Open AccessStructures prediction of Plasmodium Falciparum Signal Peptide Peptidase (PfSPP) and identification of binding Site
Author(s) -
G Priambodo,
Agus Priyono Kartono,
Irmanida Batubara,
Setyanto Tri Wahyudi
Publication year - 2019
Publication title -
iop conference series. earth and environmental science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.179
H-Index - 26
eISSN - 1755-1307
pISSN - 1755-1315
DOI - 10.1088/1755-1315/299/1/012007
Subject(s) - plasmodium falciparum , ramachandran plot , malaria , binding site , biology , biochemistry , protein structure , immunology
Malaria is a tropical parasitic disease caused by mosquitoes. Plasmodium falciparum is the species that causes the most human deaths compared to other species. Plasmodium which infects red blood cells will causes pathology and clinical manifestations in malaria sufferers. Plasmodium falciparum Signal Peptide Peptidase (PfSPP) is an important enzyme to infect red blood. I-TASSER (Iterative Threading ASSEmbly Refinement) has been used to predict the 3D structure of the PfSPP enzyme by modeling using proteins in databases. Based on data analysis such as Ramachandran plot, G-Factor, RMSD, Radius of gyration, and NAMD energy, model 5 is the best model of all I-TASSER structure prediction models. AutoLigand was used to predict the binding sites on this model and obtained 5 binding sites points with lowest free energy on each fill point. Binding sites 3, 4 and 5 have the largest volumes 345 Å 3 , 372 Å 3 , and 395 Å 3 respectively so that they have potential to bind with both ligand mefloquine and primaquine with volume 330 Å 3 and 333 Å 3 respectively. Three binding sites have the potential to inhibit PfSPP so it cannot function properly and stop the invasion of the parasite’s merozoite to other erythrocytes.