SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path
- Department of Biophysics, Graduate School of Science, Kyoto University, Kitashirakawa Oiwakecho, Japan
Figures
Figure 1 with 3 supplements
All-atom molecular dynamics (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-bond 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.
Figure 1—figure supplement 1
Time series of the number of hydrogen bonds between PfSMC ATPase and DNA derived from all-atom molecular dynamics (MD) simulations.
Figure 1—figure supplement 2
Force field dependence of tendency of hydrogen-bond formation between SMC ATPase heads and DNA.
(A) Fraction of hydrogen bond using Amber ff19SB for protein, OL15 for DNA, and OPC model for water. (B) Fraction of hydrogen bond using Amber ff99SB-ILDN for proteins, Bsc1 for DNA, and TIP4PD model for water. (C) Fraction of hydrogen bond using Amber ff99SB-ILDN for protein, Bsc1 for DNA, and TIP3P model for water.
Figure 1—figure supplement 3
Probability distribution of the coarse-grained hydrogen-bond parameters, r, θ, and φ for frequently hydrogen-bond forming residues.
The red points are optimized hydrogen-bond parameters, which correspond to peak positions.
Figure 2
Modeling of a full-length PySMC–ScpA complex.
(A–D) Template structures for homology modeling of a full-length PySMC–ScpA complex. The regions ignored in the homology modeling are indicated by transparent. (E) A coarse-grained full-length PySMC–ScpA complex model where one amino acid is represented by one bead. (F) A homology model of the engaged ATPase heads based on a crystal structure (PDB code: 1xex). The coiled-coil arms connected to the ATPase heads are modeled based on the I-shaped SMC dimer model in panel A.
Figure 3
Molecular dynamics (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-to-head distance, and hinge angle. The head-to-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.
Figure 4 with 1 supplement
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 five 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.
Figure 4—figure supplement 1
DNA-binding sites in the SMC–ScpA complex where hydrogen-bond interactions on the ATPase heads are not incorporated.
(A) Top two panels plot the local average of charges defined as the moving average with window size of five 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. The DNA that binds to the ATPase heads does not migrate to the top, staying on the side surface of the ATPase heads. (D) A representative timeseries of the distance between center of mass of the ATPase heads and DNA. (E–H) Representative snapshots during a DNA-binding event to the SMC ATPase heads.
Figure 5 with 8 supplements
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, that is, 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).
Figure 5—figure supplement 1
An initial structure of DNA translocation simulations.
An 800-bp dsDNA was placed into the kleisin ring of the disengaged state of the SMC–ScpA complex.
Figure 5—figure supplement 2
Detail snapshots during DNA translocation via DNA-segment capture.
(A) The disengaged state during t = 0 to 1.0 × 108 MD steps. (B) The engaged state during t = 1.0 × 108 to 3.0 × 108 MD steps. (C) The V-shape state during t = 3.0 × 108 to 4.0 × 108 MD steps. (D) The disengaged state t = 4.0 × 108 to 5.0 × 108 MD steps. (E) Tims series of electrostatic and hydrogen-bonding interactions between the SMC complex and DNA.
Figure 5—figure supplement 3
Detail snapshots during DNA translocation via DNA-segment capture where the DNA does not reach the hinge domain in the engaged state.
(A) The disengaged state during t = 0 to 1.0 × 108 MD steps. (B) The engaged state during t = 1.0 × 108 to 3.0 × 108 MD steps. (C) The V-shape state during t = 3.0 × 108 to 4.0 × 108 MD steps. (D) The disengaged state t = 4.0 × 108 to 5.0 × 108 MD steps. (E) Tims series of electrostatic and hydrogen-bonding interactions between the SMC complex and DNA.
Figure 5—figure supplement 4
Time series of the DNA position where each SMC and kleisin domain contacts.
DNA–protein contacts at kleisin, ATPase heads, coiled-coil, and hinge domains are plotted in red, blue, green, and orange, respectively. SMC–ScpA complex realizes a variety of step sizes such as (A) 310 bp, (B) 258 bp, (C) 204 bp, (D) 161 bp, (E) 113 bp, and (F) 42 bp.
Figure 5—figure supplement 5
Translocation step size for (A) trajectories in which the DNA reaches the hinge domain and for (B) trajectories in which the DNA does not reach the hinge in the engaged state.
Figure 5—figure supplement 6
Probability distribution of (A) electrostatic and (B) hydrogen-bonding energies between the SMC complex and DNA.
Figure 5—figure supplement 7
Detail trajectories of simulations for SMC complex and DNA without hydrogen-bonding interactions between SMC ATPase heads and DNA.
(A) The disengaged state during t = 0 to 1.0 × 108 MD steps. (B) The engaged state during t = 1.0 × 108 to 3.0 × 108 MD steps. (C) Tims series of electrostatic interactions between the SMC complex and DNA.
Figure 5—figure supplement 8
Zipping up the coiled-coil arms when transitioning from V-shape to disengaged states.
(A) The definition domains where the coiled-coil arm and ATPase heads are divided into three domains. (B) Time series of Q-scores for domains 1 and 2 for all simulations. (B) Time series of Q-scores for domains 2 and 3 for all simulations.
Figure 6 with 1 supplement
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 molecular dynamics (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.
Figure 6—figure supplement 1
Time series of the captured DNA length within the SMC ring in the engaged state during t = 1.0 × 108 to 3.0 × 108 MD steps.
(A) Captured DNA length for the trajectories that lead to the DNA translocation successfully in the subsequent states. (B) Captured DNA length for the trajectories that do not lead to the DNA translocation in the subsequent states. (C) Time series of the averaged captured DNA length.
Figure 7 with 1 supplement
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 highlighting how the kleisin path determined the direction of translocation. (C) The spatial distribution of the DNA patch on the ScpA subunit.
Figure 7—figure supplement 1
The spatial distribution of the DNA patch on the ScpA subunit that has different linker lengths.
(A) A schematic figure showing the position of the GGGGS linker introduced into the ScpA subunit. (B) The spatial distribution of the DNA patch.
Videos
Video 1
The representative trajectory of all-atom molecular dynamics (MD) simulations for engaged PfSMC ATPase heads and DNA.
Video 2
The representative trajectory of ATP-dependent conformational changes of SMC–ScpA complex.
Video 3
The representative trajectory of DNA-binding events to the top of ATPase heads.
Video 4
The representative trajectory of SMC–ScpA translocation along DNA, in which the DNA reaches the hinge domain in the engaged state.
Video 5
The representative trajectory of SMC–ScpA translocation along DNA, in which the DNA does not reach the hinge domain in the engaged state.
Video 6
The representative trajectory of zipping up the coiled-coil arm when transitioning from V-shape to disengaged states.
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SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path
eLife 14:RP106752.
https://doi.org/10.7554/eLife.106752.3
