Difference between revisions of "Part:BBa K5416000"
(→‎Variants of This Part)
 
(4 intermediate revisions by the same user not shown)
Line 7: Line 7:
 
   <figcaption><strong>Imperial-College 2024</strong></figcaption>
 
   <figcaption><strong>Imperial-College 2024</strong></figcaption>
 
</figure>
 
</figure>
 +
<p>
 +
This part is designed by Imperial_College 2024, a rubber synthase enzyme engineered to work in their composite parts to form artifical rubber-producing organelles.
 +
</p>
 
</html>
 
</html>
  
 
<b>HRT2trunc (Rubber cis-1,4-polyprenyltransferase HRT2, truncated)</b>
 
<b>HRT2trunc (Rubber cis-1,4-polyprenyltransferase HRT2, truncated)</b>
−
This part encodes the truncated version of rubber producing prenyltransferase HRT2 from the rubber tree H brasiliensis ([[Part:BBa_K1088024|K1088024]]). HRT2 uses isopentenyl diphosphate (IPP) as substrates to produce cis-1,4-polyisoprene natural rubber[2]. This enzyme has a unique unit consisting of a hydrophobic channel, where allows the polymerization of the IPP precursors to occur at the entrance and eject the polymerized natural rubber chain through the exit.
+
This part encodes the truncated version of rubber producing prenyltransferase HRT2 from the rubber tree H brasiliensis ([[Part:BBa_K1088024|K1088024]]). HRT2 uses isopentenyl diphosphate (IPP) as substrates to produce cis-1,4-polyisoprene natural rubber<sup>[1][2]</sup>. This enzyme has a unique unit consisting of a hydrophobic channel, where allows the polymerization of the IPP precursors to occur at the entrance and eject the polymerized natural rubber chain through the exit.
 
<br>
 
<br>
  
Line 24: Line 27:
 
Inspired by HRT2 parts designed by SDU_Denmark ([[Part:BBa_K1088024|K1088024]]), we applied several major modifications on protein structure of HRT2. These generate with new HRT2 with higher solubility; and prevent the formation of HRT2 dimer during expression. This modified HRT2 is coupled with multiple strategies (detailed below) during our project for higher rubber yield.
 
Inspired by HRT2 parts designed by SDU_Denmark ([[Part:BBa_K1088024|K1088024]]), we applied several major modifications on protein structure of HRT2. These generate with new HRT2 with higher solubility; and prevent the formation of HRT2 dimer during expression. This modified HRT2 is coupled with multiple strategies (detailed below) during our project for higher rubber yield.
  
−
The protein engineering process to design this part begins with identify the function of each protein domains according to the literature and protein structure database. Whereby we have identified the several domains from the original amino acid sequence of this HRT2 [2][3].
+
The protein engineering process to design this part begins with identify the function of each protein domains according to the literature and protein structure database. Whereby we have identified the several domains from the original amino acid sequence of this HRT2 <sup>[2][3]</sup>.
  
 
<html><div align="center">
 
<html><div align="center">
Line 30: Line 33:
 
   <p><small>Fig 1: Structure and domains of HRT2 from H. brasiliensis.</small></p>
 
   <p><small>Fig 1: Structure and domains of HRT2 from H. brasiliensis.</small></p>
 
</div></html>
 
</div></html>
−
In the structure of HRT2 (wt) predicted via using the ColabFold (Alphafold 2)[4]. The domains previously identified by the literatures are highlighted in different colors as follows: the N terminus and C terminus domain (coloured in blue and teal); dimerizing helix (white); major enzyme catalytic unit (green); substrate binding and catalytic residues (red); residues near the existing channel of polyisoprene chain (yellow).
+
In the structure of HRT2 (wt) predicted via using the ColabFold (Alphafold 2) <sup>[4]</sup>. The domains previously identified by the literatures are highlighted in different colors as follows: the N terminus and C terminus domain (coloured in blue and teal); dimerizing helix (white); major enzyme catalytic unit (green); substrate binding and catalytic residues (red); residues near the existing channel of polyisoprene chain (yellow).
  
 
<html><div align="center">
 
<html><div align="center">
Line 36: Line 39:
 
   <p><small>Fig 2: Strunctural alignment of HRT2 (blue) with cis-prenyltransferase from Homo sapiens.</small></p>
 
   <p><small>Fig 2: Strunctural alignment of HRT2 (blue) with cis-prenyltransferase from Homo sapiens.</small></p>
 
</div></html>
 
</div></html>
−
A protein structural alignment is hence conducted using Swiss-Model to identify the structural homologies with its homologous protein from Homo sapiens (HsCPT) [5]. In which the dimerizing helices, N terminus and C terminus domain (indicated with the arrows) appears to be less conserved after aligning the structures. Inspired by this finding, we hence truncated these domains entirely form the HRT2. Where on the scar that was left after removing the dimerizing domain, a 6xHis tag is inserted to provide the possibility of future protein purification [6].
+
A protein structural alignment is hence conducted using Swiss-Model to identify the structural homologies with its homologous protein from Homo sapiens (HsCPT) <sup>[5]</sup>. In which the dimerizing helices, N terminus and C terminus domain (indicated with the arrows) appears to be less conserved after aligning the structures. Inspired by this finding, we hence truncated these domains entirely form the HRT2. Where on the scar that was left after removing the dimerizing domain, a 6xHis tag is inserted to provide the possibility of future protein purification <sup>[6]</sup>.
  
 
<html><div align="center">
 
<html><div align="center">
Line 47: Line 50:
 
   <p><small>Fig.4 (a): Final structure of HRT2trunc, predicted by Alphafold2.</small></p>
 
   <p><small>Fig.4 (a): Final structure of HRT2trunc, predicted by Alphafold2.</small></p>
 
</div></html>
 
</div></html>
−
The amino acid sequence of the engineered HRT2 – <b>now called HRT2trunc</b>, was used to predict its final structure again with Colab Fold (alphafold2) [4]. The structure is analysed with Pymol where the hydrophobic channel is retained after the modification. Indicating a general success in this process of in silico protein engineering.
+
The amino acid sequence of the engineered HRT2 – <b>now called HRT2trunc</b>, was used to predict its final structure again with Colab Fold (alphafold2) <sup>[4]</sup>. The structure is analysed with Pymol where the hydrophobic channel is retained after the modification. Indicating a general success in this process of in silico protein engineering.
 
<br>
 
<br>
  
Line 72: Line 75:
 
   <p><small>Fig.7 The variants of this part</small></p>
 
   <p><small>Fig.7 The variants of this part</small></p>
 
</div></html>
 
</div></html>
−
We report proteins HRT2trunc-NT-ASIP ([[Part:BBa_K5416070|BBa_K5416070]]); HRT2-SP ([[Part:BBa_K5416001|BBa_K5416001]]); PhaC_HRT2trunc([[Part:BBa_K5416030|BBa_K5416030]]); to be variants of this part. For a comparison, the same domain has been colored in green.
+
We report proteins HRT2trunc-NT-ASIP ([[Part:BBa_K5416070|BBa_K5416070]]); HRT2-SP ([[Part:BBa_K5416001|BBa_K5416001]]); PhaC_HRT2trunc([[Part:BBa_K5416031|BBa_K5416031]]); to be variants of this part. For a comparison, the same domain has been colored in green.
  
 
=Reference:=
 
=Reference:=
 +
<html><p><small>
 
1. Asawatreratanakul, K., Zhang, Y.-W., Wititsuwannakul, D., Wititsuwannakul, R., Takahashi, S., Rattanapittayaporn, A. and Koyama, T. (2003). Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis. European Journal of Biochemistry, 270(23), pp.4671–4680. doi: https://doi.org/10.1046/j.1432-1033.2003.03863.x.
 
1. Asawatreratanakul, K., Zhang, Y.-W., Wititsuwannakul, D., Wititsuwannakul, R., Takahashi, S., Rattanapittayaporn, A. and Koyama, T. (2003). Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis. European Journal of Biochemistry, 270(23), pp.4671–4680. doi: https://doi.org/10.1046/j.1432-1033.2003.03863.x.
 +
<br>
 
2. Yamashita, S. and Takahashi, S. (2020). Molecular Mechanisms of Natural Rubber Biosynthesis. Annual Review of Biochemistry, 89(1), pp.821–851. doi: https://doi.org/10.1146/annurev-biochem-013118-111107.
 
2. Yamashita, S. and Takahashi, S. (2020). Molecular Mechanisms of Natural Rubber Biosynthesis. Annual Review of Biochemistry, 89(1), pp.821–851. doi: https://doi.org/10.1146/annurev-biochem-013118-111107.
 +
<br>
 
3. Takahashi S, Koyama T. Structure and function of cis‐prenyl chain elongating enzymes. The Chemical Record. 2006;6(4):194-205.
 
3. Takahashi S, Koyama T. Structure and function of cis‐prenyl chain elongating enzymes. The Chemical Record. 2006;6(4):194-205.
 +
<br>
 
4. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nature methods. 2022 Jun;19(6):679-82.
 
4. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nature methods. 2022 Jun;19(6):679-82.
 +
<br>
 
5. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic acids research. 2003 Jul 1;31(13):3381-5.
 
5. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic acids research. 2003 Jul 1;31(13):3381-5.
 +
<br>
 
6. Maree HJ, van der Walt E, Tiedt FA, Hanzlik TN, Appel M. Surface display of an internal His-tag on virus-like particles of Nudaurelia capensis ω virus (NωV) produced in a baculovirus expression system. Journal of virological methods. 2006 Sep 1;136(1-2):283-8.
 
6. Maree HJ, van der Walt E, Tiedt FA, Hanzlik TN, Appel M. Surface display of an internal His-tag on virus-like particles of Nudaurelia capensis ω virus (NωV) produced in a baculovirus expression system. Journal of virological methods. 2006 Sep 1;136(1-2):283-8.
 +
</small></p></html>
  
 
=Index=
 
=Index=
 
<html>
 
<html>
 
<p>
 
<p>
−
<span style="background-color: "#A0A0A0"><strong>
+
<span style="background-color: #A0A0A0"><strong>
 
<font color="#003300">MIPTHIAFIL DGNGRFAKKH KLPEGGGHKA GFLALLNVLT YCYELGVKYA TIYAFSIDNF RRKPHEVQYV MNLMLEKIEG MIMEESIINA YDICVRFVGN LKLLDEPLKT AADKIMRATA KNSKFVLLLA VCYT</font><font color="#ff99cc">STDEPH HHHHHPYI</font><font color = "#003300">NP YPDVLIRTSG ETRLSNYLLW QTTNCILYSP HALWPEIGLR HVVWAVQ</font>
 
<font color="#003300">MIPTHIAFIL DGNGRFAKKH KLPEGGGHKA GFLALLNVLT YCYELGVKYA TIYAFSIDNF RRKPHEVQYV MNLMLEKIEG MIMEESIINA YDICVRFVGN LKLLDEPLKT AADKIMRATA KNSKFVLLLA VCYT</font><font color="#ff99cc">STDEPH HHHHHPYI</font><font color = "#003300">NP YPDVLIRTSG ETRLSNYLLW QTTNCILYSP HALWPEIGLR HVVWAVQ</font>
 
</strong></span>
 
</strong></span>

Latest revision as of 09:14, 1 October 2024


HRT2trunc

Description of image

Imperial-College 2024

This part is designed by Imperial_College 2024, a rubber synthase enzyme engineered to work in their composite parts to form artifical rubber-producing organelles.

HRT2trunc (Rubber cis-1,4-polyprenyltransferase HRT2, truncated) This part encodes the truncated version of rubber producing prenyltransferase HRT2 from the rubber tree H brasiliensis (K1088024). HRT2 uses isopentenyl diphosphate (IPP) as substrates to produce cis-1,4-polyisoprene natural rubber[1][2]. This enzyme has a unique unit consisting of a hydrophobic channel, where allows the polymerization of the IPP precursors to occur at the entrance and eject the polymerized natural rubber chain through the exit.

Design

Protein Engineering

Too Long Didn’t Read: Here is our proposed workflow for redesigning this part where the HRT2 is edited into the HRT2trunc tested in our project.

Inspired by HRT2 parts designed by SDU_Denmark (K1088024), we applied several major modifications on protein structure of HRT2. These generate with new HRT2 with higher solubility; and prevent the formation of HRT2 dimer during expression. This modified HRT2 is coupled with multiple strategies (detailed below) during our project for higher rubber yield.

The protein engineering process to design this part begins with identify the function of each protein domains according to the literature and protein structure database. Whereby we have identified the several domains from the original amino acid sequence of this HRT2 [2][3].

Fig 1: Structure and domains of HRT2 from H. brasiliensis.

In the structure of HRT2 (wt) predicted via using the ColabFold (Alphafold 2) [4]. The domains previously identified by the literatures are highlighted in different colors as follows: the N terminus and C terminus domain (coloured in blue and teal); dimerizing helix (white); major enzyme catalytic unit (green); substrate binding and catalytic residues (red); residues near the existing channel of polyisoprene chain (yellow).

Fig 2: Strunctural alignment of HRT2 (blue) with cis-prenyltransferase from Homo sapiens.

A protein structural alignment is hence conducted using Swiss-Model to identify the structural homologies with its homologous protein from Homo sapiens (HsCPT) [5]. In which the dimerizing helices, N terminus and C terminus domain (indicated with the arrows) appears to be less conserved after aligning the structures. Inspired by this finding, we hence truncated these domains entirely form the HRT2. Where on the scar that was left after removing the dimerizing domain, a 6xHis tag is inserted to provide the possibility of future protein purification [6].

Fig.3 (a): The illustration of the engineering on HRT2 domains to produce HRT2trunc. (b) molecular surface of HRT2trunc structure predicted by Alphafold, where a channel for polyisoprene is retained (indicated with red arrows) after truncation. (c)(d): Structure of HsCPT, and the molecular surface.


Fig.4 (a): Final structure of HRT2trunc, predicted by Alphafold2.

The amino acid sequence of the engineered HRT2 – now called HRT2trunc, was used to predict its final structure again with Colab Fold (alphafold2) [4]. The structure is analysed with Pymol where the hydrophobic channel is retained after the modification. Indicating a general success in this process of in silico protein engineering.

Expression

Fig.5 SDS-PAGE, lane L Precison Plus Dual Color protein ladder marker (Bio-rad); lane 4 overnight culture of E. coli BL21 strain expressing this part. Where a band around 22kDa is vaguely identified.

Burden

Fig.6 The growth assay of this part in its E. coli BL21 transformant,under 1mM IPTG induction at 37C

The burden of this part is studied in the growth assay of its E. coli BL21 transformant, where no significant burden in cell growth is identified.

Variants of This Part

Through the path of modular engineering, Imperial-College 2024 have also designed the variants of this parts for the formation of artifical organelles.

Fig.7 The variants of this part

We report proteins HRT2trunc-NT-ASIP (BBa_K5416070); HRT2-SP (BBa_K5416001); PhaC_HRT2trunc(BBa_K5416031); to be variants of this part. For a comparison, the same domain has been colored in green.

Reference:

1. Asawatreratanakul, K., Zhang, Y.-W., Wititsuwannakul, D., Wititsuwannakul, R., Takahashi, S., Rattanapittayaporn, A. and Koyama, T. (2003). Molecular cloning, expression and characterization of cDNA encoding cis-prenyltransferases from Hevea brasiliensis. European Journal of Biochemistry, 270(23), pp.4671–4680. doi: https://doi.org/10.1046/j.1432-1033.2003.03863.x.
2. Yamashita, S. and Takahashi, S. (2020). Molecular Mechanisms of Natural Rubber Biosynthesis. Annual Review of Biochemistry, 89(1), pp.821–851. doi: https://doi.org/10.1146/annurev-biochem-013118-111107.
3. Takahashi S, Koyama T. Structure and function of cis‐prenyl chain elongating enzymes. The Chemical Record. 2006;6(4):194-205.
4. Mirdita M, Schütze K, Moriwaki Y, Heo L, Ovchinnikov S, Steinegger M. ColabFold: making protein folding accessible to all. Nature methods. 2022 Jun;19(6):679-82.
5. Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic acids research. 2003 Jul 1;31(13):3381-5.
6. Maree HJ, van der Walt E, Tiedt FA, Hanzlik TN, Appel M. Surface display of an internal His-tag on virus-like particles of Nudaurelia capensis ω virus (NωV) produced in a baculovirus expression system. Journal of virological methods. 2006 Sep 1;136(1-2):283-8.

Index

MIPTHIAFIL DGNGRFAKKH KLPEGGGHKA GFLALLNVLT YCYELGVKYA TIYAFSIDNF RRKPHEVQYV MNLMLEKIEG MIMEESIINA YDICVRFVGN LKLLDEPLKT AADKIMRATA KNSKFVLLLA VCYTSTDEPH HHHHHPYINP YPDVLIRTSG ETRLSNYLLW QTTNCILYSP HALWPEIGLR HVVWAVQ

The sequnence above is the amino acid sequenc of this part. Displayed here to make codon optimization and protein engineering easier. The sequence in deep green (html#003300) codes for the truncated major enzyme unit of the HRT2 and HRT2trunc. The sequence in pink is the 6xHis-tag introduced to this part (#ff99cc).


----- END-OF-DOCUMNETATION IMPERIAL_COLLEGE2024 -----


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]