Difference between revisions of "Part:BBa K5398020:Experience"

(→‎Protein Purification)
(→‎Adhesive test)
 
(25 intermediate revisions by the same user not shown)
Line 5: Line 5:
  
 
===Applications of BBa_K5398020===
 
===Applications of BBa_K5398020===
−
In order to obtain proteins with self-healing properties, we used the pET-29a(+) vector to express TRn5 ( BBa_K5398001) ). We tried different strategies for TRn5 protein production and purification and tested its function.
+
In order to obtain proteins with adhesive properties, we used the pET-SUMO vector to express TRn4-mfp5 ( BBa_K5398020) ). We tried different strategies for TRn4-mfp5 protein production and purification and tested its function.
 +
 
  
 
===Characterization===
 
===Characterization===
−
<p>In order to obtain proteins, test suitable expression conditions, and evaluate the function of TRn4-mfp5, we chose three different expression vectors (Fig. 1)—pET-28a(+), pET SUMO, and pET-21a(+)—and tried different strategies for TRn4-mfp5 protein production and purification.</p>
+
In order to obtain proteins, test suitable expression conditions, and evaluate the function of TRn4-mfp5, we chose three different expression vectors (Fig. 1)—pET-28a(+), pET-SUMO, and pET-21a(+)—and tried different strategies for TRn4-mfp5 protein production and purification.
 +
 
 +
 
 
<html lang="zh">
 
<html lang="zh">
 
<head>
 
<head>
Line 26: Line 29:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/plasmid-map-3.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/three-plasmid-trn4mfp5.webp" width="700" height="auto" alt="Protein purification">
 
         <p><b>Fig. 1 | Three different vectors used in protein expression.</b></p>
 
         <p><b>Fig. 1 | Three different vectors used in protein expression.</b></p>
 
         <p><b>a.</b> The plasmid map of pET-28a(+)-His-SUMO-TRn4-mfp5;
 
         <p><b>a.</b> The plasmid map of pET-28a(+)-His-SUMO-TRn4-mfp5;
−
         <b>b.</b> The plasmid map of pET SUMO-TRn4-mfp5;
+
         <b>b.</b> The plasmid map of pET-SUMO-TRn4-mfp5;
 
         <b>c.</b> The plasmid map of pET-21a(+)-TRn4-mfp5.</p>
 
         <b>c.</b> The plasmid map of pET-21a(+)-TRn4-mfp5.</p>
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
 +
 
====Protein Expression====
 
====Protein Expression====
−
<p>We expressed the protein in <i>E. coli</i> BL21 (DE3) using LB medium. After incubation at 16°C for 20 hours and then at 37°C for 4 hours, we found that the protein expressed better under the 16°C for 20 hours condition, as indicated by the stronger bands in Fig. 2. This suggests that lower temperature incubation may enhance protein solubility and proper folding, resulting in improved yield.</p>
+
<p>We expressed the protein in <i>E. coli </i> BL21(DE3) using LB medium. After incubation at 16°C for 20 h or at 37°C for 4 h, we found that the protein expressed better under the 16°C for 20 h condition, as indicated by the stronger bands in Fig. 2. This suggests that lower temperature incubation may enhance protein solubility and proper folding, resulting in improved yield.
 +
<html lang="zh">
 +
<head>
 +
    <meta charset="UTF-8">
 +
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
 +
    <style>
 +
        .module {
 +
            border: 1px solid #ccc; /* 边框 /
 +
            padding: 20px; /* 内边距 /
 +
            margin: 20px auto; /* 外边距，自动居中 /
 +
            width: 800px; /* 模块宽度 /
 +
            text-align: center; /* 内容居中 /
 +
            box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
 +
        }
 +
    </style>
 +
</head>
 +
<body>
 +
    <div class="module">
 +
        <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/16-37-lb-pet21a-new.webp" width="700" height="auto" alt="Protein purification">
 +
        <p><b>Fig. 2 | Comparison of fusion protein expression in different temperature use vector pET-21a(+).</b></p>
 +
        <p>
 +
Lane 1: Protein ladder; Lanes 2-7 (LB 37°C 4 h): Lane 2: Total liquid (IPTG); Lane 3: Supernatant
 +
(IPTG); Lane 4: Precipitate (IPTG); Lane 5: Total liquid; Lane 6: Supernatant; Lane 7: Precipitate;
 +
Lanes 8-13 (TB 16°C 20 h): Lane 8: Total liquid (IPTG); Lane 9: Supernatant (IPTG); Lane 10:
 +
Precipitate (IPTG); Lane 11: Total liquid; Lane 12: Supernatant; Lane 13: Precipitate; Lane 14:
 +
Protein ladder. </p>
 +
    </div>
 +
</body>
 +
</html>
 +
 
 +
 
 +
Since there was some discrepancy in the target band size observed in the SDS-PAGE gel, and the bands were not very distinct, we also tried another medium in an attempt to increase the expression level of the fusion protein. We additionally used TB medium and compared its expression efficiency with that of LB medium. We found that the bands in the TB medium were indeed thicker than those in the LB medium, indicating a slight increase in expression levels, although the difference was not significant.
 +
</p>
 
<html lang="zh">
 
<html lang="zh">
 
<head>
 
<head>
Line 53: Line 89:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/16-37-lb-pet21a.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/tb-lb-prt21a-new.webp" width="700" height="auto" alt="Protein purification">
−
         <p><b>Fig. 2 | Comparison of fusion protein expression in different temperature use vector pET-21a(+).</b></p>
+
         <p><b>Fig. 3 | Comparison of fusion protein expression in LB and TB media use vector pET-21a(+).</b></p>
 
         <p>
 
         <p>
−
<b>Lanes 1-6 (LB 37°C 4 h):  </b>
 
−
1. Protein ladder;
 
−
2. total liquid (+IPTG);
 
−
3. supernatant (+IPTG); 
 
−
4. precipitate (+IPTG); 
 
−
5. total liquid (-IPTG); 
 
−
6. supernatant (-IPTG); 
 
−
7. precipitate (-IPTG); 
 
  
−
<b>Lanes 8-13 (TB 16°C 20 h): </b>
+
Lanes 1-6 (LB 16°C 20 h): Lane 1: Total liquid (IPTG); Lane 2: Supernatant (IPTG); Lane 3:
−
8. Protein ladder; 
+
Precipitate (IPTG); Lane 4: Total liquid; Lane 5: Supernatant; Lane 6: Precipitate; Lane 7: Protein
−
9. total liquid (+IPTG);
+
ladder; Lanes 8-13 (TB 16°C 20 h): Lane 8: Total liquid (IPTG); Lane 9: Supernatant (IPTG); Lane
−
10. supernatant (+IPTG);
+
10: Precipitate (IPTG); Lane 11: Total liquid; Lane 12: Supernatant; Lane 13: Precipitate.
−
11. precipitate (+IPTG);
+
 
−
12. total liquid (-IPTG);
+
</p>
−
13. supernatant (-IPTG);
+
−
14. precipitate (-IPTG). </p>
+
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
−
<p>Since there was some discrepancy in the target band size observed in the protein gel image, and the bands were not very distinct, we also tried another medium in an attempt to increase the expression level of the fusion protein. We additionally used TB medium and compared its expression efficiency with that of LB medium. We found that the bands in the TB medium were indeed thicker than those in the LB medium, indicating a slight increase in expression levels, although the difference was not significant.
+
We compared protein expression between the BL21(DE3) and Rosetta <i>E. coli </i> strains. Rosetta, derived from BL21, includes a compatible chloramphenicol-resistant plasmid that provides tRNA genes for six rare codons (AUA, AGG, AGA, CUA, CCC, GGA) that are often underrepresented in <i>E. coli </i>. This modification is designed to overcome expression limitations when eukaryotic genes, which frequently use these rare codons, are expressed in a prokaryotic system. We used the pET-SUMO vector for expression.<br>
 +
 
 +
While Rosetta is optimized to address these rare codon issues and can be advantageous when expressing eukaryotic proteins with high rare codon usage, our results showed that protein expression levels were higher in the BL21(DE3) strain. This discrepancy could be due to several factors. One possibility is that our target protein does not contain a sufficient number of rare codons to significantly hinder translation in BL21(DE3). Additionally, the extra plasmid load in Rosetta could impose a metabolic burden, reducing its overall protein production efficiency. As a result, in cases where rare codon usage is not a critical factor, BL21(DE3) might provide a more efficient platform for protein expression.<br>
 +
 
 +
The results indicate that the protein expression level in the BL21(DE3) strain is higher compared to that in the Rosetta strain.<br>
 
<html lang="zh">
 
<html lang="zh">
 
<head>
 
<head>
 
     <meta charset="UTF-8">
 
     <meta charset="UTF-8">
 
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
     <meta name="viewport" content="width=device-width, initial-scale=1.0">
−
    <style>
+
  <style>
 
         .module {
 
         .module {
 
             border: 1px solid #ccc; /* 边框 */
 
             border: 1px solid #ccc; /* 边框 */
Line 94: Line 124:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/tb-lb-prt21a.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/rostta-bl21-de3-trn4-mfp-new.webp" width="700" height="auto" alt="Protein purification">
−
         <p><b>Fig. 3 | Comparison of fusion protein expression in LB and TB media use vector pET-21a(+).</b></p>
+
         <p><b>Fig. 4 | Comparison of fusion protein expression in <i>E. coli</i> strains BL21(DE3) and Rosetta.</b></p>
 
         <p>
 
         <p>
−
<b>Lanes 1-6 (LB 16°C 20 h): </b>
+
Lane 1: Protein ladder; Lanes 2-4 (BL21(DE3) LB 37℃ 4 h): Lane 2: Total liquid (IPTG);
−
1. Protein ladder; 
+
Lane 3: Supernatant (IPTG); Lane 4: Precipitate (IPTG); Lanes 5-7 (Rosetta LB 37℃ 4 h) Lane 5:
−
2. total liquid (+IPTG);
+
Total liquid (IPTG); Lane 6: Supernatant (IPTG); Lane 7: Precipitate (IPTG)  
−
3. supernatant (+IPTG);
+
−
4. precipitate (+IPTG);
+
−
5. total liquid (-IPTG); 
+
−
6. supernatant (-IPTG); 
+
−
7. precipitate (-IPTG); 
+
−
 
+
−
<b>Lanes 8-13 (TB 16°C 20 h): </b>
+
−
8. Protein ladder; 
+
−
9. total liquid (+IPTG);
+
−
10. supernatant (+IPTG);
+
−
11. precipitate (+IPTG); 
+
−
12. total liquid (-IPTG); 
+
−
13. supernatant (-IPTG); 
+
−
14. precipitate (-IPTG). 
+
 
</p>
 
</p>
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
−
We compared protein expression between the BL21(DE3) and Rosetta <i>E. coli</i> strains. Rosetta, derived from BL21, includes a compatible chloramphenicol-resistant plasmid that provides tRNA genes for six rare codons (AUA, AGG, AGA, CUA, CCC, GGA) that are lacking in <i>E. coli<i/>. This modification is intended to address expression limitations associated with the high usage frequency of these rare codons in eukaryotic genes. We used the pET SUMO vector for expression.
+
 
−
The results indicate that the protein expression level in the BL21(DE3) strain is higher compared to that in the Rosetta strain.
+
====Protein Purification====
 +
<p>
 +
After considering both expression efficiency and practical experimental constraints, we decided to express the fusion protein at 37°C for 4 h in LB medium using the pET-SUMO-TRn4-mfp5 plasmid.<br>
 +
As shown in Figures 2-4, the target protein was present in the pellet after cell lysis. Therefore, we denatured the pellet of the fusion protein TRn4-mfp5 with 8M urea overnight and renatured it through dialysis. This process resulted in some protein loss, as confirmed by SDS-PAGE analysis. <br>
 +
Consequently, we proceeded to purify the fusion protein TRn4-mfp5 using a Ni-NTA Gravity Column.<br>
 +
The target protein bands were present in lanes 2 to 5, indicating successful expression of the target protein, with a particularly strong band in the supernatant after denaturation (Fig. 5, lane 7). After purification, the target protein was mainly found in the 150 mM and 300 mM imidazole elution fractions.</p>
 +
 
 
<html lang="zh">
 
<html lang="zh">
 
<head>
 
<head>
Line 137: Line 159:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/rostta-bl21-de3-trn4-mfp5png.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/purification-trn4-mfp5-new.webp" width="700" height="auto" alt="Protein purification">
−
         <p><b>Fig. 4 | Comparison of fusion protein expression in <i>E. coli</i> strains BL21(DE3) and Rosetta.</b></p>
+
         <p><b>Fig. 5 | SDS-PAGE of purified fusion protein TRn4-mfp5(35.4 kDa) uses vector pET-SUMO.</b></p>
 
         <p>
 
         <p>
−
1. Protein ladder 
+
Lane 1: Protein-Binding buffer; Lane 2: 20 mM imidazole and 8 M urea elution; Lane 3: 50 mM
−
<i>Lanes 2-4 (BL21(DE3) LB 37℃ 4h)</i>
+
imidazole and 8 M urea elution; Lane 4: 150 mM imidazole and 8 M urea elution; Lane 5: 300 mM
−
2. total liquid (+IPTG);
+
imidazole and 8 M urea elution; Lane 6: 500 mM imidazole and 8 M urea elution; Lane 7:
−
3. supernatant (+IPTG);
+
Supernatant; Lane 8: Impurities; Lane 9: Protein ladder.
−
4. precipitate (+IPTG);
+
−
<i>Lanes 5-7 (Rosetta LB 37℃ 4h)</i>
+
−
5. total liquid (+IPTG);
+
−
6. supernatant (+IPTG);
+
−
7. precipitate (+IPTG).
+
 
</p>
 
</p>
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
 +
 +
To further confirm the expression of TRn4-mfp5, we performed a Western blot, which provided a clear and definitive conclusion, verifying the successful expression of the TRn4-mfp5 protein under the conditions mentioned above.
  
 
<html lang="zh">
 
<html lang="zh">
Line 166: Line 185:
 
             text-align: center; /* 内容居中 */
 
             text-align: center; /* 内容居中 */
 
             box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
 
             box-shadow: 0px 0px 10px rgba(0, 0, 0, 0.1); /* 阴影效果 */
−
        }
 
−
        /* Ensure no text is italic */
 
−
        p, b {
 
−
            font-style: normal; /* 确保文字不是斜体 */
 
 
         }
 
         }
 
     </style>
 
     </style>
Line 175: Line 190:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/purification-trn4-mfp5.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/wb-new.webp" width="700" height="auto" alt="Protein purification">
−
         <p><b>Fig. 4 | SDS-PAGE of purified fusion protein TRn4-mfp5 (35.4 kDa) using vector pET SUMO.</b></p>
+
         <p><b>Fig. 6 | Western Blot of purified fusion protein TRn4-mfp5(35.4 kDa) uses vector pET-SUMO.</b></p>
 
         <p>
 
         <p>
−
            Lane 1: Protein - Binding buffer;<br>
+
<p>
−
            Lane 2: 20 mM imidazole and 8 M urea elution;
+
<b>a.</b> Western blot of the pre-expressed protein. Lane 1: Total liquid (IPTG); Lane 2:
−
            Lane 3: 50 mM imidazole and 8 M urea elution;
+
Supernatant (IPTG); Lane 3: Precipitate (IPTG), <b>b.</b> Western blot after column purification
−
            Lane 4: 150 mM imidazole and 8 M urea elution;
+
of the supernatant following denaturation. Lane 1: Supernatant; Lane 2: 20 mM imidazole and 8
−
            Lane 5: 300 mM imidazole and 8 M urea elution;
+
M urea elution; Lane 3: 50 mM imidazole and 8 M urea elution; Lane 4: 150 mM imidazole and 8 M
−
            Lane 6: 500 mM imidazole and 8 M urea elution;
+
urea elution; Lane 5: 300 mM imidazole and 8 M urea elution; Lane 6: 500 mM imidazole and 8 M
−
            Lane 7: Supernatant;
+
urea elution.
−
            Lane 8: Impurities;
+
</p>
−
            Lane 9: Protein ladder.
+
−
        </p>
+
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
  
−
 
+
====Adhesive test====
−
====Protein Purification====
+
We obtained protein samples of TRn4-mfp5 by freezedrying 24 h (Fig. 7). We finally got about 25 mg protein from 1 L bacterial culture.
−
We obtained protein samples of TRn4-mfp5 by freezedrying 24 h (Fig. 6). The final yield was about 25 mg/L bacterial culture.  
+
−
 
+
 
<html lang="zh">
 
<html lang="zh">
 
<head>
 
<head>
Line 213: Line 224:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/protein-freeze-actual-picture.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/protein-freeze-actual-picture-new.webp" width="700" height="auto" alt="Protein purification">
−
         <p><b>Fig. 6 | The protein sample freeze-dried by a lyophilizer.</b></p>
+
         <p><b>Fig. 7 | The protein sample freeze-dried by a lyophilizer.</b></p>
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
  
−
Next, we dissolved protein samples in Buffer A (10 ml 20 mM Tris pH8) to reach  0.3 mg/mL, and conduct adhesive ability tests on the fusion protein(Fig. 7). 200 μL of the protein solution was applied, and the pipette tip was placed on a plastic Petri dish lid. After incubation at 37°C for 8 hours, the pipette tip successfully adhered.
+
Next, we dissolved protein samples in Buffer A (10 mL 20 mM Tris pH = 8) to reach  0.3 mg/mL, and conduct adhesive ability tests on the fusion protein(Fig. 8). 20 μL of the protein solution was applied, and the pipette tip was placed on a plastic Petri dish lid. After incubation at 37°C for 4 h, the pipette tip successfully adhered.
  
 
<html lang="zh">
 
<html lang="zh">
Line 238: Line 249:
 
<body>
 
<body>
 
     <div class="module">
 
     <div class="module">
−
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/characterization-of-fusion-protein.webp" width="700" height="auto" alt="Protein purification">
+
         <img src="https://static.igem.wiki/teams/5398/trn4-mfp5/part-fig10.webp" width="700" height="auto" alt="Protein purification">
−
         <p><b>Fig. 7 | Adhesive Ability Test of Fusion Protein on Plastic Surface</b></p>
+
         <p><b>Fig. 8 | Adhesive ability test of fusion protein on plastic surface</b></p>
 
     </div>
 
     </div>
 
</body>
 
</body>
 
</html>
 
</html>
  
−
===Reference ===
+
https://video.igem.org/videos/embed/76ade119-0738-4ded-9b7e-1af2e0326a27
−
<p>[1] Jung, H., Pena-Francesch, A., Saadat, A., et al. Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins [J]. <i>PNAS</i>, 2016, 113(23): 6478–6483.</p>
+
<p><b>Video. 1 | NAU-CHINA: TRn4-mfp5 adhesive ability test (2024)</b></p>
−
<p>[2] Zhang, C., Wu, B., Zhou, Y., et al. Mussel-inspired hydrogels: from design principles to promising applications [J]. <i>Chem Soc Rev</i>, 2020, 49: 3605-3637.</p>
+
  
−
===User Reviews===
+
<html lang="en">
−
<!-- DON'T DELETE --><partinfo>BBa_K5398020 StartReviews</partinfo>
+
<head>
−
<!-- Template for a user review
+
    <meta charset="UTF-8">
−
{|width='80%' style='border:1px solid gray'
+
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
−
|-
+
    <title>Viscosity Calculations</title>
−
|width='10%'|
+
    <style>
−
<partinfo>BBa_K5398020 AddReview number</partinfo>
+
        body {
−
<I>Username</I>
+
            font-family: Arial, sans-serif;
−
|width='60%' valign='top'|
+
        }
−
Enter the review inofrmation here.
+
        .calculation {
−
|};
+
            text-align: center;
−
<!-- End of the user review template -->
+
        }
−
<!-- DON'T DELETE --><partinfo>BBa_K5398020 EndReviews</partinfo>
+
        p {
 +
            font-size: 1.2em;
 +
        }
 +
    </style>
 +
</head>
 +
<body>
 +
 
 +
<b>Viscosity Calculations</b>
 +
 
 +
<p><b>Surface Area Calculation:</b></p>
 +
<p>The surface area for the annular region of the pipette tip is calculated as:</p>
 +
<p>
 +
<strong>S</strong> = π × (r<sub>outer</sub><sup>2</sup> - r<sub>inner</sub>
 +
<sup>2</sup>)
 +
</p>
 +
<p>
 +
Where: <br>r<sub>outer</sub> = 3 mm = 0.3 cm <br>
 +
r<sub>inner</sub> = 1.85 mm = 0.185 cm
 +
</p>
 +
<p>
 +
Substituting these values, we get:  
 +
</p>
 +
<p>
 +
<strong>S</strong> = π × (0.3<sup>2</sup> - 0.185<sup>2</sup>) = π × (0.09 - 0.034225) =  
 +
π × 0.055775 ≈ 0.1753 cm<sup>2</sup>  
 +
</p>
 +
<p><b>Force Calculation:</b></p>  
 +
<p>The total force is calculated as:</p>
 +
<p>
 +
<strong>F</strong> = (5.951 + 0.448 × 15) g × 9.8 N/kg = 12.671 g × 9.8 N/kg ≈ 0.12418 N
 +
</p>
 +
<p><b>Adhesive Force Calculation:</b></p>
 +
<p>The adhesive force produced by the protein is:</p>
 +
<p>
 +
<strong>P</strong> = <strong>F</strong> / <strong>S</strong> = 0.12418 N / 0.1753
 +
cm<sup>2</sup> ≈ 0.708 N/cm<sup>2</sup> = 7.08 kPa
 +
</p>
 +
<p><b>Adhesive Force per Milligram of Protein:</b></p>  
 +
<p>The adhesive force per milligram of protein is:</p>
 +
<p>
 +
<strong>P'</strong> = <strong>P</strong> / m = 7.08 kPa / 1 mg = 7.08 kPa/mg
 +
</p>
 +
 
 +
</div>
 +
 
 +
</body>
 +
</html>
 +
 
 +
===Reference ===
 +
<p>[1] Jung  H., Pena-Francesch  A., Saadat  A, et al. Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins[J]. <i>PNAS</i>, 2016, 113(23), 6478–6483.</p>
 +
<p>[2] Zhang C, Wu B, Zhou Y, et al. Mussel-inspired hydrogels: from design principles to promising applications[J]. <i>Chem Soc Rev</i>, 2020, 49(3605): 3605-3637.</p>

Latest revision as of 16:21, 1 October 2024


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_K5398020

In order to obtain proteins with adhesive properties, we used the pET-SUMO vector to express TRn4-mfp5 ( BBa_K5398020) ). We tried different strategies for TRn4-mfp5 protein production and purification and tested its function.


Characterization

In order to obtain proteins, test suitable expression conditions, and evaluate the function of TRn4-mfp5, we chose three different expression vectors (Fig. 1)—pET-28a(+), pET-SUMO, and pET-21a(+)—and tried different strategies for TRn4-mfp5 protein production and purification.


Protein purification

Fig. 1 | Three different vectors used in protein expression.

a. The plasmid map of pET-28a(+)-His-SUMO-TRn4-mfp5; b. The plasmid map of pET-SUMO-TRn4-mfp5; c. The plasmid map of pET-21a(+)-TRn4-mfp5.

Protein Expression

We expressed the protein in E. coli BL21(DE3) using LB medium. After incubation at 16°C for 20 h or at 37°C for 4 h, we found that the protein expressed better under the 16°C for 20 h condition, as indicated by the stronger bands in Fig. 2. This suggests that lower temperature incubation may enhance protein solubility and proper folding, resulting in improved yield.

Protein purification

Fig. 2 | Comparison of fusion protein expression in different temperature use vector pET-21a(+).

Lane 1: Protein ladder; Lanes 2-7 (LB 37°C 4 h): Lane 2: Total liquid (IPTG); Lane 3: Supernatant (IPTG); Lane 4: Precipitate (IPTG); Lane 5: Total liquid; Lane 6: Supernatant; Lane 7: Precipitate; Lanes 8-13 (TB 16°C 20 h): Lane 8: Total liquid (IPTG); Lane 9: Supernatant (IPTG); Lane 10: Precipitate (IPTG); Lane 11: Total liquid; Lane 12: Supernatant; Lane 13: Precipitate; Lane 14: Protein ladder.

Since there was some discrepancy in the target band size observed in the SDS-PAGE gel, and the bands were not very distinct, we also tried another medium in an attempt to increase the expression level of the fusion protein. We additionally used TB medium and compared its expression efficiency with that of LB medium. We found that the bands in the TB medium were indeed thicker than those in the LB medium, indicating a slight increase in expression levels, although the difference was not significant.

Protein purification

Fig. 3 | Comparison of fusion protein expression in LB and TB media use vector pET-21a(+).

Lanes 1-6 (LB 16°C 20 h): Lane 1: Total liquid (IPTG); Lane 2: Supernatant (IPTG); Lane 3: Precipitate (IPTG); Lane 4: Total liquid; Lane 5: Supernatant; Lane 6: Precipitate; Lane 7: Protein ladder; Lanes 8-13 (TB 16°C 20 h): Lane 8: Total liquid (IPTG); Lane 9: Supernatant (IPTG); Lane 10: Precipitate (IPTG); Lane 11: Total liquid; Lane 12: Supernatant; Lane 13: Precipitate.

We compared protein expression between the BL21(DE3) and Rosetta E. coli strains. Rosetta, derived from BL21, includes a compatible chloramphenicol-resistant plasmid that provides tRNA genes for six rare codons (AUA, AGG, AGA, CUA, CCC, GGA) that are often underrepresented in E. coli . This modification is designed to overcome expression limitations when eukaryotic genes, which frequently use these rare codons, are expressed in a prokaryotic system. We used the pET-SUMO vector for expression.

While Rosetta is optimized to address these rare codon issues and can be advantageous when expressing eukaryotic proteins with high rare codon usage, our results showed that protein expression levels were higher in the BL21(DE3) strain. This discrepancy could be due to several factors. One possibility is that our target protein does not contain a sufficient number of rare codons to significantly hinder translation in BL21(DE3). Additionally, the extra plasmid load in Rosetta could impose a metabolic burden, reducing its overall protein production efficiency. As a result, in cases where rare codon usage is not a critical factor, BL21(DE3) might provide a more efficient platform for protein expression.

The results indicate that the protein expression level in the BL21(DE3) strain is higher compared to that in the Rosetta strain.

Protein purification

Fig. 4 | Comparison of fusion protein expression in E. coli strains BL21(DE3) and Rosetta.

Lane 1: Protein ladder; Lanes 2-4 (BL21(DE3) LB 37℃ 4 h): Lane 2: Total liquid (IPTG); Lane 3: Supernatant (IPTG); Lane 4: Precipitate (IPTG); Lanes 5-7 (Rosetta LB 37℃ 4 h) Lane 5: Total liquid (IPTG); Lane 6: Supernatant (IPTG); Lane 7: Precipitate (IPTG)

Protein Purification

After considering both expression efficiency and practical experimental constraints, we decided to express the fusion protein at 37°C for 4 h in LB medium using the pET-SUMO-TRn4-mfp5 plasmid.
As shown in Figures 2-4, the target protein was present in the pellet after cell lysis. Therefore, we denatured the pellet of the fusion protein TRn4-mfp5 with 8M urea overnight and renatured it through dialysis. This process resulted in some protein loss, as confirmed by SDS-PAGE analysis.
Consequently, we proceeded to purify the fusion protein TRn4-mfp5 using a Ni-NTA Gravity Column.
The target protein bands were present in lanes 2 to 5, indicating successful expression of the target protein, with a particularly strong band in the supernatant after denaturation (Fig. 5, lane 7). After purification, the target protein was mainly found in the 150 mM and 300 mM imidazole elution fractions.

Protein purification

Fig. 5 | SDS-PAGE of purified fusion protein TRn4-mfp5(35.4 kDa) uses vector pET-SUMO.

Lane 1: Protein-Binding buffer; Lane 2: 20 mM imidazole and 8 M urea elution; Lane 3: 50 mM imidazole and 8 M urea elution; Lane 4: 150 mM imidazole and 8 M urea elution; Lane 5: 300 mM imidazole and 8 M urea elution; Lane 6: 500 mM imidazole and 8 M urea elution; Lane 7: Supernatant; Lane 8: Impurities; Lane 9: Protein ladder.

To further confirm the expression of TRn4-mfp5, we performed a Western blot, which provided a clear and definitive conclusion, verifying the successful expression of the TRn4-mfp5 protein under the conditions mentioned above.

Protein purification

Fig. 6 | Western Blot of purified fusion protein TRn4-mfp5(35.4 kDa) uses vector pET-SUMO.

a. Western blot of the pre-expressed protein. Lane 1: Total liquid (IPTG); Lane 2: Supernatant (IPTG); Lane 3: Precipitate (IPTG), b. Western blot after column purification of the supernatant following denaturation. Lane 1: Supernatant; Lane 2: 20 mM imidazole and 8 M urea elution; Lane 3: 50 mM imidazole and 8 M urea elution; Lane 4: 150 mM imidazole and 8 M urea elution; Lane 5: 300 mM imidazole and 8 M urea elution; Lane 6: 500 mM imidazole and 8 M urea elution.

Adhesive test

We obtained protein samples of TRn4-mfp5 by freezedrying 24 h (Fig. 7). We finally got about 25 mg protein from 1 L bacterial culture.

Protein purification

Fig. 7 | The protein sample freeze-dried by a lyophilizer.

Next, we dissolved protein samples in Buffer A (10 mL 20 mM Tris pH = 8) to reach 0.3 mg/mL, and conduct adhesive ability tests on the fusion protein(Fig. 8). 20 μL of the protein solution was applied, and the pipette tip was placed on a plastic Petri dish lid. After incubation at 37°C for 4 h, the pipette tip successfully adhered.

Protein purification

Fig. 8 | Adhesive ability test of fusion protein on plastic surface

https://video.igem.org/videos/embed/76ade119-0738-4ded-9b7e-1af2e0326a27

Video. 1 | NAU-CHINA: TRn4-mfp5 adhesive ability test (2024)

Viscosity Calculations Viscosity Calculations

Surface Area Calculation:

The surface area for the annular region of the pipette tip is calculated as:

S = π × (router2 - rinner 2)

Where:
router = 3 mm = 0.3 cm
rinner = 1.85 mm = 0.185 cm

Substituting these values, we get:

S = π × (0.32 - 0.1852) = π × (0.09 - 0.034225) = π × 0.055775 ≈ 0.1753 cm2

Force Calculation:

The total force is calculated as:

F = (5.951 + 0.448 × 15) g × 9.8 N/kg = 12.671 g × 9.8 N/kg ≈ 0.12418 N

Adhesive Force Calculation:

The adhesive force produced by the protein is:

P = F / S = 0.12418 N / 0.1753 cm2 ≈ 0.708 N/cm2 = 7.08 kPa

Adhesive Force per Milligram of Protein:

The adhesive force per milligram of protein is:

P' = P / m = 7.08 kPa / 1 mg = 7.08 kPa/mg

Reference

[1] Jung H., Pena-Francesch A., Saadat A, et al. Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins[J]. PNAS, 2016, 113(23), 6478–6483.

[2] Zhang C, Wu B, Zhou Y, et al. Mussel-inspired hydrogels: from design principles to promising applications[J]. Chem Soc Rev, 2020, 49(3605): 3605-3637.