IN SILICO CHARACTERIZATION AND MOLECULAR MODELLING OF SODIUM-DEPENDENT SEROTONIN TRANSPORTER PROTEIN FROM HOMO SAPIENS
DOI:
https://doi.org/10.22159/ajpcr.2017.v10i8.18954Keywords:
Homology modeling, In silico analysis, Protein disorder analysis, Random coilsAbstract
Objective: The objective of our investigation is to apply computational tools for a protein sodium-dependent serotonin transporter (SERT). It plays a role in sudden infant death syndrome, aggressive behavior in Alzheimer disease, and depression-susceptibility. Although various conventional and experimental therapies have been directed for the treatment, still it needs attention for more effective treatments. Toward this pursuit, we performed in silico analysis of the protein using computational tools and servers.
Methods: Homology modeling approach has been used to define the tertiary structure of the protein using SWISS-MODEL workspace. Modal validation was done to verify the generated modal. Furthermore, primary and secondary structural and functional analysis was performed to provide more perceptions into the selected protein. The protein disorder analysis was performed using PrDOS server.
Results: The results of the primary structure analyses suggested that SERT is an acidic and hydrophobic protein in nature. It is structurally stable. The secondary structural analysis results revealed that random coils dominated among secondary structure elements. The homology modeling showed that the QMEAN score of the model was −5.17, and the sequence identity was 52%. Validation protein models using Rampage revealed that more that 95.9% residues were in favored regions. The protein disorder detected by PrDOS showed the total disorder amino acid residues were 89 (14.1%).
Conclusion: The study provides valuable clues for initiation of experimental characterization of this protein and throws light on some novel insights into the structural features of sodium-dependent SERT protein from Homo sapiens. This will also helpful in conducting docking studies for the receptor protein against various drug molecules.
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