Molecular dynamics of far positioned surface mutations of Cu/Zn SOD1 promotes altered structural stability and metal-binding site: Structural clues to the pathogenesis of amyotrophic lateral sclerosis

Abstract

Cu/Zn superoxide dismutase (SOD1) mutations are associated to the motor neuron disorder, amyotrophic lateral sclerosis (ALS), which is characterized by aggregates of the misfolded proteins. The distribution of mutations all over the three-dimensional structure of SOD1 makes it complex to determine the exact molecular mechanism underlying SOD1 destabilization and the associated ALS pathology. In this study, we have examined structure and dynamics of SOD1 protein upon two ALS associated point mutations at the surface residue Glu100 (E100G and E100K), which is located far from the Cu and Zn sites and dimer interface. The molecular dynamics simulations were performed for these mutants for 50ns using GROMACS package. Our results indicate that the mutations result in structural destabilization by affecting the gate keeping role of Glu100 and loss of electrostatic interactions on the protein surface which stabilizes the β-barrel structure of the native form. Further, these mutations could increase the fluctuations in the zinc-binding loop (loop IV), primarily due to loss of hydrogen bond between Asp101 and Arg79. The relaxed conformation of Arg79 further affects the native conformation of His80 and Asp83, that results in altered zinc site geometry and the structure of the substrate channel. Our results clearly suggest that, similar to the mutations located at metal sites/dimer interface/disulfide regions, the mutations at the far positioned site (Glu100) also induce significant conformational changes that could affect the metallation and structure of SOD1 molecule, resulting in formation of toxic intermediate species that cause ALS.