Difference between revisions of "Part:BBa K5301007"
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<partinfo>BBa_K5301007 short</partinfo> | <partinfo>BBa_K5301007 short</partinfo> | ||
| − | === | + | ==Introduction== |
| + | |||
| + | The goal of BNU-China 2024 iGEM team is to fabricate nanodiscs, a kind of engineered nanoscale tool, by means of synthetic biology. Our parts collection can be mainly divided into two categories: mono-MSPs that could construct small or large nanodiscs through self-cyclization, and large cyclic MSP formed by the interaction and linkage of multiple MSPs, which are used for constructing large nanodiscs. They are closely linked together due to their common function of manufacturing nanodiscs. | ||
| + | |||
| + | <p>Through literature review, we found MSP1E3D1 as the basic MSP element for constructing nanodiscs<ref>Ilia G. Denisov, Bradley J. Baas, Yelena V. Grinkova, Stephen G. Sligar, Cooperativity in Cytochrome P450 3A4: LINKAGES IN SUBSTRATE BINDING, SPIN STATE, UNCOUPLING, AND PRODUCT FORMATION*, Journal of Biological Chemistry, Volume 282, Issue 10, 2007, Pages 7066-7076, ISSN 0021-9258, https://doi.org/10.1074/jbc.M609589200.</ref>. We further sought and obtained spNW15 and spNW50 <ref> Zhang, S., et al., One-step construction of circularized nanodiscs using SpyCatcher-SpyTag. Nature Communications, 2021. 12(1): p. 5451.</ref>that utilized the automatic covalent linkage of SpyTag and SpyCatcher to enhance the cyclization efficiency and enable the automatic cyclization of MSP, in order to manufacture nanodiscs of different diameters more simply. On this basis, taking NW15 as the basic component, we designed the multi-polymerized MSP, consisting of three linear MSP monomers. Only when three mono-MSPs interact with each other can they form cyclized MSP and achieve their function of constructing nanodiscs. It provides a more flexible solution for manufacturing large nanodiscs, while reducing the expression pressure on the chassis bacteria and avoiding the difficulty of purifying large proteins. </p> | ||
| + | |||
| + | <p>This Part Collection aims to provide a series of easily accessible and distinctively characterized MSP proteins as a toolkit for the assembly of nanodiscs. Users can easily select which MSP to produce and utilize based on their own needs to manufacture nanodiscs. The nanodiscs fabricated using the MSP we designed can be used for stabilizing amphipathic proteins, studying the structure and function of amphipathic proteins, drug delivery, developing novel antiviral drugs, etc., and possess broad application prospects<ref> Padmanabha Das, K.M., et al., Large Nanodiscs: A Potential Game Changer in Structural Biology of Membrane Protein Complexes and Virus Entry. Frontiers in Bioengineering and Biotechnology, 2020. 8.</ref>. </p> | ||
| + | |||
| + | <p>This part produces SnTST-mCh[11], as a part of the multi-polymerized MSP, to produce large nanodiscs more simply.</p> | ||
| + | |||
| + | ==Usage and Biology== | ||
In order to produce large nanodiscs more conveniently, we hope to flexibly extend the length of MSP according to demand, and thus propose the concept of multi-polymer MSP, which refers to large circular MSPs through end-to-end connections of multiple MSP fragments. | In order to produce large nanodiscs more conveniently, we hope to flexibly extend the length of MSP according to demand, and thus propose the concept of multi-polymer MSP, which refers to large circular MSPs through end-to-end connections of multiple MSP fragments. | ||
We used NW15 as the basic MSP and selected three types of linkers (Spy/Sdy/Snoop) to achieve the connection of different MSP fragments through the formation of covalent bonds, and adopted rigorous design to prevent self-cyclization of each fragment of the multi-polymer MSP. Finally, the successful cyclization of large circular MSPs is characterized by the fluorescence of mCherry after the combination of mCherry [1-10] and mCherry [11]. | We used NW15 as the basic MSP and selected three types of linkers (Spy/Sdy/Snoop) to achieve the connection of different MSP fragments through the formation of covalent bonds, and adopted rigorous design to prevent self-cyclization of each fragment of the multi-polymer MSP. Finally, the successful cyclization of large circular MSPs is characterized by the fluorescence of mCherry after the combination of mCherry [1-10] and mCherry [11]. | ||
| − | SnTST-mCh[11], the third component of multi-polymerized MSP, is a fusion protein composed of SnoopTag, | + | SnTST-mCh[11], the third component of multi-polymerized MSP, is a fusion protein composed of SnoopTag, spNW15, mCherry [11], and SpyTag, with flexible GS linkers used to connect each part. |
| + | |||
| + | <p>We also utilized AlphaFold 2 to simulate the structure of SnTST-mCh[11] and obtained the correct linear, non-cyclized protein conformation, as shown in the figure. </p> | ||
| + | |||
| + | <div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.3;overflow:hidden;"> | ||
| + | https://static.igem.wiki/teams/5301/parts/tri-3-model.png | ||
| + | </div><div class="thumbcaption"> | ||
| + | Figure 1.The structure of SnTST-mCh[11] predicted by AlphaFold2 | ||
| + | </div></div></div></div> | ||
| + | |||
| + | ==Plasmid Construction== | ||
| + | To produce multi-polymerized MSP, we first constructed plasmids to synthesize three MSPs separately. We obtained the gene sequence of NW15 from NCBI and integrated the sequences of SnoopTag and SpyTag at its N-terminus and C-terminus to form SnTST-mCh[11]. We added 5' (NcoI) and 3' (XhoI) to the ends of the gene through GENEWIZ, cloning them into the vector pET-28a(+) (Kanamycin) to construct three recombinant plasmids, which were then introduced into BL21 (DE3). Subsequently, we picked multiple single colonies from the plate for colony PCR to check if the plasmids were successfully introduced into the host bacteria. | ||
| + | <div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.5;overflow:hidden;"> | ||
| + | https://static.igem.wiki/teams/5301/parts/tri-3-pcr.png | ||
| + | </div><div class="thumbcaption"> | ||
| + | Figure 2.Colony PCR Results of Host Bacteria Introduced with pET28a_SnTST-mCh[11], All Four Colonies Successfully Obtained the Desired Band, Indicating Successful Plasmid Transformation.The theoretical sequence length is 911 bp. | ||
| + | </div></div></div></div> | ||
==Cultivation, Purification and SDS-PAGE== | ==Cultivation, Purification and SDS-PAGE== | ||
===Induction=== | ===Induction=== | ||
| − | We chose the T7 expression system as the pathway for protein expression and induced protein expression by adding IPTG at an appropriate time. To achieve efficient expression of SnTST-mCh[11], we screened the induction conditions using IPTG. We set up a gradient of four IPTG concentrations: 0.2mM, 0.5mM, 0.8mM, and 1mM. The results showed that the optimal protein expression was achieved with a concentration of | + | We chose the T7 expression system as the pathway for protein expression and induced protein expression by adding IPTG at an appropriate time. To achieve efficient expression of SnTST-mCh[11], we screened the induction conditions using IPTG. We set up a gradient of four IPTG concentrations: 0.2mM, 0.5mM, 0.8mM, and 1mM. The results showed that the optimal protein expression was achieved with a concentration of 1mM. |
<div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.5;overflow:hidden;"> | <div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.5;overflow:hidden;"> | ||
https://static.igem.wiki/teams/5301/parts/tri-3-induc.png | https://static.igem.wiki/teams/5301/parts/tri-3-induc.png | ||
</div><div class="thumbcaption"> | </div><div class="thumbcaption"> | ||
| − | Figure | + | Figure 3.SDS-PAGE analysis of SnTST-mCh[11] protein with IPTG concentration gradient induction. An IPTG concentration gradient of 0.2mM, 0.5mM, 0.8mM, and 1mM was used for 16 hours induction at 16°C. The molecular weight of SnTST-mCh[11] is 33.6 kDa. |
</div></div></div></div> | </div></div></div></div> | ||
===Purification=== | ===Purification=== | ||
After confirming the successful expression of SnTST-mCh[11], we scaled up the culture and purified the protein. During plasmid construction, we incorporated a His-tag into the sequence, allowing for purification using nickel affinity chromatography, which specifically binds to His-tagged proteins. We eluted the protein using 100mM and 500mM imidazole, and successfully obtained target protein. To verify the successful expression of the protein, we conducted a Western Blot using anti-Histag after SDS-PAGE and confirmed that we had obtained SnTST-mCh[11] with a relatively high purity. | After confirming the successful expression of SnTST-mCh[11], we scaled up the culture and purified the protein. During plasmid construction, we incorporated a His-tag into the sequence, allowing for purification using nickel affinity chromatography, which specifically binds to His-tagged proteins. We eluted the protein using 100mM and 500mM imidazole, and successfully obtained target protein. To verify the successful expression of the protein, we conducted a Western Blot using anti-Histag after SDS-PAGE and confirmed that we had obtained SnTST-mCh[11] with a relatively high purity. | ||
| − | <div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0. | + | <div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.6;overflow:hidden;"> |
| − | https://static.igem.wiki/teams/5301/parts/tri- | + | https://static.igem.wiki/teams/5301/parts/tri-3-wb.png |
</div><div class="thumbcaption"> | </div><div class="thumbcaption"> | ||
| − | Figure | + | Figure 4.Western Blot Analysis of SCSdC-mCh[1-10] Purified by Nickel Affinity Chromatography. The presence of the target protein in the 100mM imidazole elution buffer was verified through Histag antibody and the correct molecular weight of the bands. The molecular weight of SnTST-mCh[11] is 33.6 kDa. |
</div></div></div></div> | </div></div></div></div> | ||
| + | ==Structure and biological activity analysis== | ||
| + | We attempted to incubate three protein segments in vitro through different methods to link them, and successfully obtained mCherry fluorescence images.For more information on the construction of multi-polymerized MSP, go to <partinfo>BBa_K5301024</partinfo>. | ||
| + | |||
| + | ===Sequence and Features=== | ||
<!-- --> | <!-- --> | ||
| − | <span class='h3bb'> | + | <span class='h3bb'></span> |
<partinfo>BBa_K5301007 SequenceAndFeatures</partinfo> | <partinfo>BBa_K5301007 SequenceAndFeatures</partinfo> | ||
Latest revision as of 10:06, 2 October 2024
SnTST-mCh[11] is one of the components of multi-polymerized MSP.
Introduction
The goal of BNU-China 2024 iGEM team is to fabricate nanodiscs, a kind of engineered nanoscale tool, by means of synthetic biology. Our parts collection can be mainly divided into two categories: mono-MSPs that could construct small or large nanodiscs through self-cyclization, and large cyclic MSP formed by the interaction and linkage of multiple MSPs, which are used for constructing large nanodiscs. They are closely linked together due to their common function of manufacturing nanodiscs.
Through literature review, we found MSP1E3D1 as the basic MSP element for constructing nanodiscs[1]. We further sought and obtained spNW15 and spNW50 [2]that utilized the automatic covalent linkage of SpyTag and SpyCatcher to enhance the cyclization efficiency and enable the automatic cyclization of MSP, in order to manufacture nanodiscs of different diameters more simply. On this basis, taking NW15 as the basic component, we designed the multi-polymerized MSP, consisting of three linear MSP monomers. Only when three mono-MSPs interact with each other can they form cyclized MSP and achieve their function of constructing nanodiscs. It provides a more flexible solution for manufacturing large nanodiscs, while reducing the expression pressure on the chassis bacteria and avoiding the difficulty of purifying large proteins.
This Part Collection aims to provide a series of easily accessible and distinctively characterized MSP proteins as a toolkit for the assembly of nanodiscs. Users can easily select which MSP to produce and utilize based on their own needs to manufacture nanodiscs. The nanodiscs fabricated using the MSP we designed can be used for stabilizing amphipathic proteins, studying the structure and function of amphipathic proteins, drug delivery, developing novel antiviral drugs, etc., and possess broad application prospects[3].
This part produces SnTST-mCh[11], as a part of the multi-polymerized MSP, to produce large nanodiscs more simply.
Usage and Biology
In order to produce large nanodiscs more conveniently, we hope to flexibly extend the length of MSP according to demand, and thus propose the concept of multi-polymer MSP, which refers to large circular MSPs through end-to-end connections of multiple MSP fragments. We used NW15 as the basic MSP and selected three types of linkers (Spy/Sdy/Snoop) to achieve the connection of different MSP fragments through the formation of covalent bonds, and adopted rigorous design to prevent self-cyclization of each fragment of the multi-polymer MSP. Finally, the successful cyclization of large circular MSPs is characterized by the fluorescence of mCherry after the combination of mCherry [1-10] and mCherry [11]. SnTST-mCh[11], the third component of multi-polymerized MSP, is a fusion protein composed of SnoopTag, spNW15, mCherry [11], and SpyTag, with flexible GS linkers used to connect each part.
We also utilized AlphaFold 2 to simulate the structure of SnTST-mCh[11] and obtained the correct linear, non-cyclized protein conformation, as shown in the figure.
Figure 1.The structure of SnTST-mCh[11] predicted by AlphaFold2
Plasmid Construction
To produce multi-polymerized MSP, we first constructed plasmids to synthesize three MSPs separately. We obtained the gene sequence of NW15 from NCBI and integrated the sequences of SnoopTag and SpyTag at its N-terminus and C-terminus to form SnTST-mCh[11]. We added 5' (NcoI) and 3' (XhoI) to the ends of the gene through GENEWIZ, cloning them into the vector pET-28a(+) (Kanamycin) to construct three recombinant plasmids, which were then introduced into BL21 (DE3). Subsequently, we picked multiple single colonies from the plate for colony PCR to check if the plasmids were successfully introduced into the host bacteria.
Figure 2.Colony PCR Results of Host Bacteria Introduced with pET28a_SnTST-mCh[11], All Four Colonies Successfully Obtained the Desired Band, Indicating Successful Plasmid Transformation.The theoretical sequence length is 911 bp.
Cultivation, Purification and SDS-PAGE
Induction
We chose the T7 expression system as the pathway for protein expression and induced protein expression by adding IPTG at an appropriate time. To achieve efficient expression of SnTST-mCh[11], we screened the induction conditions using IPTG. We set up a gradient of four IPTG concentrations: 0.2mM, 0.5mM, 0.8mM, and 1mM. The results showed that the optimal protein expression was achieved with a concentration of 1mM.
Figure 3.SDS-PAGE analysis of SnTST-mCh[11] protein with IPTG concentration gradient induction. An IPTG concentration gradient of 0.2mM, 0.5mM, 0.8mM, and 1mM was used for 16 hours induction at 16°C. The molecular weight of SnTST-mCh[11] is 33.6 kDa.
Purification
After confirming the successful expression of SnTST-mCh[11], we scaled up the culture and purified the protein. During plasmid construction, we incorporated a His-tag into the sequence, allowing for purification using nickel affinity chromatography, which specifically binds to His-tagged proteins. We eluted the protein using 100mM and 500mM imidazole, and successfully obtained target protein. To verify the successful expression of the protein, we conducted a Western Blot using anti-Histag after SDS-PAGE and confirmed that we had obtained SnTST-mCh[11] with a relatively high purity.
Figure 4.Western Blot Analysis of SCSdC-mCh[1-10] Purified by Nickel Affinity Chromatography. The presence of the target protein in the 100mM imidazole elution buffer was verified through Histag antibody and the correct molecular weight of the bands. The molecular weight of SnTST-mCh[11] is 33.6 kDa.
Structure and biological activity analysis
We attempted to incubate three protein segments in vitro through different methods to link them, and successfully obtained mCherry fluorescence images.For more information on the construction of multi-polymerized MSP, go to BBa_K5301024.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NotI site found at 757
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 276
Illegal BglII site found at 648 - 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
- ↑ Ilia G. Denisov, Bradley J. Baas, Yelena V. Grinkova, Stephen G. Sligar, Cooperativity in Cytochrome P450 3A4: LINKAGES IN SUBSTRATE BINDING, SPIN STATE, UNCOUPLING, AND PRODUCT FORMATION*, Journal of Biological Chemistry, Volume 282, Issue 10, 2007, Pages 7066-7076, ISSN 0021-9258, https://doi.org/10.1074/jbc.M609589200.
- ↑ Zhang, S., et al., One-step construction of circularized nanodiscs using SpyCatcher-SpyTag. Nature Communications, 2021. 12(1): p. 5451.
- ↑ Padmanabha Das, K.M., et al., Large Nanodiscs: A Potential Game Changer in Structural Biology of Membrane Protein Complexes and Virus Entry. Frontiers in Bioengineering and Biotechnology, 2020. 8.