Structure and dynamics of the actin filament

Abstract

We used all-atom molecular dynamics simulations to investigate the structure and properties of the actin filament, starting with either the recent Oda model or the older Holmes model. Simulations of monomeric and polymerized actin show that polymerization changes the nucleotide-binding cleft, bringing together the Q137 side chain and bound ATP in a way that may enhance the ATP hydrolysis rate in the filament. Simulations with different bound nucleotides and conformations of the DNase I binding loop show that the persistence length of the filament depends only on loop conformation. Computational modeling reveals how bound phalloidin stiffens actin filaments and inhibits the release of gamma-phosphate from ADP-P(i) actin.

Figure 1

Actin subunit from the Oda et al. filament model in atomistic (cartoon) and coarse-grained (CG) representation. The four subdomains shown are: S1 (blue) residues 1-32, 70-144 and 338-375; S2 (red) residues 33-69; S3 (orange) residues 145-180 and 270-337; and S4 (green) residues 181-269. The cartoon representation of the protein is from PDB entry 2ZWH, and the “flatness” order parameter used for analysis is labeled.

Figure 2

Probability distributions for dihedral angle in the four-site CG model. Each panel contains the distributions for the Oda (solid) and Holmes (dashed) models for the four different nucleotide/DB loop pairs. The width of the bars is 1 deg, and the initial value for each model is labeled with a vertical line. The sample mean and skewness are listed in each panel.

Figure 3

Ramachandran plots for residues 141-142 and 336-337 in actin filaments derived from NPT MD simulations. The initial values for the Oda and Holmes filaments are represented by circle and triangles, respectively. The regions encompassing the values observed during MD simulation are marked with a dashed line (Oda) or solid line (Holmes). The lines are drawn with a contour level that encloses 100% of the observed backbone angles for the specific residues that are indicated. The Oda actin subunit is shown at the top with the residues of interest labeled in red.

Figure 4

Inter-subunit contact architecture of Oda and Holmes actin filaments derived from MD simulations. The average C^α position is depicted as a tube model to illustrate the cross-strand (i −i+1) and intra-strand (i −i+2) contacts. The initial structure is compared to the ATP/unfold and ADP/fold simulations. Contacts are shown in blue (subunit i) or black (subunits i+1 and i+2), and a contact is defined as two C^α atoms being less than 10 Å apart. Table S2 details the specific residues in contact for all of the models investigated.

Figure 5

Coordination of Q137 side chain with gamma phosphate group of bound ATP in actin filament simulations shown in stereo view. The protein is drawn with a cartoon representation, and the Q137 side chain and bound ATP molecule are shown in licorice format. Panels A and B show the initial configuration for the Oda and Holmes filament models, respectively. Panels C and D show a representative structure for the Oda and Holmes models, respectively. The distance between the NH₂ group and an O atom on the terminal PO₃ group of ATP is illustrated with a dashed line. Water molecules within 2.5 Å of the ATP molecule or Q137 side chain are shown.

Figure 6

Effect of bound phalloidin on contact architecture in actin filament simulations. The ribbon diagrams show subunits i (blue), i+1 (brown) and i+2 (green) and of phalloidin (licorice representation). Red spheres show the positions of all C^α atoms within 10.0 Å of the bound phalloidin. The two panels show stereo views for initial (top) and representative configuration (bottom) that illustrate how bound phalloidin increases the inter-strand (i − i+1) contacts in actin filaments.