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;"><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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                  <br>
Cell culture shaker: ZWYR-200D<br><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: 18px;">
Devices:<br>
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Nowadays, greenhouse effect is one of the most important problems that people are facing, which attracts great attention from researchers. CO<span style="font-size: 14px">2</span> 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 methods to control CO<span style="font-size: 14px">2</span> emissions, such as CO<span style="font-size: 14px">2</span> capture, are becoming more and more important. The main methods of CO<span style="font-size: 14px">2</span> capture include solvent absorption, physical adsorption and membrane separation, etc.
Negative control :BBa_R0040 <br>
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Solvent absorption method is mainly based on chemical absorption. Some chemical absorbents can react with CO<span style="font-size: 14px">2</span> to form compounds and separate CO<span style="font-size: 14px">2</span> 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.
Positive control :BBa_I20270 <br>  
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<br><br>
Device 1: BBa_J364000  <br>
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Physical adsorption method collects CO<span style="font-size: 14px">2</span> 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><br>
Device 2: BBa_J364001  <br>
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Membrane separation method is based on different permeability of polymeric films to different gas components 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 properties of strong selectivity for the gas components and 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, CO<span style="font-size: 14px">2</span> captured by this method is of low purity requiring multiple purification processes, which limits its application in industry.<br><br>
Device 3: BBa_J364002  <br>
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The above technologies for CO<span style="font-size: 14px">2</span> capture may have the disadvantages of high cost, low efficiency and poor cyclability, which hinder their application under industrial operating conditions. Therefore, new technologies for the absorption of CO<span style="font-size: 14px">2</span> are urgently needed, and the biomimetic approach via the use of an enzyme, namely carbonic anhydrase, may make up for the shortage of those methods.<br><br>
Device 4: BBa_J364007  <br>
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Carbonic anhydrase, a metal enzyme containing Zn<sup>2+</sup>, can catalyze CO<span style="font-size: 14px">2</span> and H<span style="font-size: 13px">2</span>O to produce HCO<sup>3-</sup> (as shown in Fig. 1). Carbonic anhydrase catalyzes faster than other types of enzymes. The range of its catalytic rates is about 10<sup>4</sup> to 10<sup>6</sup> reactions per second. Among various sources of carbonic anhydrases, human carbonic anhydrase 2 (CA2) has the highest catalytic efficiency.</p><br><br><br>
Device 5: BBa_J364008  <br>
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<div align="center"><img src="
Device 6: BBa_J364009  <br>
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https://static.igem.org/mediawiki/2018/5/58/T--AHUT_China--_background1.jpg" width="800" height="300" alt=""/></div>
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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<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;">
Calibration material: Provided in the 2018 IGEM distribution kit <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;text-align: center;">Fig1_Catalytic mechanism of carbonic anhydrase (CA2)
Microorganism: Escherichia coli DH5⍺ strains<br>
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</p>  
</p><br>
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</p>  
<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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<br><br><br>
<div align="center"><h2 class="title_color">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Results</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-size: 18px;">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 Zn<sup>2+</sup>. The structure is ellipsoidal, with a pouch cavity in the middle about 1.5nm deep and a cavity opening about 2.0nm wide. Zn<sup>2+</sup> binds at the bottom of the cavity. At present, the most commonly investigated class of carbonic anhydrase is the α form, also known as CA2. Its main secondary structure is located in its 10 β sheets of its enzyme molecule. 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 β sheets, the surface of the enzyme molecules is also distributed in the form of an α-helical structure, which is usually a short structure (Fig. 2).</p>
                  <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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<br><br><br>
</p><br>
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<div align="center"><img src="
  <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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https://static.igem.org/mediawiki/2018/3/32/T--AHUT_China--_background2.jpg" width="300" height="300" alt=""/></div>
  </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;">
  <h4>2.Particle standard curve</h4>
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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;">Fig2_The structure of carbonic anhydrase (CA2)
                  <p>
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</p>  
We obtained the two Particle Standard Curve (normal and log scale).
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</p>  
</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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<br><br><br>
<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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<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: 18px;">Compared with other methods, the technology of using carbonic anhydrase to capture CO<span style="font-size: 14px">2</span> is specific and can capture CO<span style="font-size: 14px">2</span> from other gases. In addition, this method is environmentally friendly. Carbonic anhydrase converts CO<span style="font-size: 14px">2</span> into bicarbonate, a product that can meet the growth demand of plants and microorganisms. When CO<span style="font-size: 14px">2</span> is converted to bicarbonate, bicarbonate can combine with calcium ions to form calcium carbonate, which can be stored in the ground stably.</p><br>
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 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: 18px;">Compared with other methods, carbonic anhydrase capture technology is more efficient. The main rate-limiting step of general CO<span style="font-size: 14px">2</span> capture technology is the hydration reaction of CO<span style="font-size: 14px">2</span>, while carbonic anhydrase can significantly increase the hydration reaction rate of CO<span style="font-size: 14px">2</span>, thus improving the efficiency of CO<span style="font-size: 14px">2</span> capture.</p>
</p><br>
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<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: 18px;">
<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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Although carbonic anhydrase capture technology has high efficiency, it still has some limitations. Most native carbonic anhydrases are too sensitive to the reaction environment, and are not thermally stable, however, the environment temperature is usually 65 °C, and most native carbonic anhydrase lose their activity at this temperature. Therefore, the key now is to identify thermostable carbonic anhydrase.<br><br>
  Fig. 4 Fluorescein Standard Curve
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In order to find carbonic anhydrase with high catalytic efficiency and stability, in this project, we use molecular simulation technology to design a high-efficiency and stable carbonic anhydrase by improving its catalytic properties and biological stability for CO<span style="font-size: 14px">2</span> capture, including the following parts:<br><br>
</div>
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1) Molecular simulation;<br>
<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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2) Engineered E. coli strains expressing wild-type and mutant CA2;<br>
  <div align="center" >Fig. 5 Fluorescein Standard Curve (log scale) </div>
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3) Application of mutant CA2 for CO<span style="font-size: 14px">2</span> capture.<br><br>
</div>
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</p>
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  <h4>4.Cell measurements</h4>
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  </ol>
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  <br><br>
<p>&nbsp;</p><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: 20px;color: #000000;">References:
<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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</p>
  <div align="center">Fig. 6 Fluorescence Measurements Curve</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: 18px;">
</div>
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[1]Rahman F A, Aziz M M A, Saidur R, et al. Pollution to solution: Capture and sequestration of carbon dioxide (CO<span style="font-size: 12px">2</span>) and its utilization as a renewable energy source for a sustainable future[J]. Renewable & Sustainable Energy Reviews, 2017, 71:112-126.<br>
    <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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[2]Claudiu T. Supuran. Structure and function of carbonic anhydrases[J]. Biomolecular Biochemical journal, 2016, 473(14):2023-2032.<br>
</p><br>
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[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>
 
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[4]Migliardini F, De L V, Carginale V, et al. Biomimetic CO<span style="font-size: 12px">2</span> 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.
<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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</p>
  <div align="center">Fig. 7 Raw OD600 Curve</div>
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</div>
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             </div></div>
    <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" >Fig. 8 CFU Result</div>
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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>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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Latest revision as of 16:39, 17 October 2018

Royal Hotel Royal Hotel







Project Background



Nowadays, greenhouse effect is one of the most important problems that people are facing, which attracts great attention from researchers. 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 methods to control CO2 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, etc. Solvent absorption method 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 different permeability of polymeric films to different gas components 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 properties of strong selectivity for the gas components and 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 processes, which limits its application in industry.

The above technologies for CO2 capture may have the disadvantages of high cost, low efficiency and poor cyclability, which hinder their application under industrial operating conditions. Therefore, new technologies for the absorption of CO2 are urgently needed, and the biomimetic approach via the use of an enzyme, namely carbonic anhydrase, may make up for the shortage of those methods.

Carbonic anhydrase, a metal enzyme containing Zn2+, can catalyze CO2 and H2O to produce HCO3- (as shown in Fig. 1). Carbonic anhydrase catalyzes faster than other types of enzymes. The range of its catalytic rates is about 104 to 106 reactions per second. Among various sources of carbonic anhydrases, human carbonic anhydrase 2 (CA2) 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 ellipsoidal, 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 commonly investigated class of carbonic anhydrase is the α form, also known as CA2. Its main secondary structure is located in its 10 β sheets of its enzyme molecule. 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 β sheets, the surface of the enzyme molecules is also distributed in the form of an α-helical structure, which is usually a short structure (Fig. 2).




Fig2_The structure of carbonic anhydrase (CA2)




Compared with other methods, the technology of using carbonic anhydrase to capture CO2 is specific and can capture CO2 from other gases. In addition, this method is environmentally friendly. Carbonic anhydrase converts CO2 into bicarbonate, a product that 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 can be stored in the ground stably.


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 efficiency of CO2 capture.


Although carbonic anhydrase capture technology has high efficiency, it still has some limitations. Most native carbonic anhydrases are too sensitive to the reaction environment, and are not thermally stable, however, the environment temperature is usually 65 °C, and most native carbonic anhydrase lose their activity at this temperature. Therefore, the key now is to identify thermostable carbonic anhydrase.

In order to find carbonic anhydrase with high catalytic efficiency and stability, in this project, we use molecular simulation technology to design a high-efficiency and stable carbonic anhydrase by improving its catalytic properties and biological stability for CO2 capture, including the following parts:

1) Molecular simulation;
2) Engineered E. coli strains expressing wild-type and mutant CA2;
3) Application of mutant CA2 for CO2 capture.



References:

[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.