Bioinformatics Analysis APJ Receptor And Vitrual Screening The Binding Site Of APJ

Aim: Predict the structure and function of G-protein coupled receptor APJ in bioinformatics method, to identify the potential binding site in APJ; molecular docking study on ligand binding to APJ receptor,to analyse the conformation of the ligand and the receptor; lay the foundation for APJ receptor based virtual screening and rational drug design.Methods:1. Predict Basic property of APJ: To predict phsico-chemical parameters by ProParam; to predict hydrophobic areas by BioEdit; to predict transmembrane segments by TMHMM and TMpred; to predict coiled coil by COILS Server; to predict signal peptide by Signal3.0; to predict subcellular localization by TargetP.2. Predict motifs and domaim of APJ: To predict motifs of APJ byPROSITE and Motifscan; to predict domains by SMART.3. Predict secondary structure of APJ: To predict secondary structure of APJ by Predictprotein, PRIPRED and SSPro.4. Predict tertiary structure of APJ: To homology modeling the tertiary structure of APJ by Swiss-Model; the folds recognition of APJ is done by Phyre; to assess the predicted tertiary structure by visualization tool Swiss-PdbViewer.5. Predict binding site of APJ: To predict binding sites of APJ by online software MetaPocket2.0.6. To analyse the conformation of the ligand binding to APJ receptor by molecular docking: Molecular docking of ligand apelin-13 binding to APJ receptor by Autodock Vina and MCLTools 1.5.2, to analyse the best conformation of ligand binding to APJ receptor.Results:1. Predicted results of phsico-chemical parameters of APJ: Composed of 377 amino acids, Molecular weight is 423490.0, Theoretical pI is 6.96. Predicted hydrophobicity of APJ is that APJ has six hydrophobic areas, they are located in the near position of 35,70,110,150-160,210 and 250; there are 5 hydrophilic areas, they are located in the near position of 50-60,90,130-140,170-180 and 230-240.Predicted coiled coil of APJ is that there is 1 heptad repeat in APJ. Predicted transmembrane segments of APJ is that there are 7 typical transmembrane segments in APJ, they are located in the position of 31⁵3,65⁸7,107¹29,142¹64,201²23,243²65,285³07.There is no signal peptide is predicted; predicted subcellular localization is that APJ is not located in chondriosome, it located in other organelle.2. Predicted motifs and domains show that APJ has 2 N-glycosylation sites which located in the position of 13¹6 and 173¹76; 6 Casein kinase II (CK2)phosphorylation sites which located in 15-18,54-57,87-90,189-192,336-339 and 374-377; 6 N-myristoylation sites which located in 40-45,96-101,144-149,198-203,200²05 and 331-336; 4 Protein kinase C(PKC) phosphorylation sites which located in the position of 54-56,87-89,99-101 and 174-176; 1 cAMP- and cGMP-dependent protein kinase phosphorylation site which located in the position of 58⁶1; G-protein coupled receptors family 1 signature which located in 113¹29, 7tm-1 domain located in the positon of 43³07.3. Predicded secondary structure show that APJ is a Alpha Helical Transmembrane protein; there are 15 cysteines in APJ; predicted number of disulfide bonds is 6; 3 low complexity regions are predicted, they are located in the positions of 145¹64,238²53and 329³49; 1 Nuclear localization signal is predicted in the position of 37⁴3; APJ is a compact globular protein; there is noβ-Barrel in APJ.4. Predicted tertiary structure show that the folder 1u19 is the best fold recognition for APJ. The estimated precision is 100%.5. Predicted binding site show that there are 3 obvious binding sites in APJ, 2 of them are located between chain A and chain B of APJ, there are 1 ligand binding site which is located in chain A.6. Molecular docking show that there are 9 docking mode of the ligand; Optimum conformation 1 with lowest binding energy of -8.4k cal·mol-1 was obtained from nine conformations which were produced in the molecular docking process. Conclusion:1. Bioinformatics analysis show that the folder 1u19 can be used as tertiary structure of APJ;2. Predicted three potential ligand binding sites in APJ.3. Molecular docking show that there are 9 docking mode of the ligand; Optimum conformation with lowest binding energy of -8.4k cal·mol^-1, which can be used as the mode of virtual screening and molecular drug design.