Ajith Athira, Subbiah Usha
Human Genetics Research Centre, Sree Balaji Dental College and Hospital, Bharath Institute of Higher Education and Research, Chennai, 600 100, Tamil Nadu, India.
J Genet Eng Biotechnol. 2023 Oct 6;21(1):95. doi: 10.1186/s43141-023-00551-4.
Tuftelin 1 (TUFT1) gene is important in the development and mineralization of dental enamel. The study aimed to identify potential functionally deleterious non-synonymous SNPs (nsSNPs) in the TUFT1 gene by using different in silico tools. The deleterious missense SNPs were identified from SIFT, PolyPhen-2, PROVEAN, SNPs & GO, PANTHER, and SNAP2. The stabilization, conservation, and three-dimensional modeling of mutant proteins were analyzed by I-Mutant 3.0, Consurf, and Project HOPE, respectively. The protein-protein interaction using STRING, GeneMANIA for gene-gene interaction, and DynaMut for evaluating the impact of the mutation on protein stability, conformation, and flexibility.
Eight deleterious nsSNPs (E242A, R303W, K182N, K123N, R117W, H289Q, R203W, and Q107R) out of 304 were found to have high-risk damaging effects using six in silico tools. Among them, K182N and K123N alone had increased stability, whereas E242A, R303W, R117W, H289Q, Q107R, and R203W exhibited a decrease in protein stability, based on DDG values. Meanwhile, all the eight deleterious nsSNPs altered the size, charge, hydrophobicity, and spatial organization of the amino acids and predominantly had alpha helix domains. These deleterious variants were located in highly conserved regions except R203W. Protein-protein interaction predicted that TUFT1 interacted with ten proteins that are involved in enamel mineralization and odontogenesis. Gene-gene interaction network showed that TUFT1 is involved in physical interactions, gene co-localization, and pathway interactions. DynaMut ΔΔG values predicted that five nsSNPs were destabilizing the protein, ΔΔG ENCoM values showed a destabilizing effect for all mutants, and seven nsSNPs increased the molecular flexibility of TUFT1.
Our study predicted eight functional SNPs that had detrimental effects on the structure and function of the TUFT1 gene. This will aid in the development of candidate deleterious markers as a potential target for disease diagnosis and therapeutic interventions.
成簇蛋白1（TUFT1）基因在牙釉质的发育和矿化过程中起着重要作用。本研究旨在利用不同的计算机模拟工具，识别TUFT1基因中潜在的功能有害非同义单核苷酸多态性（nsSNPs）。通过SIFT、PolyPhen-2、PROVEAN、SNPs&GO、PANTHER和SNAP2等工具识别有害错义单核苷酸多态性。分别使用I-Mutant 3.0、Consurf和Project HOPE分析突变蛋白的稳定性、保守性和三维建模。利用STRING进行蛋白质-蛋白质相互作用分析，使用GeneMANIA进行基因-基因相互作用分析，使用DynaMut评估突变对蛋白质稳定性、构象和灵活性的影响。
在304个单核苷酸多态性中，通过六种计算机模拟工具发现8个有害的非同义单核苷酸多态性（E242A、R303W、K182N、K123N、R117W、H289Q、R203W和Q107R）具有高风险的破坏作用。其中，仅K182N和K123N的稳定性增加，而根据ΔΔG值，E242A、R303W、R117W、H
