Difference between revisions of "Part:BBa K3308081"
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NOTOC__
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<partinfo>BBa_K3308081 short</partinfo>
 
<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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N1 +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 compostie part is N-terminal of primary splicing intein, gp41-1. We have denoted it as the N1 construct. The N-Terminus of this split intein is fused to a split site we have chosen in the N-terminus of a different intein, NrdJ-1. In order to choose this split site we had to consider that the N-terminal flanking sequences for gp41-1 inteins, as well as the predicted structure of the NrdJ-1 intein.]]
  
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[[File:T--Pittsburgh--Nested intein overview.png|2000px|thumb|none|alt=.|Figure 1. Nested Intein design overview]]
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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
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This construct has the first half of the N-terminal NrdJ-1 Intein, which means that it is covalently attached to the N-terminal extein, GB1<partinfo>BBa_K3308065</partinfo>. In between the N-terminus and the extein we have inserted has consensus flanking sequences, GTNPC, that are published as essential to aiding splicing of NrdJ-1, once the whole terminal comes together forming.[[#References|[2,4]]]
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The main purpose of this construct is to preserve functional splicing of gp41-1 intein.[[#References|[1]]] We had to take in consideration that gp41-1 that although we were able to match the requisites for C terminal gp41-1 intein <partinfo>BBa_K3308082</partinfo>.  
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 +
 
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The N1 position, which corresponds to the last amino acid of NrdJ-1 did not match the original sequence reported to preserve functionality in  have been predicted to need in order to preserve splicing. The N-2 amino acid was a Glycine so we assumed that the N-2 properties as EWG or EDG were not as important for this intein.[[#References|[7]]] The N-1 intein was a Lysine so we thought that this particular intein might need the resonance and hindrance of this amino acid, however this site has been changed before and able to still produce splicing. 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.
 +
 
 +
===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.
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This construct was induced and expected to react with <partinfo>BBa_K3308081</partinfo> N2  to form the spliced product, the full terminus of the N- NrdJ-1 Intein NSP ( <partinfo>BBa_K3308085</partinfo>.
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===Results===
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We were unable to complete the second round Gibson Cloning in order to transform, grow, induce, and purify the protein.
  
 
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<partinfo>BBa_K3308081 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K3308081 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_K3308081 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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[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.
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 +
This part is this set of nested Inteins constructs:
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<partinfo>BBa_K3308082</partinfo>.
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<partinfo>BBa_K3308083</partinfo>.
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<partinfo>BBa_K3308084</partinfo>.
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<partinfo>BBa_K3308085</partinfo>.
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<partinfo>BBa_K3308086</partinfo>.
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<partinfo>BBa_K3308087</partinfo>.

Revision as of 00:26, 21 October 2019

NOTOC__ 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 compostie part is N-terminal of primary splicing intein, gp41-1. We have denoted it as the N1 construct. The N-Terminus of this split intein is fused to a split site we have chosen in the N-terminus of a different intein, NrdJ-1. In order to choose this split site we had to consider that the N-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 the first half of the N-terminal NrdJ-1 Intein, which means that it is covalently attached to the N-terminal extein, GB1BBa_K3308065. In between the N-terminus and the extein we have inserted has consensus flanking sequences, GTNPC, that are published as essential to aiding splicing of NrdJ-1, once the whole terminal comes together forming.[2,4] The main purpose of this construct is to preserve functional splicing of gp41-1 intein.[1] We had to take in consideration that gp41-1 that although we were able to match the requisites for C terminal gp41-1 intein BBa_K3308082.


The N1 position, which corresponds to the last amino acid of NrdJ-1 did not match the original sequence reported to preserve functionality in have been predicted to need in order to preserve splicing. The N-2 amino acid was a Glycine so we assumed that the N-2 properties as EWG or EDG were not as important for this intein.[7] The N-1 intein was a Lysine so we thought that this particular intein might need the resonance and hindrance of this amino acid, however this site has been changed before and able to still produce splicing. 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.

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 N2 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.

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
    Illegal BsaI.rc site found at 1227
    Illegal SapI.rc site found at 1527

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_K3308082. BBa_K3308083. BBa_K3308084. BBa_K3308085. BBa_K3308086. BBa_K3308087.