Common dynamical signatures of familial amyotrophic lateral sclerosis-associated structurally diverse Cu, Zn superoxide dismutase mutants

Abstract

More than 100 structurally diverse point mutations leading to aggregation in the dimeric enzyme Cu, Zn superoxide dismutase (SOD1) are implicated in familial amyotrophic lateral sclerosis (FALS). Although SOD1 dimer dissociation is a known requirement for its aggregation, the common structural basis for diverse FALS mutations resulting in aggregation is not fully understood. In molecular dynamics simulations of wild-type SOD1 and three structurally diverse FALS mutants (A4V, G37R, and H46R), we find that a common effect of mutations on SOD1 dimer is the mutation-induced disruption of dynamic coupling between monomers. In the wild-type dimer, the principal coupled motion corresponds to a "breathing motion" of the monomers around an axis parallel to the dimer interface, and an opening-closing motion of the distal metal-binding loops. These coupled motions are disrupted in all three mutants independent of the mutation location. Loss of coupled motions in mutant dimers occurs with increased disruption of a key stabilizing structural element (the beta-plug) leading to the de-protection of edge strands. To rationalize disruption of coupling, which is independent of the effect of the mutation on global SOD1 stability, we analyze the residue-residue interaction network formed in SOD1. We find that the dimer interface and metal-binding loops, both involved in coupled motions, are regions of high connectivity in the network. Our results suggest that independent of the effect on protein stability, altered protein dynamics, due to long-range communication within its structure, may underlie the aggregation of mutant SOD1 in FALS.

Fig. 1.

Flexibility of residues in MD trajectories. (a–h) The RMSD of the MD trajectories from the original minimized crystal structure. (i–k) Relative fluctuations of residues in the mutant dimers compared with fluctuation in wild-type SOD1. Only one monomer (A in the crystal structure of the wild type) is shown for comparison. (l–o) Relative fluctuations of residues in the wild-type and mutant monomers compared with the fluctuation in the respective dimer. In l, residues experimentally found to be more/less rigid in the dimer compared with the monomer are colored red/blue, respectively.

Fig. 2.

The first eigenmode obtained from essential dynamics analysis projected on the structures of wild-type (a), A4V (b), H46R (c), and G37R (d) dimers. In the wild type, a global breathing motion of the monomers is indicated by arrows.

Fig. 3.

The network of interactions in SOD1. (a) A representation of the graph of the SOD1 dimer. Each node corresponds to a residue, and an edge exists between the nodes if they form a van der Waals contact. The dimer interface residues are colored blue, and the residues in the metal-binding sites are colored red. An example minimal path from L8 to the dimer interface and to the metal-binding sites is shown in green. The β-plug residues are colored yellow. (b and c) The distribution of normalized average minimal paths from a given residue to all other residues in the protein (b) and the betweenness of each residue (c).

Fig. 4.

A model for the aggregation of SOD1 involving the β-plug region. (a) The native SOD1 dimer. The residues 37–42 and 90–95 comprising the β-plug are colored in orange and blue, respectively. (b) An intermediate misfolded monomer observed in previous MD simulations of model SOD1 monomer unfolding (32) involving a disrupted β-plug region. (c and d) Front and top views of a nonnative SOD1 dimer observed in previous MD simulations of SOD1 misfolding (33). The residues 37–42 and 90–95 are colored in orange and blue, and pink and cyan, respectively, in the two monomers. Arrows indicate possible directions of fibril growth such that a cross-β structure results.