Computational analysis of sodium-dependent phosphate transporter SLC20A1/PiT1 gene identifies missense variations C573F, and T58A as high-risk deleterious SNPs

• Published in: Journal of biomolecular structure & dynamics 2024-05, Vol.42 (8), p.4072-4086
• Main Authors: Siva Sankari, G., James, Remya, Payva, Febby, Sivaramakrishnan, Venketesh, Vineeth Kumar, T. V., Kanchi, Subbarao, Santhy, K. S.
• Format: Article
• Language: English
• Subjects: Humans; LIG plot; missense; molecular dynamics; Molecular Dynamics Simulation; Mutation, Missense; non-synonymous; Polymorphism, Single Nucleotide; Protein Conformation; RMSD; RMSF; SLC20A1; Sodium-Phosphate Cotransporter Proteins, Type III - chemistry; Sodium-Phosphate Cotransporter Proteins, Type III - genetics; Sodium-Phosphate Cotransporter Proteins, Type III - metabolism
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2023.2218939

SLC20A1/PiT1 is a sodium-dependent inorganic phosphate transporter, initially recognized as the retroviral receptor for Gibbon Ape Leukemia Virus in humans. SNPs in SLC20A1 is associated with Combined Pituitary Hormone Deficiency and Sodium Lithium Counter transport. Using in silico techniques, we have screened the nsSNPs for their deleterious effect on the structure and function of SLC20A1. Screening with sequence and structure-based tools on 430 nsSNPs, filtered 17 nsSNPs which are deleterious. To evaluate the role of these SNPs, protein modeling and MD simulations were performed. A comparative analysis of model generated with SWISS-MODEL and AlphaFold shows that many residues are in the disallowed region of Ramachandran plot. Since SWISS-MODEL structure has a 25-residue deletion, the AlphaFold structure was used to perform MD simulation for equilibration and structure refinement. Further, to understand perturbation of energetics, we performed in silico mutagenesis and ΔΔG calculation using FoldX on MD refined structures, which yielded SNPs that are neutral (3), destabilizing (12) and stabilizing (2) on protein structure. Furthermore, to elucidate the impact of SNPs on structure, we performed MD simulations to discern the changes in RMSD, Rg, RMSF and LigPlot of interacting residues. RMSF profiles of representative SNPs revealed that A114V (neutral) and T58A (positive) were more flexible & C573F (negative) was more rigid compared to wild type, which is also reflected in the changes in number of local interacting residues in LigPlot and ΔΔG. Taken together, our results show that SNPs can lead to structural perturbations and impact the function of SLC20A1 with potential implications for disease. Communicated by Ramaswamy H. Sarma