Activation Robot Structural Analysis Professional 2014
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Activation Robot Structural Analysis Professional 2014
to confirm that the mutations that abrogate activity are truly loss of function mutations, we also tested the effect of these mutations on the 3-d structure of aep. because many of the catalytic residues are not located at the surface of aep, we cannot use crystallography to identify the positions of the residues that influence the enzymatic activity. instead, we used molecular dynamics simulation to measure the distance between the catalytic residues and the distance of the mutated residues from the active center. to determine the distance between the mutated residues and the active center, the distance from the mutated residue to the catalytic cys191 residue was measured. the results indicated that d233 and h150 are closest to the active center, which is consistent with the fact that they are located on the surface of aep ( figure 4c ). the r46, v110 and s217/s218 residues are also close to the active center because they are on the surface of aep, but they are not absolutely conserved. interestingly, the mutation of the absolutely conserved residues h47, s39, e189 and d149 did not alter the distance of these residues from the active center. thus, our results indicate that these residues are not located close to the catalytic center, which is consistent with the fact that they do not affect the activity of aep. however, the n44, y45, e216, y222 and s267 residues are located close to the active center, and some of them are absolutely conserved. interestingly, the mutant c221a, which is absolutely conserved, did not affect the distance of the residue to the active center, suggesting that c221 has a different role from other absolutely conserved residues. the results of our analysis are consistent with the 3-d structure of aep and our experimental results, demonstrating that our computational strategy can be used to efficiently predict the effects of mutations on enzyme activity.
in addition to the pro-aep, recombinant aepph7.5 and aepph4.0 were also prepared for co-crystallization trials. the recombinant proteins were produced in e. coli and purified to near-homogeneity ( supplementary information, figure s1d ). the purified proteins were concentrated to ∼35 mg/ml before crystallization. intriguingly, aepph7.0 formed in the presence of peg 3350 exhibited different crystal forms, namely rectangular and hexagonal, respectively ( supplementary information, table s1 ). the rectangular crystal form of aepph7.5 (space group p2~1~2~1~2~1~) diffracted to 2.5 å resolution, whereas the hexagonal crystal form of aepph4.0 (space group p6~5~22) diffracted to 1.35 å resolution ( supplementary information, table s1 ). when the hexagonal crystal form of aepph4.0 was soaked with citric acid (ph 4.0), crystals were formed in the presence of 40 mm citric acid and 5 mm edta (ph 4.5) that diffracted to 3.3 å resolution ( supplementary information, table s1 ). thus, the hexagonal crystal form of aepph4.0 was crystallized in the presence of citric acid, and both the co-crystallization and activation experiments were performed in the presence of 5 mm edta. the crystal structure of aepph4.5 was determined to 2.6 å resolution ( figure 2c and supplementary information, table s2 ). although the crystals were grown in the presence of 1 mm dtt, the corresponding structure was very similar to those with 5 mm dtt. this is because the structure of aepph4.5 in the absence of dtt was determined previously at 1.8 å resolution ( figure 2c and supplementary information, table s3 ).
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