps of ClpY.
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