Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis

Abstract

The structural and mechanical properties of monomeric actin (G-actin), the trimer nucleus, and actin filaments (F-actins) are determined as a function of the conformation of the DNase I-binding loop (DB loop) by using all-atom molecular dynamics simulations and coarse-grained (CG) analysis. Recent x-ray structures of ADP-bound G-actin (G-ADP) by Otterbein et al. [Otterbein, L. R., Graceffa, P. & Dominguez, R. (2001) Science 293, 708-711] and ATP-bound G-actin (G-ATP) by Graceffa and Dominguez [Graceffa, P. & Dominguez, R. (2003) J. Biol. Chem. 278, 34172-34180] indicate that the DB loop of actin does not have a well defined secondary structure in the ATP state but folds into an alpha-helix in the ADP state. MD simulations and CG analysis indicate that such a helical DB loop significantly weakens the intermonomer interactions of actin assemblies and thus leads to a wider, shorter, and more disordered filament. The computed persistence lengths of F-actin composed of G-ATP (16 microm) and of G-ADP (8.5 microm) agree well with the experimental values for the two states. Therefore, the loop-to-helix transition of the DB loop may be one of the factors that lead to the changes in structural and mechanical properties of F-actin after ATP hydrolysis. This result may provide a direct connection between the conformational changes of an actin monomer and the structural and mechanical properties of the cytoskeleton. The information provided by MD simulations also helps to understand the possible origin of the special features of actin dynamics.

Fig. 1.

The conformation of G-ATP and G-ADP. (a) A schematic representation of the x-ray structures (12) of an ATP-bound actin monomer. Each subdomain of G-actin is colored differently, and the subdomain definition in Holmes et al. (14) is used. D1, including residues 1–32, 70–144, and 338–375, is colored cyan; D2, including residues 33–69, is colored tan; D3, including residues 145–180 and 270–337, is colored lime; and D4, including residues 181–269, is colored mauve. The bound ATP is shown in a licorice representation. The x-ray structures of G-ADP are very similar to those of G-ATP except for the structure of the DB loop (residues 40 – 48) in D2 (13). Residues 38–50 of D2, including the DB loop of G-ADP, are overlaid with those of G-ATP and are shown in white. (b) A 90° rotation of residues 38–50 in D2. It can be seen that the DB loop adopts a loop conformation in G-ATP (12) but folds into an α-helix in G-ADP (13). (c) A CG representation of G-actin. The adenosine group of ATP and ADP is CG into D3, and the phosphate groups are assigned to D1. A total of six internal coordinates are included. b1, the D1–D2 bond; b2, the D1–D3 bond; b3, the D3–D4 bond; a1, the D1-D3-D4 angle; a2, the D2-D1-D3 angle; d1, the D2-D1-D3-D4 dihedral angle.

Fig. 2.

The conformation of a G-actin trimer at the ATP and ADP states. (a and b) Schematics of a snapshot during the MD simulations of G-ATP (a) and G-ADP (b) trimers. (c) The coarse representation of the actin trimers. Each ball corresponds to a subdomain of G-actin (see Fig. 1). Monomers are numbered 1-3 starting at the + end. Monomer 1 is in ice blue, monomer 2 is in mauve, and monomer 3 is in lime. Residues with strong intermonomer interactions are shown in a tube representation and are colored differently. The DB loop, residues 40 – 48, is colored white, the plug-in loop, residues 264–271, is colored yellow, residues 62–64 are colored purple, residues 283–289 are colored cyan, and residues 372–375 are colored orange. A total of five effective bonds are assigned in the CG model for two monomers across a strand: iD2–(i + 1)D3, iD2–(i + 1)D4, iD4–(i + 1)D1, iD4–(i + 1)D3, and iD3–(i + 1)D3. Italic number indicates the number identity of a monomer, and D1–D4 denote the subdomains. In the cases of the trimer nucleus, i = 1 or 2. For two monomers along the same strand, a total of three effective bonds are assigned in the CG actin trimers: iD2–(i + 2)D1, iD2–(i + 2)D3, and iD4–(i + 2)D3. Other effective bonds between monomers follow the same convention of nomenclature.

Fig. 3.

The conformation of F-ATP and F-ADP. (a) A snapshot of F-ATP (Left) and F-ADP (Center) in a ribbon representation. The initial structure of F-ADP (Right) based on the Holmes model is shown for comparison. One of the two strands is colored cyan; the other is colored pink. (b) A zoom-in version of F-ATP and F-ADP from a. The arrows indicate the resulting effects of a helical DB loop in F-ADP on the structures of the filament. See the text for details.

Fig. 4.

The cosine correlation functions of the angles between tangent vectors as a function of the contour length, s, for F-ATP and F-ADP. The effects of spontaneous curvatures are excluded by means of the procedures described in Supporting Text. Estimation of the initial slope of decay is shown as dashed lines.