Difference between revisions of "Part:BBa K5301006"
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<partinfo>BBa_K5301006 short</partinfo> | <partinfo>BBa_K5301006 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 SnCSdT, 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]. | ||
SnCSdT, the second component of multi-polymerized MSP, is a fusion protein composed of SnoopCatcher, NW15, and SdyTag, with flexible GS linkers used to connect each part. | SnCSdT, the second component of multi-polymerized MSP, is a fusion protein composed of SnoopCatcher, NW15, and SdyTag, with flexible GS linkers used to connect each part. | ||
| + | |||
| + | <p>We also utilized AlphaFold 2 to simulate the structure of SnCSdT 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-2-model.png | ||
| + | </div><div class="thumbcaption"> | ||
| + | Figure 1.The structure of SnCSdT 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 SnoopCatcher and SdyTag at its N-terminus and C-terminus to form SnCSdT. 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 and confirmed that the plasmids were successfully introduced into the host bacteria. | ||
==Cultivation, Purification and SDS-PAGE== | ==Cultivation, Purification and SDS-PAGE== | ||
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We chose the T7 expression system as the pathway for protein expression and induced protein expression by adding IPTG at an appropriate time. Through experimental validation, we added the IPTG solution at a concentration of 0.8mM when the OD value of the bacterial suspension reached 0.6-0.8, resulting in substantial expression of soluble proteins. | We chose the T7 expression system as the pathway for protein expression and induced protein expression by adding IPTG at an appropriate time. Through experimental validation, we added the IPTG solution at a concentration of 0.8mM when the OD value of the bacterial suspension reached 0.6-0.8, resulting in substantial expression of soluble proteins. | ||
<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- | + | https://static.igem.wiki/teams/5301/parts/tri-2-induction.png |
</div><div class="thumbcaption"> | </div><div class="thumbcaption"> | ||
| − | Figure | + | Figure 2.SDS-PAGE analysis of SnCSdT protein with IPTG induction. An IPTG concentration of 0.8mM was used for 16 hours induction at 16°C. The molecular weight of SnCSdT is 42.1 kDa. |
</div></div></div></div> | </div></div></div></div> | ||
===Purification=== | ===Purification=== | ||
| − | After confirming the successful expression of SnCSdT, 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 300mM and 500mM imidazole, respectively, and obtained a large amount of target protein in both cases, as shown in figure | + | After confirming the successful expression of SnCSdT, 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 300mM and 500mM imidazole, respectively, and obtained a large amount of target protein in both cases, as shown in figure 3. |
<div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.4;overflow:hidden;"> | <div class="center"><div class="thumb tnone"><div class="thumbinner" style="width:min-content;"><div style="zoom:0.4;overflow:hidden;"> | ||
| − | https://static.igem.wiki/teams/5301/parts/tri- | + | https://static.igem.wiki/teams/5301/parts/tri-2-purification.png |
</div><div class="thumbcaption"> | </div><div class="thumbcaption"> | ||
| − | Figure | + | Figure 3.SDS-PAGE Analysis of SnCSdT Purified by Nickel Affinity Chromatography. Both 300mM and 500mM imidazole elution resulted in the acquisition of a significant amount of target protein. The molecular weight of SnCSdT is 42.1 kDa. |
</div></div></div></div> | </div></div></div></div> | ||
==Structure and biological activity analysis== | ==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_K5301006 SequenceAndFeatures</partinfo> | <partinfo>BBa_K5301006 SequenceAndFeatures</partinfo> | ||
Latest revision as of 10:09, 2 October 2024
SnCSdT 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 SnCSdT, 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]. SnCSdT, the second component of multi-polymerized MSP, is a fusion protein composed of SnoopCatcher, NW15, and SdyTag, with flexible GS linkers used to connect each part.
We also utilized AlphaFold 2 to simulate the structure of SnCSdT and obtained the correct linear, non-cyclized protein conformation, as shown in the figure.
Figure 1.The structure of SnCSdT 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 SnoopCatcher and SdyTag at its N-terminus and C-terminus to form SnCSdT. 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 and confirmed that the plasmids were successfully introduced into the host bacteria.
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. Through experimental validation, we added the IPTG solution at a concentration of 0.8mM when the OD value of the bacterial suspension reached 0.6-0.8, resulting in substantial expression of soluble proteins.
Figure 2.SDS-PAGE analysis of SnCSdT protein with IPTG induction. An IPTG concentration of 0.8mM was used for 16 hours induction at 16°C. The molecular weight of SnCSdT is 42.1 kDa.
Purification
After confirming the successful expression of SnCSdT, 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 300mM and 500mM imidazole, respectively, and obtained a large amount of target protein in both cases, as shown in figure 3.
Figure 3.SDS-PAGE Analysis of SnCSdT Purified by Nickel Affinity Chromatography. Both 300mM and 500mM imidazole elution resulted in the acquisition of a significant amount of target protein. The molecular weight of SnCSdT is 42.1 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
- 10INCOMPATIBLE WITH RFC[10]Illegal PstI site found at 1021
- 12INCOMPATIBLE WITH RFC[12]Illegal PstI site found at 1021
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 203
Illegal BglII site found at 575 - 23INCOMPATIBLE WITH RFC[23]Illegal PstI site found at 1021
- 25INCOMPATIBLE WITH RFC[25]Illegal PstI site found at 1021
Illegal AgeI site found at 100
Illegal AgeI site found at 860 - 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.