Modeling ectodomain of dengue glycoprotein

Project Acheivement

A recent Cryo-electron microscopy reconstruction structure of the glycoprotein E of dengue-2 Virus (1P58.PDB) included the backbone C alpha co-ordinates of the complete protein (res no 1-496). Using this 9.5 Angstrom structure as a seed, the side chain coordinates were built using the program MaxSprout at EMBL, Heidelberg The structure so built, along with the X-ray crystal structures available for dengue-2 virus (1TG8.PDB and 1OKE.PDB) were used for further rebuilding of the model and loop refinement using the homology modeling tool Modeller. The model was evaluated using PROCHECK, Prosa and other tools. The RMSD between the final model for 1P58 and the templates was of the order of 0.9 Angstrom. Super imposition of three structures viz. 1TG8, 1OKE and the final model for 1P58.PDB revels that the 1P58 model has a 3D structure, which resembles that of 1OKE more than that of 1TG8.

Conclusion

The structure of the model including the C-terminus ectodomain stem region (396-449) was seen to be energetically favorable. The model developed thus predicts the structure of the ectodomain stem region of the envelope protein in dengue type 2 virus that can form the basis for further characterization and function annotation using docking methods.

Related Publication

Prabhakar G, C. Rebecca Pearl, Sarah Cherian “Modeling of the complete structure of Dengue Virus Type 2 envelope glycoprotein using C alpha trace from Cryo-electron microscopy as seed” at the Raman Memorial Conference, Dept, of Physics, University of Pune. (Feb 24-25, 2006)