Structure prediction of A.thaliana G protein alpha subunit using bioinformatics tools based on sequence alignments

Official URL: http://risc01.sabanciuniv.edu/record=b1064264 (Table of Contents)

Identification and characterization of plant G-proteins are mainly based on sequence homology with their mammalian counterparts. Studies with mutant plants have confirmed the assigned functional roles of these proteins and possible signaling pathways involving G-proteins (Fujisawa Y et al., 2001). The work presented in this thesis, reports detailed sequence alignment analyses of A. Thaliana G-protein a subunit (GPA1) with its mammalian counterpart rat transducin a subunit (PDB entry 1gg2). Alignment of GPA1 with the other known Ga sequences, from plants, reveal a high degree of homology. Same analyse are extended to A. Thaliana b and g subunits. Results of sequence analyses were used as a basis for secondary structure prediction and for modeling 3D structure of GPA1. secondary structure prediction was carried for b and g subunits as well. Modeling calculations were based on the sequence alignment, secondary structure prediction, known structure of rat transducin a subunit, and carried out using the MODELLER moduler within insightII program. The best model predicted 76% correct folding within confidence limits determined using ERRAT. The accuracy of this model can be improved with further optimization of the loop regions. Further work in progress for over-expression of recombinant GPA1 so that the structure can also be determined experimentally.