title: A theoretical study on Zn binding loop mutants instigating destabilization and metal binding loss in human SOD1 protein.
abstract: Mutations in Cu/Zn superoxide dismutase 1 (SOD1) protein are a major cause of the devastating neurodegenerative disorder Amyotrophic lateral sclerosis. Evidence suggests that SOD1 functions as a free radical scavenger in humans. However, neither the mechanism nor a cure for this neurodegenerative disease are yet known. In the present study, we explored the effect of mutations on the mechanistic action on the Zn binding loop of SOD1 through discrete molecular dynamics. The results were analyzed in detail using statistical potential (BACH) to find the mutant structures having the least potential energy. Subsequently, we studied the impact of those mutations on metal ions bound in SOD1 using the program Check My Metal. Remarkably, our results recognized certain mutants, viz. His80Arg and Asp83Gly, that were more damaging to the Zn binding loop than all other mutants, leading to a loss of Zn binding with altered coordination of the Zn ion. Furthermore, the conformational stability, compactness, and secondary structural alteration of the His80Arg and Asp83Gly mutants were monitored using distinct parameters. Hence, at low computational expense, our study provides helpful insight into this emergent neurodegenerative disorder affecting mankind.
authors.affiliation: Bioinformatics Laboratory, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
authors.forename: E
authors.initials: E
authors.lastname: Srinivasan
authors.affiliation: Bioinformatics Laboratory, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India.
authors.forename: Rao
authors.initials: R
authors.lastname: Sethumadhavan
authors.affiliation: Bioinformatics Laboratory, Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, 632014, Tamil Nadu, India. rrajasekaran@vit.ac.in.
authors.forename: R
authors.initials: R
authors.lastname: Rajasekaran
mesh_terms: D000690:Amyotrophic Lateral Sclerosis / Q000201:enzymology*; D019295:Computational Biology; D006801:Humans; D056004:Molecular Dynamics Simulation; D020125:Mutation, Missense; D000072417:Protein Domains; D000072105:Superoxide Dismutase-1 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D015032:Zinc
chemical_list: C000606290:SOD1 protein, human; D000072105:Superoxide Dismutase-1; D015032:Zinc
keywords: ALS; Check My Metal; DMD; SOD1; Zn binding loop