Burnham-Brandeis Helical Package

<p>Software for three-dimensional reconstruction of helical structures from images obtained by electron microscopy.</p

Comparison between actin decorated with wild-type smooth muscle myosin S1 and actin decorated with a R403Q smooth muscle myosin mutant.

<p>A: Wild-type smooth muscle actomyosin in the presence of ADP. The top row shows a 4-nm thick central slice perpendicular to the filament axis. The second row shows a 4-nm thick central slice parallel to the filament axis (cutting plane indicated by the left line in top row). The pointed end is to the top of the figure in the two lower rows. The bottom row shows an adjacent 4-nm thick slice (cutting plane indicated by right line in top row). This slice goes primarily through the S1 molecules. B: R403Q mutant smooth muscle actomyosin in the presence of ADP. Organization of rows as in (A). C: Wild-type smooth muscle actomyosin in the absence of nucleotide (apo). The approximate location of the motor domain (MD) and the light chain (LC) regions are labeled in each view. Organization of rows as in A. The approximate outline of the actin portion of the filament is indicated. D: Apo R403Q mutant smooth muscle actomyosin. Organization of rows as in (A). Bar:10 nm.</p

Difference and structural variability maps.

<p>4-nm wide slices perpendicular to the helix axis of several maps are shown on the left. Only peaks significant at a confidence level of 99.99% are shown. A: Wild-type smooth muscle actomyosin in the absence of nucleotide. The motor domain (MD) and light-chain (LC) regions are labeled. A faint ghost image of this map is also overlaid on C and E to aid visualization. B: A difference map generated by subtracting the R403Q mutant smooth muscle actomyosin apo state reconstruction from the R403Q mutant smooth muscle actomyosin ADP state reconstruction. A clear difference peak can be identified in the light-chain region. A faint ghost image of the wild-type ADP state reconstruction is overlaid to aid visualization. This image is also overlaid on D and F. C: Difference map between two independently generated R403Q mutant apo state reconstructions. Only occasional, randomly distributed, isolated pixels can be seen, no coherent difference peaks exist. D: Difference map between two independently generated R403Q mutant ADP state reconstructions. E: Structural variability (AVID map) of R403Q mutant apo state reconstruction. Only randomly distributed peaks can be seen, there is no consistent structural variability in any confined region. F: Structural variability (AVID map) of R403Q mutant ADP state reconstruction. Bar:10 nm. G: Surface representation of the difference map shown in B. The cyan density represents additional density in the R403Q mutant ADP state reconstruction if compared to the R403Q mutant apo state reconstruction. The apo state (pink) and ADP state (blue wireframe) wild-type reconstructions are also shown. The difference between the mutant reconstructions is located in the light-chain region and correlates with the changes observed in wild-type smooth muscle actomyosin.</p

Data collection

a<p>This counts split data (i.e. far and near side) as different data sets (see text for details).</p>b<p>All statistics are calculated over the respective number of data sets.</p>c<p>The phase residual is a measure for the homogeneity and quality of the data. Values below 45° are considered excellent; values below 55° are acceptable.</p

Proximity of residue Arg⁴⁰⁶ (Arg⁴⁰³ in cardiac myosin) to the actin interface.

<p>Arg⁴⁰⁶ (red spheres) is immediately adjacent to residues of the cardiomyopathy loop that were previously implicated in actin binding by docking studies (407–414; green). While the conformation of the Arg⁴⁰⁶ in the smooth muscle myosin crystal structure points away from the interface (A), it can easily reach actin by simple, stereochemically permitted bond angle rotations (B). The resulting conformation does not generate serious clashes with other myosin residues. Myosin is shown in blue, the interacting actin filament subunits in grey. Residue Pro³³³ of actin, the closest to myosin Arg⁴⁰⁶, is shown as spheres.</p

Mechanism of Filament Nucleation and Branch Stability Revealed by the Structure of the Arp2/3 Complex at Actin Branch Junctions

<div><p>Actin branch junctions are conserved cytoskeletal elements critical for the generation of protrusive force during actin polymerization-driven cellular motility. Assembly of actin branch junctions requires the Arp2/3 complex, upon activation, to initiate a new actin (daughter) filament branch from the side of an existing (mother) filament, leading to the formation of a dendritic actin network with the fast growing (barbed) ends facing the direction of movement. Using genetic labeling and electron microscopy, we have determined the structural organization of actin branch junctions assembled in vitro with 1-nm precision. We show here that the activators of the Arp2/3 complex, except cortactin, dissociate after branch formation. The Arp2/3 complex associates with the mother filament through a comprehensive network of interactions, with the long axis of the complex aligned nearly perpendicular to the mother filament. The actin-related proteins, Arp2 and Arp3, are positioned with their barbed ends facing the direction of daughter filament growth. This subunit map brings direct structural insights into the mechanism of assembly and mechanical stability of actin branch junctions.</p> </div

Localization of the Labels Attached to Arp2, Arp3, Arc40/ARPC1, and Arc18/ARPC3 at the Actin Branch Junction

<div><p>Color codes used: Arp2 (pink), Arp3 (orange), Arc40/ARPC1 (green), and Arc18/ARPC3 (red).</p> <p>(A) 2D average projection maps of the branches obtained with Arp2-GFP (row 1), Arp3-GFP (row 2), Arc40/ARPC1-YFP (row 3), and Arc18/ARPC3-GFP (row 4).</p> <p>(B) Difference maps calculated between maps obtained with labeled and unlabeled complexes.</p> <p>(C) Difference maps superimposed with the projection maps. The position of the difference peaks was cross-validated (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030383#s3" target="_blank">Materials and Methods</a>).</p> <p>(D) The average projection map obtained with the unlabeled complex.</p> <p>(E) The main difference peaks are superimposed with the unlabeled projection map.</p> <p>(F and G) Circles of 3.9-nm radius centered on the difference peaks indicate the possible locations of the C-termini of each labeled subunit. The GFP/YFP label was attached to the C-terminus of the relevant subunit with an eight-amino-acid flexible linker that in fully extended conformation can reach a length of up to approximately 3.2 nm. The distance of the N-terminus of GFP or YFP from the center of mass of its beta-barrel (14 × 8 × 8 nm) is approximately 2.5 nm. The centers of the peaks determined from the difference maps probably coincide with the center of mass.</p> <p>Bar = 10 nm.</p></div

Structure Models of the Arp2/3 Complex at Actin Branch Junction

<div><p>Color codes used: Arp2 (light pink), Arp3 (orange), Arc40/ARPC1 (green), Arc35/ARPC2 (cyan), Arc19/ARPC4 (blue), Arc18/ARPC3 (dark pink), and Arc15/ARPC5 (yellow). Gray arrows indicate the mother and daughter filaments.</p> <p>(A) Orientation of the Arp2/3 complex relative to the mother and daughter filaments as determined using the labeling constraints.</p> <p>(B) Model rotated vertically anticlockwise by 90° from view in (A) and tilted so that the mother filament coincides with the vertical axis. The gray arrow is positioned to pass through the center of the complex.</p> <p>(C) Model rotated vertically by 180° from the view in (A).</p> <p>(D) Label positions and their corresponding C-termini localization. GFP or YFP, shown as ribbon diagram with the same color coding as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030383#pbio-0030383-g003" target="_blank">Figure 3</a>, were superimposed on the respective difference peak (<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030383#pbio-0030383-g003" target="_blank">Figure 3</a>) with their orientation matching the peak shape.</p> <p>(E) Model superimposed on the projection density map (white corresponds to high density).</p> <p>(F) Model and ribbon diagram of a daughter filament (white) as it would grow after small relative rotations of Arp2 and Arp3 (see text) superimposed on the projection density map.</p> <p>(G and H) Model proposed by Beltzner and Pollard [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030383#pbio-0030383-b06" target="_blank">6</a>] (G) and by Aguda et al. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030383#pbio-0030383-b05" target="_blank">5</a>] (H) shown for comparison. Note that in (G), the daughter filament will be oriented out of the paper plane toward the reader.</p> <p>(I)Arp2/3 crystal structure in the same orientation as originally presented in Robinson et al. [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030383#pbio-0030383-b12" target="_blank">12</a>].</p></div

Surface representations of smooth muscle actomyosin constructs.

<p>The pointed end of the filaments is towards the top of the figure. A: Wild-type smooth muscle actomyosin in the presence of ADP. B: Wild-type smooth muscle actomyosin in the apo state. The contour level for A and B is chosen to represent the correct molecular mass. Note the well defined density and angle of the light-chain region (LC) C: R403Q mutant smooth muscle actomyosin in the presence of ADP. D: R403Q mutant smooth muscle actomyosin in the apo state. The contour level for C and D is chosen to show as much of the light chain domains as possible without completely obscuring the shape of the motor domain. E: Overlay of the maps in A–D. Color code and contouring as in A–D. F, G: Watershed segmentation of the maps in C (F) and D (G). These results reconfirm the orientation of the light-chain domains that correspond to those of the wild-type reconstructions (sketches) and the better definition of boundaries in the center of the filaments: the actin subunits are well segmented while there is no sub-segmentation of myosin domains as can be obtained for wild-type reconstructions <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0001123#pone.0001123-Volkmann4" target="_blank">[33]</a>. The sketches show central lines extracted from the density of the wild-type (grey) and the segmentation of the R403Q (black). Only the line segments extracted for the corresponding light-chain regions (LC) are shown, line segments corresponding to the motor domain region (MD) overlap almost completely for all maps.</p

Visualization of NPFs in the Actin Branch Junction by Difference Mapping

<div><p>(A-F) WASp protein dissociate from the actin branch. 2D average projection obtained (A) using the unlabeled yeast Arp2/3 complex and N-WASp WA, and (B) using the full-length GST-N-WASp complexed with its activator GST-Nck. (C) Difference map between (A) and (B). 2D average projection obtained using (D) the amoeba Arp2/3 complex and Scar WA, and (E) MBP-Scar1WA. (F) Difference map between (D) and (E).</p> <p>(G-I) Cortactin is present in the actin branch. (G) 2D average projection obtained using GST-cortactin and the amoeba Arp2/3 complex. (H) Difference map between (G) and (D). (I) The peak in the difference map shown in yellow superimposed with the projection map.</p> <p>Bar = 10 nm.</p></div