Team:AHUT-ZJU-China/Improved parts
AHUT-ZJU-China
Improved Parts
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 |
Our 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.