Development of In Silico Analysis and Molecular Dynamics Simulation on L67P and D76Y Mutants of the Human Superoxide Dismutase 1(hSOD1) Related to Amyotrophic Lateral Sclerosis

Payam Baziyar; Bagher Seyedalipour; Saman Hosseinkhani; Ehsan Nazifi

doi:10.30498/ijb.2022.310249.3178

Development of In Silico Analysis and Molecular Dynamics Simulation on L67P and D76Y Mutants of the Human Superoxide Dismutase 1(hSOD1) Related to Amyotrophic Lateral Sclerosis

Iran J Biotechnol. 2022 Oct 1;20(4):e3178. doi: 10.30498/ijb.2022.310249.3178. eCollection 2022 Oct.

Authors

Payam Baziyar¹, Bagher Seyedalipour¹, Saman Hosseinkhani², Ehsan Nazifi³

Affiliations

¹ Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
² Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
³ Department of Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.

Abstract

Background: One neurodegenerative disorder that is caused by a mutation in the hSOD1 gene is Amyotrophic lateral sclerosis (ALS).

Objectives: The current study was developed in order to evaluate the effect exerted by two ALS-associated point mutations, L67P and D76Y are located in the metal-binding loop, on structural characterization of hSOD1 protein using molecular dynamics (MD) simulations and computational predictions.

Materials and methods: In this study, GROMACS was utilized to perform molecular dynamics simulations along with 9 different algorithms such as Predict SNP, PhD-SNP, MAPP, PolyPhen-1, Polyphen-2, SNP, SIFT, SNP&GO, and PMUT for predicting and also evaluating the mutational effect on the structural and conformational characterization of hSOD1.

Results: Our study was done by several programs predicting the destabilizing and harmful effect exerted by mutant hSOD1. The deleterious effect of L67P mutation was predicted by MAPP and PhD-SNP algorithms, and D76Y mutation was predicted by 9 algorithms. Comparative studies that were conducted on mutants and wild-type indicated the altar in flexibility and protein conformational stability influenced the metal-binding loop's conformation. The outcomes of the MD exhibited an increase and decrease of flexibility for D76Y and L67P mutants compared to the wild type, respectively. On the other hand, analysis of the gyration radius indicated lower and higher compactness for D76Y and L67P, respectively, suggesting that replacing amino acid at the metal-binding loop can alter the protein compactness compared with the protein the wild type.

Conclusions: Overall, these findings provided insight into the effect of mutations on the hSOD1, which leads to neurodegeneration disorders in humans. The results show that the mutations of L67P and D76Y influence the stability of protein conformational and flexibility associated with ALS disease. Thus, results of such mutations are can be a prerequisite to achieve a thorough understanding of ALS pathogenicity.

Keywords: Amyotrophic lateral sclerosis (ALS); D76Y and L67P variants; Human superoxide dismutase-1 (hSOD1); Metal-binding loop (MBL); Molecular dynamics (MD) Simulation.