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Team:UST Beijing/Modeling
From 2014.igem.org
RFP Parts Evaluation
Evaluation and characterization of a highly engineered RFP gene (BBa_J04450): thermo sensitive expression pattern and secondary structure of mRNA.
Synthetic GLO gene is translated into protein, the primary structure of which was uploaded onto SWISS-Model website for 3D structure construction. Next the constructed 3D model was loaded into Chimera 8.1 and prepared. FAD was docked into model using auto dock vina; next pre-vitamin C, vitamin C and xylitol was individually docked into the catalytic site with FAD in situ. The table above shows the relative binding affinity of each putative substrate. The 3D model was calculated according to xylitol oxidase crystal structure (PDB code 2vfs). The result suggests that the 3D model was nearly accurate enough to distringuish putative substrates.
