Difference between revisions of "Part:BBa K3308082"

 
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<partinfo>BBa_K3308082 short</partinfo>
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<partinfo>BBa_K3308081 short</partinfo>
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===N1-construct===
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===Overview===
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[[File:Coded- Nested intein diagram.png|300px|thumb|right| ]] The Pittsburgh iGEM team 2019 designed a modular protein circuit system consisting of split Intein-based logic gates. This composite part is an input of the proposed nested intein system. This system is composed of two-independent splicing events reconstituting function functional half of a nested intein. Each nested intein’s chain (N and C terminus) will be split at one  location by another split intein rendering it nonfunctional. Consequently only splicing of the “inner inteins”, will reconstruct the functional intein that is fused to the desired extein. [[#References|[5]]]In this system, the primary splicing events taking place at each split site of the nested intein halves, will serve an AND gate. Each AND is composed of two inputs, the N- and C- terminals of matching inteins.[[#References|[1]]]
  
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n2 +MBP
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[[File:pvs45- 51 general diagram.png|900px|thumb|center|'''Figure 2: Nesting NrdJ-1 Inteins with gp41-1 and TvoVMA split inteins.''' This set of constructs is identical to  BBa_K3308007-13; however,this this composite part contains a solubility tag (maltose binding protein) that is expected to aide in the solubilization of the parts inside the cell. The addition of this tag is said to decrease aggregation of proteins. [[#References|[3]]]. This composite part contains the C-terminal of primary splicing intein, gp41-1. We have denoted it as the N2 construct. The C-Terminus of this split intein is fused to a split site we have chosen in the N-terminus of the intein NrdJ-1. In order to choose this split site we had to consider that the C-terminal flanking sequences for gp41-1 inteins, as well as the predicted structure of the NrdJ-1 intein.]]
  
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<!-- Add more about the biology of this part here
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===Design===
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===Usage and Biology===
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After expression and attempted purification of <partinfo>BBa_K3308007</partinfo>, We decided that we would conduct Gibson Assembly of the part into a different plasmid backbone <partinfo>BBa_K3308093</partinfo> consisting of Maltose Binding Protein[[#References|[3,5]]].  Maltose Bidning Protein is a relatively large 42 kDa
 +
This construct has C terminal of gp41-1 Intein, which means that it is covalently attached to the second half of the N-terminal NrdJ-1 Intein<partinfo>BBa_K3308069</partinfo>. This sepcific split site was chosen in N-NrdJ-1  because it provided the C1 requisite C or S amino acid.[[#References|[2,3,4]]]
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The main purpose of this construct is to preserve functional splicing of gp41-1 C intein.[[#References|[1]]]
 +
 
 +
When looking into the block B site of gp41-1, we saw that there were many acid and base amino acid since this block is involved in the first step as reviewed above we thought that it would be more important than the N-1 intein here. [[#References|[2]]] Considering these things and the fact that any percent yield would still be considered a success for our current methods we decided that this site would be a strong candidate for success.
 +
 
 +
This construct was predicted to splice in the presence of its partner, <partinfo>BBa_K3308081</partinfo>, to form fully fucntional N-terminus NrdJ-1 (BBa_K3308085).
 +
If splicing occurs as planned betweenn these two constructs then, addition of <partinfo>BBa_K3308081</partinfo>, <partinfo>BBa_K3308082</partinfo>, and <partinfo>BBa_K3308086</partinfo> should result in the effective reconstruction of the full extein (GB1-GTNPC-SEIVL-gpD)- <partinfo>BBa_K3308087</partinfo>
 +
===Usage===
 +
Each construct of the set was labeled with 6XHis tag, for the purposes of purification via Ni-NTA resin(1ul/mL of culture). Following the His-tag the composite part also consists of a Tev7 Protease binding site, indicated the three dashed lines. It is important to note that the addition of the tag and cleavage site was not expected to have any impact on the splicing mechanisms of the intein.
 +
 
 +
This construct was induced and expected to react with <partinfo>BBa_K3308081</partinfo> N1  to form the spliced product, the full terminus of the N- NrdJ-1 Intein NSP ( <partinfo>BBa_K3308085</partinfo>.
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 +
===Results===
 +
We were unable to complete the second round Gibson Cloning in order to transform, grow, induce, and purify the protein. We would have epected the addition of MBP to this construct specifically because it contains a C-terminal intein gp41-1 C, would have increased solubility.
  
 
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<partinfo>BBa_K3308082 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3308082 SequenceAndFeatures</partinfo>
  
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===References===
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[1] Gramespacher, J. A., Stevens, A. J., Thompson, R. E., & Muir, T. W. (2018). Improved protein splicing using embedded split inteins. Protein Science, 27(3), 614–619. https://doi.org/10.1002/pro.3357
  
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<!-- Uncomment this to enable Functional Parameter display
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[2] Beyer, H.M., Mikula, K.M., Li, M.,Wlodawer, A., Iwai, H., (2019) The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from a cis-splicing intein.BioRxiv. https://doi.org/10.1101/546465
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===Functional Parameters===
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<partinfo>BBa_K3308082 parameters</partinfo>
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[3] Kimple, M. E., Brill, A. L., & Pasker, R. L. (2013). Overview of affinity tags for protein purification. Current protocols in protein science, 73, Unit–9.9. doi:10.1002/0471140864.ps0909s73
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<!-- -->
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[4]  Amitai, G., Callahan, B. P., Stanger, M. J., Belfort, G., & Belfort, M. (2009). Modulation of intein activity by its neighboring extein substrates. Proceedings of the National Academy of Sciences, 106(27), 11005–11010. https://doi.org/10.1073/pnas.0904366106
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[5] Costa, S., Almeida, A., Castro, A., & Domingues, L. (2014). Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system. Frontiers in Microbiology, 5. doi: 10.3389/fmicb.2014.00063
 +
 
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[6] Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s gift to protein chemists. Chemical Science, 5(2), 446–461. https://doi.org/10.1039/c3sc52951g
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[7] Øemig, J. S. (2013)Structural Studies on Intein. (Published Doctoral Dissertation). University of Helsinki. Helsinki, Finland Retrieved from https://pdfs.semanticscholar.org/3c6a/b9fa31488316df5f421869163101ba13037e.pdf
 +
 
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===Contribution Markup===
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This page was was last updated by Pittsburgh 2019 team.
 +
 
 +
This part is this set of nested Inteins constructs:
 +
<partinfo>BBa_K3308081</partinfo>.
 +
<partinfo>BBa_K3308083</partinfo>.
 +
<partinfo>BBa_K3308084</partinfo>.
 +
<partinfo>BBa_K3308085</partinfo>.
 +
<partinfo>BBa_K3308086</partinfo>.
 +
<partinfo>BBa_K3308087</partinfo>.

Revision as of 00:44, 21 October 2019


GB1-GTNPC-[NrdJ-1 N (1-4)]-[gp41-1 N]

N1-construct

Overview

Coded- Nested intein diagram.png
The Pittsburgh iGEM team 2019 designed a modular protein circuit system consisting of split Intein-based logic gates. This composite part is an input of the proposed nested intein system. This system is composed of two-independent splicing events reconstituting function functional half of a nested intein. Each nested intein’s chain (N and C terminus) will be split at one location by another split intein rendering it nonfunctional. Consequently only splicing of the “inner inteins”, will reconstruct the functional intein that is fused to the desired extein. [5]In this system, the primary splicing events taking place at each split site of the nested intein halves, will serve an AND gate. Each AND is composed of two inputs, the N- and C- terminals of matching inteins.[1]
Figure 2: Nesting NrdJ-1 Inteins with gp41-1 and TvoVMA split inteins. This set of constructs is identical to BBa_K3308007-13; however,this this composite part contains a solubility tag (maltose binding protein) that is expected to aide in the solubilization of the parts inside the cell. The addition of this tag is said to decrease aggregation of proteins. [3]. This composite part contains the C-terminal of primary splicing intein, gp41-1. We have denoted it as the N2 construct. The C-Terminus of this split intein is fused to a split site we have chosen in the N-terminus of the intein NrdJ-1. In order to choose this split site we had to consider that the C-terminal flanking sequences for gp41-1 inteins, as well as the predicted structure of the NrdJ-1 intein.

Design

After expression and attempted purification of BBa_K3308007, We decided that we would conduct Gibson Assembly of the part into a different plasmid backbone BBa_K3308093 consisting of Maltose Binding Protein[3,5]. Maltose Bidning Protein is a relatively large 42 kDa This construct has C terminal of gp41-1 Intein, which means that it is covalently attached to the second half of the N-terminal NrdJ-1 InteinBBa_K3308069. This sepcific split site was chosen in N-NrdJ-1 because it provided the C1 requisite C or S amino acid.[2,3,4] The main purpose of this construct is to preserve functional splicing of gp41-1 C intein.[1]

When looking into the block B site of gp41-1, we saw that there were many acid and base amino acid since this block is involved in the first step as reviewed above we thought that it would be more important than the N-1 intein here. [2] Considering these things and the fact that any percent yield would still be considered a success for our current methods we decided that this site would be a strong candidate for success.

This construct was predicted to splice in the presence of its partner, BBa_K3308081, to form fully fucntional N-terminus NrdJ-1 (BBa_K3308085). If splicing occurs as planned betweenn these two constructs then, addition of BBa_K3308081, BBa_K3308082, and BBa_K3308086 should result in the effective reconstruction of the full extein (GB1-GTNPC-SEIVL-gpD)- BBa_K3308087

Usage

Each construct of the set was labeled with 6XHis tag, for the purposes of purification via Ni-NTA resin(1ul/mL of culture). Following the His-tag the composite part also consists of a Tev7 Protease binding site, indicated the three dashed lines. It is important to note that the addition of the tag and cleavage site was not expected to have any impact on the splicing mechanisms of the intein.

This construct was induced and expected to react with BBa_K3308081 N1 to form the spliced product, the full terminus of the N- NrdJ-1 Intein NSP ( BBa_K3308085.

Results

We were unable to complete the second round Gibson Cloning in order to transform, grow, induce, and purify the protein. We would have epected the addition of MBP to this construct specifically because it contains a C-terminal intein gp41-1 C, would have increased solubility.

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 408
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 106

References

[1] Gramespacher, J. A., Stevens, A. J., Thompson, R. E., & Muir, T. W. (2018). Improved protein splicing using embedded split inteins. Protein Science, 27(3), 614–619. https://doi.org/10.1002/pro.3357

[2] Beyer, H.M., Mikula, K.M., Li, M.,Wlodawer, A., Iwai, H., (2019) The crystal structure of the naturally split gp41-1 intein guides the engineering of orthogonal split inteins from a cis-splicing intein.BioRxiv. https://doi.org/10.1101/546465

[3] Kimple, M. E., Brill, A. L., & Pasker, R. L. (2013). Overview of affinity tags for protein purification. Current protocols in protein science, 73, Unit–9.9. doi:10.1002/0471140864.ps0909s73

[4]  Amitai, G., Callahan, B. P., Stanger, M. J., Belfort, G., & Belfort, M. (2009). Modulation of intein activity by its neighboring extein substrates. Proceedings of the National Academy of Sciences, 106(27), 11005–11010. https://doi.org/10.1073/pnas.0904366106

[5] Costa, S., Almeida, A., Castro, A., & Domingues, L. (2014). Fusion tags for protein solubility, purification and immunogenicity in Escherichia coli: the novel Fh8 system. Frontiers in Microbiology, 5. doi: 10.3389/fmicb.2014.00063

[6] Shah, N. H., & Muir, T. W. (2014). Inteins: Nature’s gift to protein chemists. Chemical Science, 5(2), 446–461. https://doi.org/10.1039/c3sc52951g

[7] Øemig, J. S. (2013)Structural Studies on Intein. (Published Doctoral Dissertation). University of Helsinki. Helsinki, Finland Retrieved from https://pdfs.semanticscholar.org/3c6a/b9fa31488316df5f421869163101ba13037e.pdf

Contribution Markup

This page was was last updated by Pittsburgh 2019 team.

This part is this set of nested Inteins constructs: BBa_K3308081. BBa_K3308083. BBa_K3308084. BBa_K3308085. BBa_K3308086. BBa_K3308087.