Difference between revisions of "Team:AHUT China/Background"

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                 <div align="center"> <h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Introduction</h2></div>
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                 <p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆'; font-style: normal; font-weight: 400; font-size: 36px; text-align: center;">&nbsp;&nbsp;&nbsp;&nbsp;<strong style="font-family: Segoe, 'Segoe UI', 'DejaVu Sans', 'Trebuchet MS', Verdana, sans-serif; font-style: normal; font-weight: 400;color: #000000;"> Project Background
                  <p>We took part in the Fifth International InterLab Measurement Study which ains to achieve the purpose of comparative measurement. The goal of this study is to obtain large amounts of data from labs across the world,to develop absolute units for measurements GFP in a plate reader to eliminate variation between labs.</p><br>
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</strong></h2>
<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Materials</h2></div>
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                <hr>
                  <p>Plate reader: Synergy H1 (Biotek)<br>
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                <nbsp><nbsp>
Plate reader plates: Corning 3603 96-Well Microplates (black plates with clear flat bottom)<br>
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                  <p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆'; font-size: 14px;"> <span style="font-size: 16px"><span style="font-size: 24px">Background</span>  </span></p>
Cell culture shaker: ZWYR-200D<br><br>
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<br>
Devices:<br>
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Negative control :BBa_R0040 <br>
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Positive control :BBa_I20270 <br>
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Device 1: BBa_J364000  <br>
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Device 2: BBa_J364001  <br>
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Device 3: BBa_J364002  <br>
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Device 4: BBa_J364007  <br>
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Device 5: BBa_J364008  <br>
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Device 6: BBa_J364009  <br>
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Note: for Device 5, we have not transformed it into DH5⍺ competent cells successfully for many times, therefore, we thank IGEM team of Nanjing University for providing the Device 5.<br>
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Calibration material: Provided in the 2018 IGEM distribution kit <br>
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Microorganism: Escherichia coli DH5⍺ strains<br>
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</p><br>
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<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Methods</h2></div>
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                  <p>Following iGEM requirements, Team AHUT_China performed measurements according to these 2018 InterLab Protocols <a href="https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf">https://static.igem.org/mediawiki/2018/0/09/2018_InterLab_Plate_Reader_Protocol.pdf</a> </p><br>
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<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Results</h2></div>
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                  <h4>1.OD 600 reference point</h4><p>
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Using OD 600 and H2O to generate the conversion factor for the transformation later. The average of OD600 is 0.063; the correction factor (OD600/ABS600) is 3.500
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</p><br>
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  <div align="center"><img src="https://static.igem.org/mediawiki/2018/c/cb/T--AHUT_China--_LUDOX_correct_result.jpg" width="317" height="234" alt=""/></div><br><div align="center">Fig. 1 LUDOX correct value
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  </div>
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  <h4>2.Particle standard curve</h4>
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                  <p>
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We obtained the two Particle Standard Curve (normal and log scale).
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</p><br>
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  <div align="center"><img src="https://static.igem.org/mediawiki/2018/6/65/T--AHUT_China--_Fig._2_Particle_Standard_Curve.jpg" width="701" height="440" alt=""/></div><br><div align="center">Fig. 2 Particle Standard Curve
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  </div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/7/7e/T--AHUT_China--_Fig._3_Particle_Standard_Curve_%28log_scale%29.jpg" width="701" height="440" alt=""/></div><br><div align="center">
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  Fig. 3 Particle Standard Curve (log scale)
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</div>
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<h4>3.Fluorescein standard curve</h4><p>
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Dilution serious of fluorescein were prepared and measured in a 96 well plate. A standard curve is generated to correct the cell based readings to an equivalent fluorescein concentration.<br>
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We obtained the two Fluorescein Standard Curve (normal and log scale).
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</p><br>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/2/24/T--AHUT_China--_Fig._4_Fluorescein_Standard_Curve.jpg" width="701" height="440" alt=""/></div><br><div align="center">
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  Fig. 4 Fluorescein Standard Curve
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</div>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/a/a9/T--AHUT_China--_Fig._5_Fluorescein_Standard_Curve_%28log_scale%29.jpg" width="701" height="440" alt=""/></div><br><div align="center">
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  <div align="center" >Fig. 5 Fluorescein Standard Curve (log scale) </div>
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</div>
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  <h4>4.Cell measurements</h4>
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  </ol>
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<p>&nbsp;</p><br>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/2/21/T--AHUT_China--_Fig._6_Fluorescence_Measurements_Curve_.jpg" width="732" height="492" alt=""/></div><br><div align="center">
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  <div align="center">Fig. 6 Fluorescence Measurements Curve</div>
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</div>
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    <p>Test devices 1 and 4 show high fluorescence intensity. Test devices 2 show a modest fluorescence intensity alone with positive control group, while devices3,5,6 barely show low fluorescence intensity alone with the negative control group.
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  </p><br>
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/3/36/T--AHUT_China--_Fig._7_Raw_OD600_Curve_.jpg" width="724" height="484" alt=""/></div><br><div align="center">
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  <div align="center">Fig. 7 Raw OD600 Curve</div>
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</div>
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    <h4>5.We obtained the Colony Forming Units per 0.1 OD600 E. coli cultures</h4>  
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<div align="center"><img src="https://static.igem.org/mediawiki/2018/f/f1/T--AHUT_China--_Fig._8_CFU_Result.jpg" width="724" height="420" alt=""/></div><br>
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    <div align="center"><img src="https://static.igem.org/mediawiki/2018/e/e5/T--AHUT_China--_Fig._8_CFU_Result1.jpg" width="732" height="492" alt=""/></div><br>
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    <div align="center">
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  <div align="center" >Fig. 8 CFU Result</div>
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  <p >&nbsp;</p>
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<div align="center"><h2 class="title_color">Discussion</h2></div>
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                <p>For Figure 3, the log graph isn’t a straight line but not 1:1 slope. In figure 6, highest fluorescence was obtained from device 4, closely followed by test device 1. Test device 2 and positive control group show a modest fluorescence intensity and device 5,6 show low fluorescence intensity, while test devices 3 barely have any fluorescence signal as well as the negative group.
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  </p>            
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<div align="center"><h2 class="title_color">Conclusion</h2></div>
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                <p>It was certainly a technical challenge to Participate in the InterLab Study. Performing the prescribed protocols with adherence to all the InterLab guidelines yielded parts of expected results, and with the completed InterLab Google Forms, confirms our team participation in this InterLab Study.
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</p>
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                  <p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 16px;">&nbsp;&nbsp;&nbsp;&nbsp;
            </div>
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Nowadays, greenhouse effect is the most important problem that people are facing, which attracts great attention from governments. CO2 accounts for about two-thirds of the total greenhouse gas, and it is the most important gas which causes the greenhouse effect. As a result, various measures to control carbon dioxide emissions, such as CO2 capture, are becoming more and more important. The main methods of CO2 capture include solvent absorption, physical adsorption and membrane separation.<br>
          </div>
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&nbsp;&nbsp;&nbsp;&nbsp;Solvent absorption is mainly based on chemical absorption. Some chemical absorbents can react with CO2 to form compounds and separate CO2 from the flue gas containing the absorbent. However, this method also has the following disadvantages: the solution is easy to oxidize and decompose; the solution is highly corrosive and easy to corrode the instrument; large energy consumption and high operation cost.<br>
 +
Physical adsorption method collects CO2 according to the adsorption characteristics of different components of gas to solid adsorbent. However, this method requires a large number of adsorbent to maintain the operation of this process, and the adsorbent has poor selectivity, low adsorption capacity and low efficiency, resulting in high operating costs and few practical applications.<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;Membrane separation method is based on the polymer film to different gas components of different permeability to achieve the purpose of separation of different gas components. The membranes used can be divided into organic membranes and inorganic membranes. Among them, the organic membrane has strong selectivity for the gas components, simple assembly, but poor heat resistance and corrosion resistance. The inorganic membrane, on the contrary, has good heat resistance and corrosion resistance, but its assembly is complex. In general, CO2 captured by this method is of low purity, requiring multiple purification and less application in industry.<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;The above CO2 capture technologies all have the disadvantages of high cost, low efficiency and poor circulability. These unavoidable disadvantages hinder their application in production and life. Therefore, new technologies are urgently needed, and the technology of carbonic anhydrase (CA) capture makes up for the shortage of other methods.
 +
Carbonic anhydrase, a metal enzyme containing Zn2+, can catalyze CO2 and H2O to produce HCO3- (as shown in figure 1). Carbonic anhydride catalyzes faster than other types of enzymes. The range of carbonic anhydrase catalytic rates is 104 to 106 reactions per second. Among various sources of carbonic anhydrase, human carbonic anhydrase has the highest catalytic efficiency.</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;<img src="
 +
https://static.igem.org/mediawiki/2018/8/8f/T--AHUT_China--_report3.jpg" width="300" height="300" alt=""/></div>
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<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 14px;text-align: center;">
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<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 14px;text-align: center;">Fig1_Catalytic mechanism of carbonic anhydrase (CA2)
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</p>   
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</p>   
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      </div>
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<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 16px;">&nbsp;&nbsp;&nbsp;&nbsp;The molecular weight of carbonic anhydrase is about 30KDa, which is composed of a single peptide chain and contains about 260 amino acids. Each enzyme molecule contains one Zn2+. The structure is ellipsoid, with a pouch cavity in the middle about 1.5nm deep and a cavity opening about 2.0nm wide. Zn2+ binds at the bottom of the cavity. At present, the most studied type of carbonic anhydrase is cosine-family CA, also known as CA2. Its main secondary structure is in its enzyme molecule 10 pali-fold. It is because of their existence that the enzyme structure is divided into two parts. Many key amino acid residues in enzyme molecules are related to their activity. In addition to extension-folding, the surface of the enzyme molecules is also distributed in the form of an icy-helical structure, which is usually a short structure (Fig 2).</p>
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<div align="center">&nbsp;&nbsp;&nbsp;&nbsp;<img src="
 +
https://static.igem.org/mediawiki/2018/8/8f/T--AHUT_China--_report3.jpg" width="300" height="300" alt=""/></div>
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<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 14px;text-align: center;">
 +
<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 14px;text-align: center;">Fig2_The structure of carbonic anhydrase (CA2)
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</p>   
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</p>   
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      </div>       
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<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 16px;">&nbsp;&nbsp;&nbsp;&nbsp;Compared with other methods, carbonic anhydrase capture technology is specific and can capture CO2 from other gases. In addition, this method is environmentally friendly. Carbonic anhydrase converts CO2 into bicarbonate, which can meet the growth demand of plants and microorganisms. When CO2 is converted to bicarbonate, bicarbonate can combine with calcium ions to form calcium carbonate, which is stably stored underground.</p>
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 +
<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 16px;">&nbsp;&nbsp;&nbsp;&nbsp;Compared with other methods, carbonic anhydrase capture technology is more efficient. The main rate-limiting step of general CO2 capture technology is the hydration reaction of CO2, while carbonic anhydrase can significantly increase the hydration reaction rate of CO2, thus improving the CO2 capture efficiency.</p>
 +
 +
<p style="font-family: 'Arial Unicode MS', 'Microsoft YaHei UI', 'Microsoft YaHei UI Light', '华文细黑', '微软雅黑', '幼圆';  font-size: 16px;">&nbsp;&nbsp;&nbsp;&nbsp;
 +
Although carbonic anhydrase capture technology has high efficiency, it still has some limitations. Because most natural carbonic anhydrase environmental sensitivity in the reaction, and do not have heat stability, carbonic anhydrase in CO2 capture, however, the environment temperature is 65 ℃, and natural carbonic anhydrase in the temperature cannot remain stable, after many times circulation loss of enzyme activity. The price of carbonic anhydrase is relatively expensive, and frequent replacement will greatly increase the cost of capture, which limits the wide spread of carbonic anhydrase capture technology. So the key now is to look for the thermal stability of carbonic anhydrase.<br>
 +
In order to find the high efficiency catalysis and high stability of carbonic anhydrase, in this project, we use the high efficiency catalysis characteristic of human carbonic anhydrase 2 (hereinafter referred to as CA2), use molecular simulation method to optimize its amino acid sequence, and design the CA2 mutant with high activity and high stability. The project includes the following aspects:<br>
 +
1) molecular simulation;<br>
 +
2) construction of escherichia coli strains expressing wild-type and mutant CA2;<br>
 +
3) expression and purification of CA2;<br>
 +
4) practical application of CA2: CO2 capture.<br><br>
 +
 
 +
1. Rahman F A, Aziz M M A, Saidur R, et al. Pollution to solution: Capture and sequestration of carbon dioxide (CO2) and its utilization as a renewable energy source for a sustainable future[J]. Renewable & Sustainable Energy Reviews, 2017, 71:112-126.<br>
 +
2. Claudiu T. Supuran. Structure and function of carbonic anhydrases[J]. Biomolecular Biochemical journal, 2016, 473(14):2023-2032.<br>
 +
3. Lionetto M G, Caricato R, Erroi E, et al. Potential application of carbonic anhydrase activity in bioassay and biomarker studies [J]. Chemistry & Ecology, 2006, 22(sup1): S119-S25.<br>
 +
4. Migliardini F, De L V, Carginale V, et al. Biomimetic CO2 capture using a highly thermostable bacterial α-carbonic anhydrase immobilized on a polyurethane foam [J]. Journal of Enzyme Inhibition & Medicinal Chemistry, 2014, 29(1): 146.</p>
 +
  <br><br><br>
 
             </div>
 
             </div>
 
         </section>
 
         </section>

Revision as of 00:33, 11 October 2018

Royal Hotel Royal Hotel







     Project Background


Background


     Nowadays, greenhouse effect is the most important problem that people are facing, which attracts great attention from governments. CO2 accounts for about two-thirds of the total greenhouse gas, and it is the most important gas which causes the greenhouse effect. As a result, various measures to control carbon dioxide emissions, such as CO2 capture, are becoming more and more important. The main methods of CO2 capture include solvent absorption, physical adsorption and membrane separation.
    Solvent absorption is mainly based on chemical absorption. Some chemical absorbents can react with CO2 to form compounds and separate CO2 from the flue gas containing the absorbent. However, this method also has the following disadvantages: the solution is easy to oxidize and decompose; the solution is highly corrosive and easy to corrode the instrument; large energy consumption and high operation cost.
Physical adsorption method collects CO2 according to the adsorption characteristics of different components of gas to solid adsorbent. However, this method requires a large number of adsorbent to maintain the operation of this process, and the adsorbent has poor selectivity, low adsorption capacity and low efficiency, resulting in high operating costs and few practical applications.
    Membrane separation method is based on the polymer film to different gas components of different permeability to achieve the purpose of separation of different gas components. The membranes used can be divided into organic membranes and inorganic membranes. Among them, the organic membrane has strong selectivity for the gas components, simple assembly, but poor heat resistance and corrosion resistance. The inorganic membrane, on the contrary, has good heat resistance and corrosion resistance, but its assembly is complex. In general, CO2 captured by this method is of low purity, requiring multiple purification and less application in industry.
    The above CO2 capture technologies all have the disadvantages of high cost, low efficiency and poor circulability. These unavoidable disadvantages hinder their application in production and life. Therefore, new technologies are urgently needed, and the technology of carbonic anhydrase (CA) capture makes up for the shortage of other methods. Carbonic anhydrase, a metal enzyme containing Zn2+, can catalyze CO2 and H2O to produce HCO3- (as shown in figure 1). Carbonic anhydride catalyzes faster than other types of enzymes. The range of carbonic anhydrase catalytic rates is 104 to 106 reactions per second. Among various sources of carbonic anhydrase, human carbonic anhydrase has the highest catalytic efficiency.

    

Fig1_Catalytic mechanism of carbonic anhydrase (CA2)

    The molecular weight of carbonic anhydrase is about 30KDa, which is composed of a single peptide chain and contains about 260 amino acids. Each enzyme molecule contains one Zn2+. The structure is ellipsoid, with a pouch cavity in the middle about 1.5nm deep and a cavity opening about 2.0nm wide. Zn2+ binds at the bottom of the cavity. At present, the most studied type of carbonic anhydrase is cosine-family CA, also known as CA2. Its main secondary structure is in its enzyme molecule 10 pali-fold. It is because of their existence that the enzyme structure is divided into two parts. Many key amino acid residues in enzyme molecules are related to their activity. In addition to extension-folding, the surface of the enzyme molecules is also distributed in the form of an icy-helical structure, which is usually a short structure (Fig 2).

    

Fig2_The structure of carbonic anhydrase (CA2)

    Compared with other methods, carbonic anhydrase capture technology is specific and can capture CO2 from other gases. In addition, this method is environmentally friendly. Carbonic anhydrase converts CO2 into bicarbonate, which can meet the growth demand of plants and microorganisms. When CO2 is converted to bicarbonate, bicarbonate can combine with calcium ions to form calcium carbonate, which is stably stored underground.

    Compared with other methods, carbonic anhydrase capture technology is more efficient. The main rate-limiting step of general CO2 capture technology is the hydration reaction of CO2, while carbonic anhydrase can significantly increase the hydration reaction rate of CO2, thus improving the CO2 capture efficiency.

     Although carbonic anhydrase capture technology has high efficiency, it still has some limitations. Because most natural carbonic anhydrase environmental sensitivity in the reaction, and do not have heat stability, carbonic anhydrase in CO2 capture, however, the environment temperature is 65 ℃, and natural carbonic anhydrase in the temperature cannot remain stable, after many times circulation loss of enzyme activity. The price of carbonic anhydrase is relatively expensive, and frequent replacement will greatly increase the cost of capture, which limits the wide spread of carbonic anhydrase capture technology. So the key now is to look for the thermal stability of carbonic anhydrase.
In order to find the high efficiency catalysis and high stability of carbonic anhydrase, in this project, we use the high efficiency catalysis characteristic of human carbonic anhydrase 2 (hereinafter referred to as CA2), use molecular simulation method to optimize its amino acid sequence, and design the CA2 mutant with high activity and high stability. The project includes the following aspects:
1) molecular simulation;
2) construction of escherichia coli strains expressing wild-type and mutant CA2;
3) expression and purification of CA2;
4) practical application of CA2: CO2 capture.

1. Rahman F A, Aziz M M A, Saidur R, et al. Pollution to solution: Capture and sequestration of carbon dioxide (CO2) and its utilization as a renewable energy source for a sustainable future[J]. Renewable & Sustainable Energy Reviews, 2017, 71:112-126.
2. Claudiu T. Supuran. Structure and function of carbonic anhydrases[J]. Biomolecular Biochemical journal, 2016, 473(14):2023-2032.
3. Lionetto M G, Caricato R, Erroi E, et al. Potential application of carbonic anhydrase activity in bioassay and biomarker studies [J]. Chemistry & Ecology, 2006, 22(sup1): S119-S25.
4. Migliardini F, De L V, Carginale V, et al. Biomimetic CO2 capture using a highly thermostable bacterial α-carbonic anhydrase immobilized on a polyurethane foam [J]. Journal of Enzyme Inhibition & Medicinal Chemistry, 2014, 29(1): 146.