Gating mechanisms during actin filament elongation by formins
- The University of Chicago, United States
- University of Minnesota, United States
- Yale University, United States
Figures
Figure 1
Processive association of formin with the barbed end of a growing filament.
(A) End-on and side views of formin FH1FH2 domains interacting with the barbed end of an actin filament (gray) in closed (FH2 domain in red color) and open (FH2 domain in green color) states. The …
Figure 2
Homology models of FH2 domains on the barbed end of actin filaments.
(A) Overall quality of the homology models of Cdc12, Bni1 and mDia1 FH2 domains after 200 ns of MD simulations. The graph compares the z-scores of the three homology models with the z-scores of all …
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Figure 2—source data 1
Cdc12 FH2 interacting with a seven-mer filament.
PDB file of the structure of Cdc12 FH2 domain interacting with an actin filament composed of seven actin subunits, obtained at 500 ns of the all-atom MD simulation.
- https://doi.org/10.7554/eLife.37342.004
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Figure 2—source data 2
Bni1 FH2 interacting with a seven-mer filament.
PDB file of the structure of Bni1 FH2 domain interacting with an actin filament composed of seven actin subunits, obtained at 500 ns of the all-atom MD simulation.
- https://doi.org/10.7554/eLife.37342.005
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Figure 2—source data 3
mDia1 FH2 interacting with a seven-mer filament.
PDB file of the structure of mDia1 FH2 domain interacting with an actin filament composed of seven actin subunits, obtained at 500 ns of the all-atom MD simulation.
- https://doi.org/10.7554/eLife.37342.006
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Figure 2—source data 4
Cdc12 FH2 interacting with a five-mer filament.
PDB file of the structure of Cdc12 FH2 domain interacting with an actin filament composed of five actin subunits, obtained at 350 ns of the all-atom MD simulation.
- https://doi.org/10.7554/eLife.37342.007
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Figure 2—source data 5
Bni1 FH2 interacting with a five-mer filament.
PDB file of the structure of Bni1 FH2 domain interacting with an actin filament composed of five actin subunits, obtained at 350 ns of the all-atom MD simulation.
- https://doi.org/10.7554/eLife.37342.008
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Figure 2—source data 6
mDia1 FH2 interacting with a five-mer filament.
PDB file of the structure of mDia1 FH2 domain interacting with an actin filament composed of five actin subunits, obtained at 350 ns of the all-atom MD simulation.
- https://doi.org/10.7554/eLife.37342.009
Figure 3
Steric clashes of FH2 dimers with incoming actin subunits during all-atom simulations of seven-mer and five-mer filaments.
(A–C) FH2 dimers on seven-mer filaments including actin A1. (A) Time course of volume fractions of actin subunit (+A1) occupied by FHL during 500 ns simulations. Measurements start at 0 ns for Cdc12 …
Figure 4 with 1 supplement
Effect of FH2 domains on the barbed end configurations of actin seven-mer filaments.
The panels show helical twist angles between subunits at the barbed ends of actin filaments associated with three different formin FH2 dimers during all-atom MD simulations. (A–C) The angles between …
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Figure 4—source data 1
Twist angles between actin subunits as a function of time.
Helical twist angles between subunits of seven-mer filaments (A1–A2, A2–A3, A3–A4, A4–A5 and A5–A6) associated with three different formin FH2 dimers during all-atom MD simulations. The angles are outputted at every 40 ps during the time intervals given in Figure 4.
- https://doi.org/10.7554/eLife.37342.013
Figure 4—figure supplement 1
Effect of FH2 domains on the configurations of actin seven-mer filaments.
Comparison of the distributions of angles between the actin pair of subunits during three different time intervals. (A,D,G) t = 100–120 ns for Cdc12 and mDia1, and t = 160–180 ns for Bni1. (B,E,H) t …
Figure 5 with 2 supplements
Effect of FH2 domains on the barbed end configurations of actin five-mer filaments before the addition of actin subunit A1.
(A) The helical twist angles between actin subunits A2 and A3 as a function of time during 350 ns of all-atom MD simulations (replica 1) of the FH2 domains of Bni1, Cdc12 and mDia1 associated with …
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Figure 5—source data 1
Twist angles between actin subunits as a function of time.
Helical twist angles between subunits of five-mer filaments (A2–A3, A3–A4 and A4–A5) associated with three different formin FH2 dimers during all-atom MD of two independent simulations (replica 1 and replica 2). The angles are outputted at every 20 ps during the time intervals given in Figure 5.
- https://doi.org/10.7554/eLife.37342.017
Figure 5—figure supplement 1
The interactions of FH2 domains (post regions) with an actin filament and the barbed end configuration.
The correlations for the number of contacts between the post regions of the FH2 domains and actin subunits (A2 and A3) and the distributions of twist angles of A2-A3 during 350 ns all-atom MD …
Figure 5—figure supplement 2
The interactions of FH2 domains (lasso and knob regions) with an actin filament and the barbed end configuration.
The correlations for the number of contacts between the lasso and knob regions of the FH2 domains and actin subunits (A2 and A3) and the distributions of twist angles of A2-A3 during 350 ns all-atom …
Figure 6
Free-energy sampling of the conformational mobility of FHT domains interacting with five-mer filaments.
(A) Two independent metabasin metadynamics (MBMetaD) simulations for each formin were carried out (run for 80 ns) to understand the conformational mobility of the FHT domain. The collective …
Figure 7 with 1 supplement
Interactions of FH2 domains with actin filament seven-mers.
The time-averaged number of contacts over the last 20 ns of the 200 ns simulations between the three actin subunits at the barbed ends of the filaments and the FH2 domains of mDia1 (red), Bni1 …
Figure 7—figure supplement 1
Interactions of each region in FH2 domains with an actin filament. The number of contacts between the lasso, linker, knob and post regions of the FH2 domains and actin subunits (A1, A2 and A3) as a function of time during last 50 ns of 500 ns all-atom MD simulations.
https://doi.org/10.7554/eLife.37342.020
Figure 8
Construction and simulations of coarse-grained (CG) models of FH2 domains.
(A) Assignment of coarse-grained (CG) sites of the Cdc12 FH2 domain dimer by the EDCG method (FHL is green and FHT is orange). (B) Connection of CG sites by harmonic bonds defined by heteroENM and …
Figure 9
Conformational changes of FH2 domains on the barbed ends of actin filament seven-mers during coarse-grained (CG) simulations.
(A) Side and (B) bottom views of structures of Cdc12, Bni1, and mDia1 FH2 domains interacting with the barbed ends of actin filaments at the end (t = 2000 ns) of the CG simulations (dielectric …
Tables
Table 1
Stability of salt bridges between formin FH2 domains and actin subunits.
Stability was measured as the percent of the time that a salt bridge formed between knob helices of the three FH2 domains and actin barbed end grooves of actin subunits A2 or A3 during (A) the last …
| Cdc12 knob helices/Actin barbed end groove | ||||||
|---|---|---|---|---|---|---|
| FH2 residue | FH2 domain | Actin residue | Actin subunit | (A) Percent formed | (B) Percent formed | (C) Percent formed |
| K1068 | FHL | D25 | A2 | 78.2 | 76.9 | 86.5 |
| E1090 | FHL | R147 | A2 | - | 63.1 | 13.1 |
| E1093 | FHL | R147 | A2 | 99.4 | - | - |
| K1099 | FHL | E167 | A2 | - | - | 41.2 |
| K1105 | FHL | E167 | A2 | - | 52.6 | 77.1 |
| K1107 | FHL | E167 | A2 | 41.5 | - | - |
| K1068 | FHT | D25 | A3 | 95.2 | 70.7 | 82.4 |
| K1072 | FHT | D25 | A3 | 64.3 | 71.4 | 85.3 |
| K1072 | FHT | D24 | A3 | - | 15.6 | 12.8 |
| E1093 | FHT | R147 | A3 | 94.8 | 97.3 | 99.8 |
| K1099 | FHT | E167 | A3 | - | 47.2 | 18.1 |
| Bni1 knob helices/Actin barbed end groove | ||||||
| E1463 | FHL | R147 | A2 | 83.6 | 89.5 | 88.6 |
| R1423 | FHL | E167 | A2 | 0.401 | 0.541 | - |
| E1463 | FHT | R147 | A3 | 90.0 | 88.5 | 93.8 |
| K1467 | FHT | E167 | A3 | 97.4 | 95.7 | - |
| mDia1 knob helices/Actin barbed end groove | ||||||
| R851 | FHL | D25 | A2 | 97.8 | 93.5 | - |
| E871 | FHL | R147 | A2 | 8.42 | 18.8 | - |
| K879 | FHL | E167 | A2 | 25.3 | 3.69 | - |
| K838 | FHT | E167 | A3 | 98.6 | 98.6 | 25.7 |
Table 2
Salt bridges between formin FH2 domains and actin subunits.
Percentage of the time that salt bridges formed between the lasso and linker regions of Cdc12, Bni1 and mDia1 FH2 domains and actin subunits during the last 20 ns of AA simulations spanning 200 ns …
| FH2 residue | FH2 domain | Actin residue | Actin subunit | % Formed |
|---|---|---|---|---|
| Cdc12/actin | ||||
| R990 | FHL-lasso | D363 | A2 | 100. |
| K992 | FHT-lasso | E125 | A1 | 99.6 |
| K1038 | FHL-linker | E99 | A2 | 71.5 |
| K1041 | FHL-linker | E100 | A2 | 52.5 |
| K1045 | FHL-linker | E2 | A2 | 72.3 |
| K1045 | FHL-linker | D3 | A2 | 93.2 |
| K1046 | FHL-linker | E4 | A2 | 50.3 |
| K1038 | FHT-linker | D363 | A1 | 20.6 |
| Bni1/actin | ||||
| K1357 | FHL-lasso | D363 | A2 | 85.2 |
| K1357 | FHT-lasso | D363 | A1 | 23.0 |
| K1359 | FHT-lasso | E125 | A1 | 99.2 |
| R1402 | FHL-linker | E99 | A2 | 99.4 |
| E1403 | FHL-linker | K359 | A2 | 95.0 |
| K1410 | FHL-linker | E4 | A2 | 24.0 |
| K1410 | FHL-linker | E100 | A2 | 81.8 |
| K1412 | FHL-linker | D3 | A2 | 57.5 |
| R1402 | FHT-linker | D363 | A1 | 98.4 |
| mDia1/actin | ||||
| R764 | FHL-lasso | D363 | A2 | 23.4 |
| K807 | FHL-linker | E125 | A2 | 49.9 |
| K813 | FHL-linker | E4 | A2 | 37.9 |
| K813 | FHL-linker | E99 | A2 | 20.4 |
| K826 | FHL-linker | D3 | A2 | 70.9 |
| K826 | FHL-linker | E2 | A2 | 43.3 |
| K827 | FHL-linker | E2 | A2 | 13.2 |
| K828 | FHL-linker | E2 | A2 | 11.4 |
| K807 | FHT-linker | E125 | A1 | 23.0 |
| K810 | FHT-linker | E83 | A1 | 43.7 |
| K810 | FHT-linker | E125 | A1 | 46.7 |
| K813 | FHT-linker | D51 | A1 | 99.0 |
| E816 | FHT-linker | R37 | A1 | 96.8 |
| K828 | FHT-linker | E2 | A3 | 25.1 |
Additional files
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Supplementary file 1
Definitions of features of Cdc12, Bni1 and mDia1 FH2 domains.
The columns show feature name and residues comprising corresponding feature.
- https://doi.org/10.7554/eLife.37342.025
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Supplementary file 2
Template modeling scores (TM-scores) of the FH2 domain homology models based on different templates.
TM-score is used to determine the similarity of protein structures. Based on statistics, TM-score between 0.0 and 0.17 indicates random structural similarity and TM-score between 0.5 and 1.00 indicates having about the same fold [43]. TM-scores were obtained through this website: https://zhanglab.ccmb.med.umich.edu/TM-align/
- https://doi.org/10.7554/eLife.37342.026
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Supplementary file 3
Correlations between interactions of FH2 domain with an actin filament and the barbed end configuration.
Pearson correlation coefficients for the number of contacts between the lasso, knob and post regions of the FH2 domains and actin subunits (A2 and A3) and the distributions of twist angles of A2-A3 (given in Figure 5—figure supplement 2 and Figure 5—figure supplement 1) during 350 ns all-atom MD simulations of five-mer filaments.
- https://doi.org/10.7554/eLife.37342.027
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Supplementary file 4
Average interactions of different FH2 regions with an actin filament.
The average number of contacts (with standard deviations and t-statistics) between the lasso, knob and post regions of the FH2 domains and actin subunits (A2 and A3) from 350 ns of the all-atom MD simulations of five-mer filaments.
- https://doi.org/10.7554/eLife.37342.028
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Transparent reporting form
- https://doi.org/10.7554/eLife.37342.029
