Difference between revisions of "Part:BBa K2547004:Experience"

 
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===Applications of BBa_K2547004===
 
===Applications of BBa_K2547004===
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<h3>Construction of mutant human carbonic anhydrase 2 (CA2 (L203K)) expression plasmid
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</h3>
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<p>Because wild-type CA2 has the fastest reaction rate at 37 °C and loses its activity at 50 °C, so it may be not suitable for using wide type CA2 to capture CO2 under industrial operating conditions. Therefore, we use molecular simulation to design new high-efficiency and stable carbonic anhydrases by improving their catalytic properties and stability. Basing on the simulation results above, we finally determined that the suitable mutation site of CA2 with high and stable activity was L203K (the 203th leucine mutated into lysine).
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<br></p>
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<p>Therefore, we constructed an expression vector containing CA2 (L203K) coding sequence for following activity assay (Fig. 1). The obtained recombinant vector was verified by restriction enzyme digestion (Fig. 2) and sequencing.
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</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;https://static.igem.org/mediawiki/parts/7/7f/T--AHUT_China--_par1t.jpg
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</div>
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<center>Fig. 1 Map of CA2 (L203K) recombinant vector
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</center>
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<div align="center">https://static.igem.org/mediawiki/parts/e/ee/T--AHUT_China--_par2t.jpg</div>
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<center>Fig. 2 Agarose Gel Electrophoresis of CA2(L203K) recombinant plasmid and its identification by enzyme digestion (NdeⅠand Hind Ⅲ). Lane M: DNA marker; Lane 1: CA2 (L203K) recombinant plasmid; Lane 2: enzyme digestion band of CA2 (L203K), the length was 825 bp (the arrow indicated).
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</center>
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<h3>Induced expression of CA2 (L203K) protein
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</h3>
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<p>The CA2 (L203K) expression plasmid was transformed into E. coli BL21 (DE3), and its expression was induced with IPTG, and identified by SDS-PAGE analysis. The results showed that CA2 (L203K) could be expressed in BL21 (DE3) strain and existed in soluble form in the cell lysate supernatant (Fig. 3).
 +
</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;https://static.igem.org/mediawiki/parts/d/d6/T--AHUT_China--78947578.jpg</div>
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<center>Fig. 3 SDS-PAGE analysis for CA2 (L203K) cloned in pET-30a(+) vector and expressed in BL21(DE3) strain.
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</center>
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<h3>Purification of CA2 (L203K) protein
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</h3>
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<p>In order to detect the enzyme activity of CA2 (L203K) protein, we further purify the crude protein extract by nickel column to obtain purified CA2 (L203K) protein. CA2 (L203K) was purified with high purity as indicated by a significant single protein band after SDS-PAGE and Western blot (Fig. 4).
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</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;
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https://static.igem.org/mediawiki/parts/1/1d/T--AHUT_China--_par9t.jpg</div>
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<center>Fig. 4 SDS-PAGE and Western blot analysis of CA2 (L203K) protein. Lane 1: Negative control; Lane 2: purified CA2 (L203K) protein.
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</center>
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<h3>Enzyme activity assay of CA2-WT and CA2 (L203K) protein
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</h3>
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<p>Next, we determined the enzymatic activities of wild-type and mutant CA2 by colorimetric and esterase methods. As indicated in Fig. 5, specific activity of mutant CA2 was about 2 times greater than that of wild-type enzyme. The kinetic constants (Km and Vmax) were calculated for esterase activity assay, and the result showed that CA2 (L203K) protein has a higher activity than CA2-WT (Fig. 6).
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</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;
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https://static.igem.org/mediawiki/parts/6/68/T--AHUT_China--_par5t.jpg</div>
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<center>Fig. 5 Colorimetric assay of CA2 activity
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</center>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;
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https://static.igem.org/mediawiki/parts/8/86/T--AHUT_China--_par6t.jpg</div>
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<center>Fig. 6 Esterase activity analysis of CA2 protein
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</center>
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<h3>
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Thermal stability studies of CA2-WT and CA2 (L203K) protein
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</h3>
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<p>We then investigated the effect of temperature on CA2 activity by esterase activity assay. As shown in Fig. 7, as the temperature increases, especially at 55 °C and 65 °C, the enzymatic activity of CA2-WT was significantly decreased, while the mutant CA2 still retain relatively high activity, indicating that CA2 (L203K) was more stable at high temperature and retained its activity.
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</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;
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https://static.igem.org/mediawiki/parts/f/fc/T--AHUT_China--_par7t.jpg</div>
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<center>Fig. 7 Activity of purified CA2-WT and CA2 (L203K) protein under indicated temperatures and time points.
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</center>
  
 
===User Reviews===
 
===User Reviews===
 
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<I>AHUT-ZJU-China</I>
 
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Enter the review inofrmation here.
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This year, basing on the existing part (<span class="plainlinks">[https://parts.igem.org/Part:BBa_K2547004 BBa_K2547004]</span>, Carbonic anhydrase 2 (L203K) we designed in 2018, in order to further improve its catalytic activity, we designed a new part (<span class="plainlinks">[https://parts.igem.org/Part:BBa_K3656310 BBa_K3656310]</span>, CA2 (L203K)-P247K) by mutation of the 247th proline to lysine was developed based on molecular simulation.
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Using software PyMOL and Auto Dock, based on CA2(L203K)protein structure (Fig. 1), we conducted molecular simulations.
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[[File:T--AHUT-ZJU-China--BBaK3656310_1.png|500px|thumb|center|Fig. 1 Structure of CA2 (L203K)]]
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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 ((<span class="plainlinks">[https://parts.igem.org/Part:BBa_K3656310 BBa_K3656310]</span>) CA2 (L203K)-P247K) with higher catalytic activity was obtained.
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[[File:T--AHUT-ZJU-China--BBaK3656310_2.png|500px|thumb|center|Fig. 2 Structure of CA2 (L203K)-P247K ]]
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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.
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<center>
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{| class="wikitable" style="text-align:center"
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|+ Table 1 Docking Analysis results of CA2 (L203K) and CA2 (L203K)-P247K by Auto Dock software
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|-
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! Name                !! CA2(L203K)                !! CA2 (L203K)-P247K             
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|-
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! Part Number          !! Original part BBa_K2547004 !! Improved new part BBa_K3656310
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|-
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| binding_energy      || -4.17                      || -4.59                         
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|-
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| ligand_efficiency    || -1.04                      || -1.15                         
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|-
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| inhib_constant      || 875.8                      || 435.27                         
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|-
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| inhib_constant_units || uM                        || uM                             
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|-
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| intermol_energy      || -4.77                      || -5.18                         
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|-
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| vdw_hb_desolv_energy || -1.7                      || -1.95                         
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|-
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| electrostatic_energy || -3.07                      || -3.24                         
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|-
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| total_intermal      || 0.03                      || 0.05                           
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|-
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| torsional_energy    || 0.6                        || 0.6                           
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|-
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| unbound_energy      || 0.03                      || 0.05                           
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|}
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</center>
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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 CO<sub>2</sub> produced by coal chemical industry and so on. We will continue to create more commercial or public products that have greater influence on CO<sub>2</sub> capture.
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Latest revision as of 02:52, 28 October 2020


This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K2547004

Construction of mutant human carbonic anhydrase 2 (CA2 (L203K)) expression plasmid

Because wild-type CA2 has the fastest reaction rate at 37 °C and loses its activity at 50 °C, so it may be not suitable for using wide type CA2 to capture CO2 under industrial operating conditions. Therefore, we use molecular simulation to design new high-efficiency and stable carbonic anhydrases by improving their catalytic properties and stability. Basing on the simulation results above, we finally determined that the suitable mutation site of CA2 with high and stable activity was L203K (the 203th leucine mutated into lysine).

Therefore, we constructed an expression vector containing CA2 (L203K) coding sequence for following activity assay (Fig. 1). The obtained recombinant vector was verified by restriction enzyme digestion (Fig. 2) and sequencing.

    T--AHUT_China--_par1t.jpg
Fig. 1 Map of CA2 (L203K) recombinant vector
T--AHUT_China--_par2t.jpg
Fig. 2 Agarose Gel Electrophoresis of CA2(L203K) recombinant plasmid and its identification by enzyme digestion (NdeⅠand Hind Ⅲ). Lane M: DNA marker; Lane 1: CA2 (L203K) recombinant plasmid; Lane 2: enzyme digestion band of CA2 (L203K), the length was 825 bp (the arrow indicated).

Induced expression of CA2 (L203K) protein

The CA2 (L203K) expression plasmid was transformed into E. coli BL21 (DE3), and its expression was induced with IPTG, and identified by SDS-PAGE analysis. The results showed that CA2 (L203K) could be expressed in BL21 (DE3) strain and existed in soluble form in the cell lysate supernatant (Fig. 3).

    T--AHUT_China--78947578.jpg
Fig. 3 SDS-PAGE analysis for CA2 (L203K) cloned in pET-30a(+) vector and expressed in BL21(DE3) strain.

Purification of CA2 (L203K) protein

In order to detect the enzyme activity of CA2 (L203K) protein, we further purify the crude protein extract by nickel column to obtain purified CA2 (L203K) protein. CA2 (L203K) was purified with high purity as indicated by a significant single protein band after SDS-PAGE and Western blot (Fig. 4).

     T--AHUT_China--_par9t.jpg
Fig. 4 SDS-PAGE and Western blot analysis of CA2 (L203K) protein. Lane 1: Negative control; Lane 2: purified CA2 (L203K) protein.

Enzyme activity assay of CA2-WT and CA2 (L203K) protein

Next, we determined the enzymatic activities of wild-type and mutant CA2 by colorimetric and esterase methods. As indicated in Fig. 5, specific activity of mutant CA2 was about 2 times greater than that of wild-type enzyme. The kinetic constants (Km and Vmax) were calculated for esterase activity assay, and the result showed that CA2 (L203K) protein has a higher activity than CA2-WT (Fig. 6).

     T--AHUT_China--_par5t.jpg
Fig. 5 Colorimetric assay of CA2 activity
     T--AHUT_China--_par6t.jpg
Fig. 6 Esterase activity analysis of CA2 protein

Thermal stability studies of CA2-WT and CA2 (L203K) protein

We then investigated the effect of temperature on CA2 activity by esterase activity assay. As shown in Fig. 7, as the temperature increases, especially at 55 °C and 65 °C, the enzymatic activity of CA2-WT was significantly decreased, while the mutant CA2 still retain relatively high activity, indicating that CA2 (L203K) was more stable at high temperature and retained its activity.

     T--AHUT_China--_par7t.jpg
Fig. 7 Activity of purified CA2-WT and CA2 (L203K) protein under indicated temperatures and time points.

User Reviews

UNIQ5be79eedf429b69a-partinfo-00000000-QINU

No review score entered. AHUT-ZJU-China

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.

;

UNIQ5be79eedf429b69a-partinfo-00000002-QINU