All-atom MD simulations of engaged PfSMC ATPase heads and DNA.

(A) A representative trajectory of all-atom MD. (Upper) Left and right depict the initial and final snapshots, respectively. (Lower) Time series of the number of hydrogen bonds between ATPase heads and DNA. (B) The fraction of hydrogen formation between amino acid residues in the ATPase heads and DNA. (C) A representative snapshot of the hydrogen-bond forming residues. (Left) Hydrogen bond network between the ATPase heads and DNA for representative basic residues. (Right) The hydrogen bond forming residues are positioned on the top surface of ATPase heads.

MD simulations for ATP-dependent conformational changes of SMC-ScpA complex.

(A) A representative trajectory of ATP-dependent conformational changes in the SMC complex by switching the reference structures in the AICG2+ model. (Top) Typical snapshots of SMC-ScpA complex for the disengaged (t = 0 step), engaged (t = 8.5×107 steps), V-shape (t = 1.2×108 steps), and disengaged (t = 1.8×108 steps) states. (Bottom) Times series of Q-scores for the disengaged and engaged structure, head-head distance, and hinge angle. The head-head distance is defined as the center of distance between two ATPase head domains. The hinge angle is calculated for three selected points; The center of mass of the hinge dimerization domain defines one point. The other two points are defined by the center of mass of the sequential 10 amino acid residues in the coiled-coil middle region for each chain. (B) Average distances between intermolecular amino acid residues with the same index number for the disengaged (red), engaged(blue), and V-shape (green) structures.

Identification of DNA binding sites in the SMC-ScpA complex.

(A) Top two panels plot the local average of charges defined as the moving average with a window size of 5 residues. Bottom panel plots the contact probability between DNA and SMC-ScpA complex. (B) DNA contact probability mapped on the SMC-ScpA structure. (C) A typical snapshot of DNA binding to the SMC-ScpA complex. (D) Upper panel plots timeseries of the distance between center of mass of the ATPase heads and DNA. Lower panel plots timeseries of the hydrogen-bond energy. (E-H) Representative snapshots during a DNA binding event to the top of the SMC ATPase heads.

SMC translocation along DNA via DNA-segment capture.

(A-D) A representative trajectory of DNA translocation by the SMC-ScpA complex coupled with the conformational change depending on the nucleotide states. The DNA reaches the hinge domain in the engaged state. (E-H) A representative trajectory of DNA translocation by the SMC-ScpA complex coupled with the conformational change depending on the nucleotide states. The DNA does not reach the hinge in the engaged state. (I-J) Time series of the DNA position where each SMC domain contacts with. DNA-Protein contacts at kleisin, ATPase heads, coiled-coil, and hinge domains are plotted in red, blue, green, and orange, respectively. (K) Analysis of translocation step size. (L) The length of the captured DNA segment in the engaged state for successful (left) and unsuccessful (right) translocation trajectories. (M) Q-scores, i.e., the fraction of native contacts, between the intermolecular coiled-coil arm and ATPase head domains, revealing the zipping motion of the coiled-coil arm when transitioning from the V-shape to the disengaged state. The coiled-coil arm was divided into three domains: hinge side (green), middle region (red), and ATPase heads side (blue).

Diverse DNA dynamics during ATP hydrolysis cycle.

The numbers at the top left represent the number of trajectories observed. (A) Initial configuration of the simulations. (B) The results of disengaged MD simulations. (C) The results of engaged MD simulations. Each simulation was restarted from the final snapshot of each disengaged MD simulation. (D) The results of V-shape MD simulations. Multiple simulations were conducted by restarting from the DNA-segment capture trajectories in the engaged state€) The results of disengaged MD simulations. The simulations were restarted from the V-shape conformations maintaining the DNA loop within the SMC ring.

Asymmetric kleisin path makes unidirectionality of SMC translocation.

(A) Typical snapshots of the moment when the SMC-ScpA complex captured a DNA segment within its ring structure in the engaged state. Particles marked in green on the ScpA indicate DNA patches. (B) Schematic figures highliting how the kleisin path determined the direction of translocation. (C) The spatial distribution of the DNA patch on the ScpA subunit.