Difference between revisions of "Part:BBa K2686000"

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===Mass Spectrometry===
 
===Mass Spectrometry===
  
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We sent Coomassie stained gel to the Proteomics Core Facility.
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[[File:PCFGel.png|thumb|center|upright=3|The Coomassie stained gel sent to the Proteomics Core Facility. The two bands that were used for mass spec are surrounded by black rectangles and are <bbpart>BBa_K2686002</bbpart> (on the left) and <bbpart>BBa_K2686000</bbpart> (on the right).]]
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We sent the Coomassie stained gel to the Proteomics Core Facility.
  
 
The Proteomics Core Facility then washed the gel we provided, reduced and alkylated it, digested the proteins using trypsin and extracted the peptides to perform MALDI-TOF mass spec. The analysis of the results was also performed by the facility and we were provided the peptide sequence alignments onto the HexaHistidine Encapsulin-OT1 construct.
 
The Proteomics Core Facility then washed the gel we provided, reduced and alkylated it, digested the proteins using trypsin and extracted the peptides to perform MALDI-TOF mass spec. The analysis of the results was also performed by the facility and we were provided the peptide sequence alignments onto the HexaHistidine Encapsulin-OT1 construct.
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[[File:AlignmentOT1FDR.png|thumb|center|upright=3|This image was taken in Scaffold Viewer 4, where the peptides identified from mass spec are aligned to the HexaHistidine Encapsulin-OT1 sequence using a peptide cutoff threshold of 1% FDR. The OT1 peptide has alignments with peptides at the encapsulin’s C terminus which indicates that the OT1 peptide is successfully expressed.]]
 
[[File:AlignmentOT1FDR.png|thumb|center|upright=3|This image was taken in Scaffold Viewer 4, where the peptides identified from mass spec are aligned to the HexaHistidine Encapsulin-OT1 sequence using a peptide cutoff threshold of 1% FDR. The OT1 peptide has alignments with peptides at the encapsulin’s C terminus which indicates that the OT1 peptide is successfully expressed.]]
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[[File:(K)FSIINFEK(-)1%spectrum.PNG|thumb|center|upright=3|Spectrum of FSIINFEKL at 1% FDR threshold.]]
 
[[File:(K)FSIINFEK(-)1%spectrum.PNG|thumb|center|upright=3|Spectrum of FSIINFEKL at 1% FDR threshold.]]
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[[File:(K)FSIINFEK(-)95spectrum.PNG|thumb|center|upright=3|Spectrum of FSIINFEK at 95% probability threshold.]]
 
[[File:(K)FSIINFEK(-)95spectrum.PNG|thumb|center|upright=3|Spectrum of FSIINFEK at 95% probability threshold.]]
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[[File:(K)FSIINFEK(-)95fragmentation.PNG|thumb|center|upright=3|Fragmentation table of FSIINFEK at 95% probability threshold.]]
 
[[File:(K)FSIINFEK(-)95fragmentation.PNG|thumb|center|upright=3|Fragmentation table of FSIINFEK at 95% probability threshold.]]

Revision as of 00:04, 18 October 2018


Encapsulin with HexaHistidine insert and C-terminal OT1

This part encodes a modified Thermotoga maritima Encapsulin protein BBa_K2686001with an additional HexaHistidine (GGGGGGHHHHHHGGGGG) insert between amino acids 43 and 44 BBa_K2686002, forming a loop on the interior surface of the encapsulin monomer providing higher heat resistance and stability, and better hydrodynamic properties (Moon et al., 2014). The C-terminus of the encapsulin is fused to a SIINFEKL (OT1) peptide which is displayed on the exterior surface of the encapsulin monomer as an antigen (Choi et al., 2016). SIINFEKL was chosen as it is a very popular model antigen sequence in research and a variety of antibodies targeting it are available, furthermore it is used as a tumor antigen model in scientific research and has been used in conjunction with encapsulin (Choi et al., 2016).

The part was obtained from BBa_K2686005 by inserting a OT1 coding sequence.

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 77
    Illegal BglII site found at 492
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal SapI.rc site found at 426
    Illegal SapI.rc site found at 457


Characterization

A variety of different characterization techniques were used to assess the properties of the encapsulin protein cage.

Expression

A cell free expression system was used to synthesize the encapsulin proteins in vitro. The TX-TL cell free system is a robust way to express proteins (Sun et al., 2013), and we used the protocol developed by the 2017 EPFL iGEM team Aptasense.

SDS PAGE of encapsulins expressed in cell free TX-TL system with Lysine-BODIPY fluorescent tRNA's (Imager settings used were for measuring fluorescein λex=494nm, λem=512nm ). The two different sets of lanes correspond to different heat denaturation temperatures (70C and 100C for 15 minutes). Stars (✦) show lanes where 60-mers are present. From left to right: (L) Positive control with DNA coding for Luciferase (37kDa), (H) HexaHistidine Encapsulin (BBa_K2686002) showing bands for the encapsulin multimer high on the gel lanes (✦) as well as the monomer around 31kDa, (R) Encapsulin (BBa_K2686001) without HexaHistidine linker also has a band for the 60-mer (✦), (N) Negative control (cell-free TX-TL expression without DNA and 100C denaturation), (Ladder) LC5928 BenchMark™ Fluorescent Protein Standard, (L) Positive control with DNA coding for Luciferase (37kDa), (H) HexaHis Encapsulin (BBa_K2686002) showing bands for the encapsulin multimer high on the gel lanes (✦) as well as the monomer around 31kDa, (R) Encapsulin (BBa_K2686001) without HexaHistidine linker also showing the multimer (✦), (N) Negative control (cell-free TX-TL expression without DNA and 70C denaturation)
SDS PAGE of the different encapsulin proteins expressed by iGEM EPFL 2018. Cell-free mixture Before (B) heat purification procedure outlined above, the pellet after the heat purification procedure (P) and the supernatant after the heat purification procedure (S). Triangles ▲ signify the location of encapsulin 60-mer bands to the right, whereas stars ✦ show encapsulin monomer bands to their right. From left to right: (1-3) Negative control (cell-free TX-TL expression without DNA), (4-6) HexaHistidine Encapsulin (BBa_K2686002) showing bands for the encapsulin multimer high on the gel lanes ▲ as well as the monomer around 31kDa ✦. (7) HexaHistidine-OT1 Encapsulin (BBa_K2686000) where bands are not easily discernible, (8) Ladder Precision Plus Protein™ All Blue Prestained Protein Standards #1610373 , (9) HexaHistidine-OT1 Encapsulin (BBa_K2686000) where the monomer band is visible at 31kDa ✦, (10-12) HexaHistidine Encapsulin (BBa_K2686002) where the bands for the 60-mer ▲ and monomer can be identified✦. (13-15) HexaHistidine-OT1 Encapsulin (BBa_K2686000)

Purification

After having tested a variety of purification procedures, heat purification at 70C for 20 minutes followed by cooling on ice for 15 minutes and a subsequent centrifugation at 12000g for 10 minutes was found to be the most efficient way of isolating the encapsulin (encapsulin ends up in supernatant).

Assembly

The self assembly of the encapsulin 60-mer was first examined using PAGE, where the monomer is seen around 32.9kDa as well as a high band due to the high molecular weight and size of the 1.98MDa complex, showing that the 60-mer is present.

Native PAGE gel of sfGFP, HexaHistidine-OT1 Encapsulin and HexaHistidine-OT1 Encapsulin sfGFP-tag. On the left is the fluorescent image of the gel and o the right is the gel after Coomassie staining. Before (B) heat purification procedure outlined in Purification section, Supernatant (S) after the heat purification procedure. Stars ★ show the bands for monomers of HexaHistidine-OT1 Encapsulin (BBa_K2686000,BBa_K2686006) with sfGFP-tag bound to them, increasing the molecular weight of the complex when compared to sfGFP alone. Triangles ▲ signify a 60-mer band to the right. From left to right: (1-2) Negative control (cell-free TX-TL expression without DNA), (2-4) HexaHistidine-OT1 Encapsulin (BBa_K2686000) shown by a ★. The difference in height between the bands of sfGFP compared to the ★ is striking and suggests that the sfGFP-tag binds to the HexaHistidine-OT1 Encapsulin monomers. In addition there seems to be a small amount of 60-mer indicated by ▲. (9-10) Encapsulin (BBa_K2686001) does assemble to form the 60-mer ▲ as seen on the stained gel. (11) HexaHistidine-OT1 Encapsulin and sfGFP-tag (BBa_K2686006), on the left the presumed ★ protein dimer is seen to be higher than the sfGFP in lane 12, no particular bands can be identified on the right. (12) sfGFP, fluorescent band is seen to be lower than for lane 11.

Mass Spectrometry

The Coomassie stained gel sent to the Proteomics Core Facility. The two bands that were used for mass spec are surrounded by black rectangles and are BBa_K2686002 (on the left) and BBa_K2686000 (on the right).

We sent the Coomassie stained gel to the Proteomics Core Facility.

The Proteomics Core Facility then washed the gel we provided, reduced and alkylated it, digested the proteins using trypsin and extracted the peptides to perform MALDI-TOF mass spec. The analysis of the results was also performed by the facility and we were provided the peptide sequence alignments onto the HexaHistidine Encapsulin-OT1 construct.

Alignment of peptides to HexaHistidine ENcapsulin-OT1

1% FDR cutoff
This image was taken in Scaffold Viewer 4, where the peptides identified from mass spec are aligned to the HexaHistidine Encapsulin-OT1 sequence using a peptide cutoff threshold of 1% FDR. The OT1 peptide has alignments with peptides at the encapsulin’s C terminus which indicates that the OT1 peptide is successfully expressed.
Spectrum of FSIINFEKL at 1% FDR threshold.
Fragmentation table of FSIINFEKL at 1% FDR threshold.
95% probability cutoff
This image was taken in Scaffold Viewer 4, where the peptides identified from mass spec are aligned to the HexaHistidine Encapsulin-OT1 sequence using a peptide threshold of 95% probability. The OT1 peptide excluding the last amino acid has alignments with peptides at the encapsulin’s C terminus which suggests that the OT1 peptide is successfully expressed.
Spectrum of FSIINFEK at 95% probability threshold.
Fragmentation table of FSIINFEK at 95% probability threshold.

Alignment of peptides to HexaHis Encapsulin

1% FDR cutoff
Here the HexaHistidine Encapsulin BBa_K2686002 sample's fragmentation results are aligned against the sequence of HexaHistidine Encapsulin-OT1 BBa_K2686000 using a peptide cutoff of 1% FDR. There are no peptides aligning to the SIINFEKL part which is the desired result since BBa_K2686002 does not have a OT1 peptide at its C terminus.
95% probability cutoff
Here the HexaHistidine Encapsulin BBa_K2686002 sample's fragmentation results are aligned against the sequence of HexaHistidine Encapsulin-OT1 BBa_K2686000 using a peptide cutoff of 95% probability cutoff. There are no peptides aligning to the SIINFEKL part which is the desired result since BBa_K2686002 does not have a OT1 peptide at its C terminus.

Dendritic Cell Uptake

DC3.png
C4-P1 RI.png
L15.png
LW8.png

References

Choi, B., Moon, H., Hong, S., Shin, C., Do, Y., Ryu, S. and Kang, S. (2016). Effective Delivery of Antigen–Encapsulin Nanoparticle Fusions to Dendritic Cells Leads to Antigen-Specific Cytotoxic T Cell Activation and Tumor Rejection. ACS Nano, 10(8), pp.7339-7350.

Moon, H., Lee, J., Min, J. and Kang, S. (2014). Developing Genetically Engineered Encapsulin Protein Cage Nanoparticles as a Targeted Delivery Nanoplatform. Biomacromolecules, 15(10), pp.3794-3801.

Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K. and Ueda, T. (2001). Cell-free translation reconstituted with purified components. Nature Biotechnology, 19(8), pp.751-755.

Sun, Z., Hayes, C., Shin, J., Caschera, F., Murray, R. and Noireaux, V. (2013). Protocols for Implementing an Escherichia coli Based TX-TL Cell-Free Expression System for Synthetic Biology. Journal of Visualized Experiments, (79).