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. 2008 Dec;95(11):5324-33.
doi: 10.1529/biophysj.108.143313. Epub 2008 Sep 19.

Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex

Jim Pfaendtner  1 , Gregory A Voth
Affiliations

Molecular dynamics simulation and coarse-grained analysis of the Arp2/3 complex

Jim Pfaendtner et al. Biophys J. 2008 Dec.

Abstract

A molecular dynamics investigation and coarse-grained analysis of inactivated actin-related protein (Arp) 2/3 complex is presented. It was found that the nucleotide binding site within Arp3 remained in a closed position with bound ATP or ADP, but opened when simulation with no nucleotide was performed. In contrast, simulation of the isolated Arp3 subunit with bound ATP, showed a fast opening of the nucleotide binding cleft. A homology model for the missing subdomains 1 and 2 of Arp2 was constructed, and it was also found that the Arp2 binding cleft remained closed with bound nucleotide. Within the nucleotide binding cleft a distinct opening and closing period of 10 ns was observed in many of the simulations of Arp2/3 as well as isolated Arp3. Substitution studies were employed, and several alanine substitutions were found to induce a partial opening of the ATP binding cleft in Arp3 and Arp2, whereas only a single substitution was found to induce opening of the ADP binding cleft. It was also found that the nucleotide type did not cause a substantial change on interfacial contacts between Arp3 and the ArpC2, ArpC3 and ArpC4 subunits. Nucleotide-free Arp3 had generally less stable contacts, but the overall contact architecture was constant. Finally, nucleotide-dependent coarse-grained models for Arp3 are developed that serve to further highlight the structural differences induced in Arp3 by nucleotide hydrolysis.

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Figures

FIGURE 1
FIGURE 1
Molecular representation of the entire Arp2/3 complex with bound ATP in the Arp2 and Arp3 subunits. The subunits are labeled in the figure using standard coloring and notation. Figure created using VMD (27).
FIGURE 2
FIGURE 2
Molecular and coarse-grained representations of Arp3. The molecular representation is colored to display the CG mapping, and the CG sites are labeled and correspond to the four sites described in the methods section. There are six effective CG geometric parameters labeled in the figure: three bonds, two angles, and one dihedral. Figure created using VMD (27).
FIGURE 3
FIGURE 3
Effect of bound nucleotide on the overall RMSD of Arp2/3. The error bars are shown as the RMSD for each subunit as a function of nucleotide state. If no error bars are shown, then the variation in RMSD is smaller than the symbol.
FIGURE 4
FIGURE 4
Opening of the nucleotide binding cleft of the Arp3 subunit as a function of the bound nucleotide. Each line in A represents the results of a simulation of Arp2/3 with bound ATP (blue), ADP (red), or nucleotide free (green), additionally shown is a simulation of the isolated Arp3 complex with bound ATP (black). B gives a detailed view of the behavior of ADP-bound Arp2/3. The degree of opening and closing is measured by the Gly-15 – Asp-172 Cα distance (B2).
FIGURE 5
FIGURE 5
View of the nucleotide binding site of Arp3 with bound ADP taken at a simulation time of 16 ns. The bound ADP molecule and several key residues (labeled in the figure) are shown with licorice representation. Nonbonded interactions discussed in the text are labeled with a black dashed line. Figure created using VMD (27).
FIGURE 6
FIGURE 6
Opening and closing of the nucleotide binding cleft in Arp3 with bound ADP (A) and bound ATP (B). The behavior of the wild-type and the three point substitutions is shown. Opening and closing is characterized using the bond B2 as described in Fig. 4. All results are taken from simulations of the full Arp2/3 complex.
FIGURE 7
FIGURE 7
Protein-protein contact maps for the interface between Arp3 and the ArpC2 subunits. The residue number of the primary amino acid sequence is labeled on each axis of the contact map, and one contact map is shown for each nucleotide state. The sidebar shows the correspondence between the degree of shading and the amount of contact, as defined by Eq.1.
FIGURE 8
FIGURE 8
Protein-protein contact maps for the interface between Arp3 and the ArpC3 subunits (see Fig. 7 legend for detailed description).
FIGURE 9
FIGURE 9
Protein-protein contact maps for the interface between Arp3 and the ArpC4 subunits (see Fig. 7 for detailed description).
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