Difference between revisions of "Part:BBa K3351015"
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<partinfo>BBa_K3351015 short</partinfo>
 
<partinfo>BBa_K3351015 short</partinfo>
 
===Summary===
 
===Summary===
−
PhaP contains a hydrophobic granule binding domain and a cytosol-facing hydrophilic domain. PhaP-tagged proteins could interact with various types of hydrophobic surfaces. A (Gly4Ser2)2 flexible linker is inserted between PhaP and HD5d5 to facilitate attaching of HD5d5 on surface and displaying sufficient flexibility of this peptide.  
+
PhaP contains a hydrophobic granule binding domain and a cytosol-facing hydrophilic domain. Complete biodegradable nature of PhaP. PhaP-tagged proteins could interact with various types of hydrophobic surfaces. A (Gly4Ser2)2 flexible linker is inserted between PhaP and HD5d5 to facilitate attaching of HD5d5 on surface and displaying sufficient flexibility of this peptide.<br>
 +
The noncationic and nonhydrophobic residues of HD5 were replaced with electropositive Arg to increase the antibacterial activity of HD5 derivative that contains a Cys2-4 bond, obtaining another derivative termed HD5d5. The in vitro antibacterial assay and irradiation-wound-infection animal experiment both showed that HD5d5 was much more effective than HD5 at eliminating MDRAb.
 +
<html>
 +
<img style="display: block;
 +
    width: 60%;height: 60%;" src="https://2020.igem.org/wiki/images/9/9c/T--NWU-CHINA-A--p-hd5d5-design.png"><div> </div></html>
 +
 
 +
===Imagine===
 +
The fusion protein PhaP-HD5d5 was expressed in E. coli strain Transetta (DE3).Because PhaP-tagged proteins could interact with various types of hydrophobic surfaces. PhaP-HD5d5 will  anchor to hydrophobic polymer surface efficiently to make band-aids with antibacterial functions.
 +
 
 +
===Design===
 +
1.HD5d5: Mining Gene Information from the Literature.<br>
 +
2.The HD5d5 fragment was subcloned into the pWDX plasmid using the SpeⅠand BamHⅠ sites to produce the pWDX-PhaP-HD5d5 plasmid.<br>
 +
<html>
 +
<img style="display: block;
 +
    width: 60%;height: 60%;" src="https://2020.igem.org/wiki/images/4/47/T--NWU-CHINA-A--p-hd5d5-plasmid.png"><div> </div></html>
 +
3.The plasmids were then transformed into E. coli BL21(DE3), and transformant clones were screened.<br>
 +
4.E. coli BL21 (DE3) was used as the protein expression host.<br>
 +
5.Extraction and Purification of Proteins (PhaP-HD5d5) from E. coli BL21 (DE3).<br>
 +
6.The in vitro antibacterial activities of PhaP-HD5d5 was measured against S. aureus using the filter paper disc diffusion method.<br>
 +
7.PhaP-HD5d5 will be adhered to the surface of PHA/PLA.<br>
 +
8.The bactericidal activity of PhaP, PhaP-Tac, and their coated PHA/PLA films will be tested against selected bacteria.<br>
 +
 
 +
===Research and design cycle===
 +
1.Positive colonies (E. coli BL21 (DE3) pWDX(+)::PhaP-HD5d5) from 12.09.2020 were transferred to test tubes with 2 mL LB+amp and incubated at 37°C, 200 rpm overnight.One 250 mL Erlenmeyer flask with 100 mL LB and 100µL amp/kan was inoculated with 1 mL of one culture above in a 250 mL flask, which both were incubated at 37°C, 200 rpm.OD measurement after three hours showed an OD(600) = 0.6. E. coli BL21 cultures were induced with 100 µL IPTG for incubated at 37°C, 200 rpm overnight.<br>
 +
2.The incubated medium was transferred to 50 mL centrifuge tube and the supernatant collected after centrifuging (6791×g) for 3 min at 4°C. After removal of the supernatant by centrifugation (6791×g, 15 min), it was collected precipitate.<br>
 +
3.The bacterias were crushed with an ultrasonic (ultrasonic power: 400 W, crushing time: 1 s, interval time: 1s) on ice for 2 min. ( A volume of 20 ml of the Bacterial lysates was added to each baterial precipitat, Bacterial lysates 2.0: 20mM/L tris-HCl  150mM/L NaCl)<br>
 +
4.PhaP-HD5d5 was not observed in the supernatant analyzed by SDS-PAGE.<br>
 +
Through analysis, the reason we thought was the Bacterial lysates or the ultrasonic power/total time,so we change the Bacterial lysates and ultrasonic total time.<br>
 +
The bacterias were crushed with an ultrasonic (ultrasonic power: 400 W, crushing time: 1 s, interval time: 1s) on ice for 15 min. ( A volume of 20 ml of the Bacterial lysates was added to each baterial precipitat, Bacterial lysates 2.0: 20mM/L tris-HCl  150mM/L NaCl).But PhaP-HD5d5 also was not observed in the supernatant analyzed by SDS-PAGE.<br>
 +
<br>
 +
This time,we increased the power of ultrasound and the time to crush the bacteria,which were crushed with an ultrasonic (ultrasonic power: 500 W, crushing time: 3 s, interval time: 5s) on ice for 30 min.it is pity that we couldn’t observed the PhaP-HD5d5 in in the supernatant analyzed by SDS-PAGE.<br>
 +
So we increased the total time of ultrasound to 45 min, the bacterias were crushed with an ultrasonic (ultrasonic power: 500 W, crushing time: 3 s, interval time: 5s) on ice for 45 min.
 +
The sonicated bacterial lysate was centrifuged 6791 × g for 15 min at 4°C. Equivalent amounts of supernatant and precipitate were subjected to SDS-PAGE analysis. The supernatant, containing target proteins(PhaP-HD5d5).<br>
 +
<br>
 +
<html><img style="display: block;
 +
    width: 60%;height: 60%;" src="https://2020.igem.org/wiki/images/8/83/T--NWU-CHINA-A--p-hd5d5-gel.png"><div> </div></html>
 +
 
 +
===Bacteriostatic experimen===
 +
It was noticed that the and PhaP-HD5d5 showed the antibacterial effects when examined on S. aureus.<br>
 +
<html>
 +
<img style="display: block;
 +
    width: 60%;height: 60%;" src="https://2020.igem.org/wiki/images/e/ef/T--NWU-CHINA-A--anti-p-hd5d5-1.png"><div> </div><br>
 +
<img style="display: block;
 +
    width: 60%;height: 60%;" src="https://2020.igem.org/wiki/images/3/3e/T--NWU-CHINA-A--anti-p-hd5d5-2.png"><div> </div><br><img style="display: block;
 +
    width: 60%;height: 60%;" src="https://2020.igem.org/wiki/images/f/f7/T--NWU-CHINA-A--anti-p-hd5d5-3.png"><div> </div><br>
 +
</html>
 +
 
  
 
===Characterization===
 
===Characterization===

Revision as of 02:29, 24 October 2020


HisTag-PhaP-linker-HD5d5-HisTag

Summary

PhaP contains a hydrophobic granule binding domain and a cytosol-facing hydrophilic domain. Complete biodegradable nature of PhaP. PhaP-tagged proteins could interact with various types of hydrophobic surfaces. A (Gly4Ser2)2 flexible linker is inserted between PhaP and HD5d5 to facilitate attaching of HD5d5 on surface and displaying sufficient flexibility of this peptide.
The noncationic and nonhydrophobic residues of HD5 were replaced with electropositive Arg to increase the antibacterial activity of HD5 derivative that contains a Cys2-4 bond, obtaining another derivative termed HD5d5. The in vitro antibacterial assay and irradiation-wound-infection animal experiment both showed that HD5d5 was much more effective than HD5 at eliminating MDRAb.

Imagine

The fusion protein PhaP-HD5d5 was expressed in E. coli strain Transetta (DE3).Because PhaP-tagged proteins could interact with various types of hydrophobic surfaces. PhaP-HD5d5 will anchor to hydrophobic polymer surface efficiently to make band-aids with antibacterial functions.

Design

1.HD5d5: Mining Gene Information from the Literature.
2.The HD5d5 fragment was subcloned into the pWDX plasmid using the SpeⅠand BamHⅠ sites to produce the pWDX-PhaP-HD5d5 plasmid.

3.The plasmids were then transformed into E. coli BL21(DE3), and transformant clones were screened.
4.E. coli BL21 (DE3) was used as the protein expression host.
5.Extraction and Purification of Proteins (PhaP-HD5d5) from E. coli BL21 (DE3).
6.The in vitro antibacterial activities of PhaP-HD5d5 was measured against S. aureus using the filter paper disc diffusion method.
7.PhaP-HD5d5 will be adhered to the surface of PHA/PLA.
8.The bactericidal activity of PhaP, PhaP-Tac, and their coated PHA/PLA films will be tested against selected bacteria.

Research and design cycle

1.Positive colonies (E. coli BL21 (DE3) pWDX(+)::PhaP-HD5d5) from 12.09.2020 were transferred to test tubes with 2 mL LB+amp and incubated at 37°C, 200 rpm overnight.One 250 mL Erlenmeyer flask with 100 mL LB and 100µL amp/kan was inoculated with 1 mL of one culture above in a 250 mL flask, which both were incubated at 37°C, 200 rpm.OD measurement after three hours showed an OD(600) = 0.6. E. coli BL21 cultures were induced with 100 µL IPTG for incubated at 37°C, 200 rpm overnight.
2.The incubated medium was transferred to 50 mL centrifuge tube and the supernatant collected after centrifuging (6791×g) for 3 min at 4°C. After removal of the supernatant by centrifugation (6791×g, 15 min), it was collected precipitate.
3.The bacterias were crushed with an ultrasonic (ultrasonic power: 400 W, crushing time: 1 s, interval time: 1s) on ice for 2 min. ( A volume of 20 ml of the Bacterial lysates was added to each baterial precipitat, Bacterial lysates 2.0: 20mM/L tris-HCl 150mM/L NaCl)
4.PhaP-HD5d5 was not observed in the supernatant analyzed by SDS-PAGE.
Through analysis, the reason we thought was the Bacterial lysates or the ultrasonic power/total time,so we change the Bacterial lysates and ultrasonic total time.
The bacterias were crushed with an ultrasonic (ultrasonic power: 400 W, crushing time: 1 s, interval time: 1s) on ice for 15 min. ( A volume of 20 ml of the Bacterial lysates was added to each baterial precipitat, Bacterial lysates 2.0: 20mM/L tris-HCl 150mM/L NaCl).But PhaP-HD5d5 also was not observed in the supernatant analyzed by SDS-PAGE.

This time,we increased the power of ultrasound and the time to crush the bacteria,which were crushed with an ultrasonic (ultrasonic power: 500 W, crushing time: 3 s, interval time: 5s) on ice for 30 min.it is pity that we couldn’t observed the PhaP-HD5d5 in in the supernatant analyzed by SDS-PAGE.
So we increased the total time of ultrasound to 45 min, the bacterias were crushed with an ultrasonic (ultrasonic power: 500 W, crushing time: 3 s, interval time: 5s) on ice for 45 min. The sonicated bacterial lysate was centrifuged 6791 × g for 15 min at 4°C. Equivalent amounts of supernatant and precipitate were subjected to SDS-PAGE analysis. The supernatant, containing target proteins(PhaP-HD5d5).

Bacteriostatic experimen

It was noticed that the and PhaP-HD5d5 showed the antibacterial effects when examined on S. aureus.





Characterization

Figure.1 growth curve

Reference

[1] Xue Q, Liu XB, Lao YH, Wu LP, Wang D, Zuo ZQ, Chen JY, Hou J, Bei YY, Wu XF, Leong KW, Xiang H, Han J. Anti-infective biomaterials with surface-decorated tachyplesin I. Biomaterials. 2018 Sep;178:351-362. doi: 10.1016/j.biomaterials.2018.05.008. Epub 2018 May 9. PMID: 29778319. Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]