Bioinformatics Analysis and Homology Modeling of HMGR Protein from Hevea brasiliensis
Zhang XiaoFei · Chinese Journal of Tropical Agriculture · 2009
The characters of HMGR protein such as the constitution of amino acids,theoretical pI,alienation/proximity water area,secondary structure in Hevea brasiliensis were analyzed by a series of bioinformatics software,and then compared with those of Litchi chinensis,Arabidopsis thaliana and Oryza sativa.The three-dimensional structure of this protein was constructed by homology modeling,analyzed and then validated.The results show that HMGR protein of H.brasiliensis had 575 amino acids with the pI being 6.44.In the secondary structure α-helix,β-sheet and random coil made up 45.91%,13.04% and 35.83%,respectively.The validation of modeling accords with the stereochemistry.Moreover,appropriate binding sites of SIM and ADP in the structural space of HMGR were predicted by using this modeling,and relative residues which can possibly form H-bonds or interact with SIM and ADP were positioned.