View source for Part:BBa K4152214


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<partinfo>BBa_K4152214 short</partinfo>

These elements are the target PK gene we constructed, which would be used to insert the Proteinase K gene into pPIC9.

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===Usage and Biology===

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<span class='h3bb'>Sequence and Features</span>
<partinfo>BBa_K4152214 SequenceAndFeatures</partinfo>


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===Functional Parameters===
<partinfo>BBa_K4152214 parameters</partinfo>
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===Origin(organism)===
Tritirachium album limber
===Structure Design===
*1. Use PyMOL to mutate some residues of Proteinase K, and analyze the possibility of the formation of new interaction forces like hydrogen bond, salt bond, disulfide bond, and π-π interaction. 
*2. Use AlphaFold v2.1.0 to predict the structure of the mutated PK.
<p style="text-align: center;">
[[File:mt14-alphafold.png|400px]]<br>
'''Figure 1.'''   The mutated PK structure compared to the Wild type PK.<br>
</p>
*3. Use FoldX to calculate the Gibbs Free Energy compared to wild-type PK with Ca<sup>2+</sup>. (PDB ID: 1ic6) The result of this mutated PK's ΔΔG is '''-13.81''' kcal/mol.
===Molecular cloning===
We used the wild-type Proteinase K(Hereinafter referred to as PK) DNA gene to overlap our mutated PK gene. 
<p style="text-align: center;">
[[File:mt14-total of pcr'.png|600px]]<br>
'''Figure 2.'''   The process of PCR for our mutated PK gene.<br>
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*1. Use mutated PK primers to clone our small fragments. 
<p style="text-align: center;">
[[File:mt14-pcr1'.png|400px]]<br>
'''Figure 3.'''   Fragments of mutated PK gene are PCR-amplified independently.<br>
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<p style="text-align: center;">
[[File:Mt14-pcr2'.png|250px]]<br>
'''Figure 4.'''   Fragments of mutated PK gene are PCR-amplified independently.<br>
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*2. Fuse the segments in a subsequent reaction by High-fidelity thermostable DNA polymerase.
<p style="text-align: center;">
[[File:Mt14-pcr3'.png|250px]]<br>
'''Figure 5.'''   PCR Mutagenesis by Overlap Extension to obtain the mutated PK gene.<br>
</p>
*3. Use restriction endonuclease XhoⅠ and EcoRⅠ to double digest our mutated PK gene and pPIC9.
<p style="text-align: center;">
[[File:Mt14-dd1'.png|250px]]<br>
'''Figure 6.'''   Double digestion of mutated PK.<br>
</p>
<p style="text-align: center;">
[[File:Mt14-dd2'.png|250px]]<br>
'''Figure 7.'''   Double digestion of pPIC9.<br>
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*4. Use Ligase to link our mutated PK and pPIC9 after double digestion. <br>
*5. Transform the constructed plasmid into competent DH5α cells to expand the plasmid largely <br>
*6. Extract the recombinant pPIC9-PK, verify it by double digestion (XhoⅠ and EcoRⅠ), and sequence it to verify mutation sites.
<p style="text-align: center;">
[[File:Mt14-dd3'.png|400px]]<br>
'''Figure 8.'''   Double digestion verification of Recombinant pPIC9-PK.<br>
</p>
After verification, it was determined that the construction is successful. We transformed the constructed plasmid into competent DH5α cells to expand the plasmid largely<br>
===Expression in <i>Pichia Pastoris</i>===
'''Linearization of Recombinant pPIC9-PK:'''<br>
We used restriction endonuclease SalⅠ to linearize our recombinant plasmid.
<p style="text-align: center;">
[[File:Mt14-linearization.png|500px]]<br>
'''Figure 9.'''   Linearization of Recombinant pPIC9-PK.<br>
</p>
'''Electrotransformation:'''<br>
Add several μg linearized pPIC9-PK to GS115 competence cells, then use a 1.5kV electric pulse to drill holes to let the gene get in.<br> 
'''Screen positive colonies and culture preservation:'''<br>
* 1. Use MD solid medium to screen positive GS115 cells which can grow without Histidine. (Because GS115 cannot grow at medium without Histidine except our gene was introduced in).<br>
* 2. Extract the genomic DNA of recombinant GS115 and verify the sequence of Recombinant pPIC9-PK (from AOX1 promoter to AOX1 Terminator, about 1500bp). 
<p style="text-align: center;">
[[File:Mt14-genome pcr.png|300px]]<br>
'''Figure 10.'''   Genome PCR genomic DNA in Recombinant GS115.<br>
</p>
* 3. Transfer the positive clones and preserve them in Glycerin (sterile), storing them at -80°C.<br>
'''Express PK with Methanol:'''<br>
Transfer some Glycerin recombinant GS115 to YPD, and culture overnight. Then transfer some YPD culture to BMG, culture overnight. Transfer some BMG culture to BMM, add 0.6% Methanol daily, express PK for several days, then collect the supernatant and concentrate it. At last, we do SDS-PAGE to make sure that the mutated PK has expressed successfully, and take the standard samples to do Western blot and quantitative analysis of stripes with ImageJ, then figure out the mass of PK.<br>
<p style="text-align: center;">
[[File:Mt14-SDS-PAGE-1.png|450px]]<br>
'''Figure 11.'''   SDS-PAGE-1.<br>
</p>
<p style="text-align: center;">
[[File:Mt14-SDS-PAGE-2.png|450px]]<br>
'''Figure 12.'''   SDS-PAGE-2.<br>
</p>
===Enzyme activity and thermostability determination===
We use an Enzyme-labeled instrument to measure the Abs of OD<sub>660nm</sub> of the product of L-Tyrosine of the reaction. We use 1% Casein as our substrate, and Tris-HCl (pH8.0) as our Buffer, and react at 55°C for several minutes. Then add trichloroacetic acid (TCA) to end the reaction, and centrifuge to collect the supernatant that contains our product of L-Tyrosine. Next step, we use Na<sub>2</sub>CO<sub>3</sub> to provide the alkaline environment, then add the supernatant and Folin-phenol reagent to colorate L-Tyrosine. In the end, we detect the Abs of OD<sub>660nm</sub> to assess the enzyme activity of our PK. <br>
We store our PK at Room temperature for several days and detect the remains of it, then assess the thermostability of PK.
<p style="text-align: center;">
[[File:Mt14.png|300px]]<br>
'''Figure 13.'''   Enzyme activity determination, compared with wild type.
</p>
===Conclusion===
In conclusion,the thermostability of the Mutated PK has improved '''在这里填东西''' times with Ca<sup>2+</sup>, improved '''在这里填东西''' times without Ca<sup>2+</sup> compared with wild type of PK.