Coding

Part:BBa_K3656310:Experience

Designed by: Zi Liu   Group: iGEM20_AHUT-ZJU-China   (2020-10-27)


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Applications of BBa_K3656310

This year, basing on the existing part (BBa_K2547004, Carbonic anhydrase 2 (L203K) we designed in 2018, in order to further improve its catalytic activity, we designed a new part (BBa_K3656310, CA2 (L203K)-P247K) by mutation of the 247th proline to lysine was developed based on molecular simulation.

Using software PyMOL and Auto Dock, based on CA2(L203K)protein structure (Fig. 1), we conducted molecular simulations.


Fig. 1 Structure of CA2 (L203K)

we set the mutation site and substitution residue, carry out molecular docking of the recombinase, and then compare the enzyme-substrate docking conformation before and after the recombination. Basing on the simulation results above, we finally determined that the suitable mutation site of CA2(L203K) was P247K (the 247th Proline mutated into lysine) (Fig. 2), and an improved new part (BBa_K3656310 CA2 (L203K)-P247K) with higher catalytic activity was obtained.

Fig. 2 Structure of CA2 (L203K)-P247K

Through molecular simulations of Auto Dock, we obtain the following data results. As shown in Table 1, we found that the binding energy of CA2 (L203K)-P247K was improved compared with that of CA2 (L203K), indicating enhanced catalytic activity of our new part than the original existing part.

Table 1 Docking Analysis results of CA2 (L203K) and CA2 (L203K)-P247K by Auto Dock software
Name CA2(L203K) CA2 (L203K)-P247K
Part Number Original part BBa_K2547004 Improved new part BBa_K3656310
binding_energy -4.17 -4.59
ligand_efficiency -1.04 -1.15
inhib_constant 875.8 435.27
inhib_constant_units uM uM
intermol_energy -4.77 -5.18
vdw_hb_desolv_energy -1.7 -1.95
electrostatic_energy -3.07 -3.24
total_intermal 0.03 0.05
torsional_energy 0.6 0.6
unbound_energy 0.03 0.05

The team prepares to further study the function of CA2 (L203K)-P247K in the future, express and purify its protein, and test the activity. We also try to combine our research results with practical applications, including automobile exhaust emissions, industrial production exhaust emissions and CO2 produced by coal chemical industry and so on. We will continue to create more commercial or public products that have greater influence on CO2 capture.

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