Source:
Generated By: https://synbiohub.org/public/igem/igem2sbol/1
Created by: Shijun Zhao
Date created: 2016-10-08 11:00:00
Date modified: 2016-10-12 11:19:30
Triplespycatcher with His-tag
| Types | DnaRegion |
| Roles | Composite engineered_region |
| Sequences | BBa_K1989001_sequence (Version 1) |
Description
Triplespycatcher with His-tag
Usage and Biology
In the last few years, hydrogens made from natural or synthetic polymers have been investigated due to their extensive application in clinical medicine and synthetic biology. Compared to traditional biological material, protein-based multifunctional biological material is low-cost, facile and eco-friendly. However, strategies for assembling 3D molecular networks synthesized only by protein molecular remain underdeveloped. The reason why investigating this technology is still tough is lack of protein-based cross linking agents. Inspired by the self-catalysis of isopeptide bond between Lys and Asp in Streptococcus pyogenes fibronectin-binding protein FbaB, researchers split the catalytic domain and obtained two peptide called SpyTag(the short one) and SpyCatcher(the long one) which are able to form isopeptide bond with the other without any assistant. By fusing SpyTag and SpyCatcher with functional domains respectively, researchers solved the problem tactfully. In order to using Spytag and Spycatcher system as scaffold, we fused three Spycatcher spaced by (VPGVG)15 with 6xHistag in N-terminal.
Based on our results, the fused protein His-3B possess isopeptide bond forming ability. Thus, using His-3B with multiplespytag, we can obtain multifunctional biomaterial.
You can find triplespyag with SUP and His-tag here http://parts.igem.org/Part:BBa_K1989000".
Cultivation, Purification and SDS-PAGE
Cultivation
The part was assembled with T7 promoter and RBS in pET28a plasmid vector. E. coli strain BL21(DE3) harboring the appropriate plasmid was grown at 37 ??C in 2xYT medium overnight with suitable concentration of antibiotic. The culture was diluted 100 fold into fresh medium with antibiotic and grown at 37??C to an optical density of 0.6~0.8 at 600 nm, the protein expression was induced with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) and cells were grown overnight at 25??C.
Purification
Cells were centrifuged at 8000rpm for 15min at 4??C. Resuspend the cell paste expressing recombinant protein in binding buffer (20 mM Tris-HCl, 0.5 M NaCl, 20 mM imidazole, 1mM β-mercaptoethanol, pH7.4), containing SIGMAFAST??? Protease Inhibitor Cocktail Tablets (SIGMA-ALORICH). Disrupt the cells with sonication for 20 min with suitable power on ice and centrifuge at 18000 rpm for 40 min at 4??C. Remove remaining particles by passing the supernatant through a 0.22 μm filter.
The HisTrap??? column (GE Healthcare, Inc.) was equilibrated with binding buffer. Load the sample and wash the column with binding buffer.
Elute the target protein with a linear gradient starting with binding buffer and ending with the same buffer including 500mM imidazole. The eluted fraction containing the target protein were concentrated by Amicon?? Ultra Centrifugal Filters (Merck) with a 10 kDa cutoff, then frozen by liquid nitrogen and stored at -80??C.
SDS-PAGE
Protein purification was checked by SDS-PAGE and the resulting protein is quantified by Braford analysis.
Activity Analysis
Gel Formation
Basic Exploration
Exploring the polymerization of our crosslinking network is significant to subsequent application. We must know what our Spy Network is like, and how long they need to complete their reactions, which would offer us a kind of intuition of their crosslinking ability.
To answer the questions shown above, we have analyzed the crosslinking ability of our fundamental monomers, 3A, 3A-SUP, 3A-mSA and 3B. They were firstly diluted to certain concentration, and were made to react under the restriction that the number of A was equal to B. The monomers containing A were conducted to react with 3B at 25℃ and pH=7.3 with the duration of 2 hours.
配图方法：一张胶图配一张分析图（不用分析，标出疑似产物即可）
Fig. 1. Exploration of the polymerization ability of the 3A/3A-SUP/3A-mSA with 3B A: 3A+3B, B: 3A-SUP+3B, C: 3A-mSA+3B.
We found that some new bands appeared above the band of 3B when it was mixed with monomers containing A, which demonstrated that our idea of forming functional network was executable. The products were mainly oligomers (Fig. 2 A-F, Table 1), for it is easy to form loops, which hindered the linkage between different monomers at such low concentration. Interestingly, with the restriction that A is equal to B in number, and the content of 3B was constant initially, the crosslinking ability at low concentration of these monomers were different with each other by comparing the surplus content of 3B. What???s more, it was surprising that the position of 3B band (~62kDa) was not accord with its theoretical weight (55.4kDa). Further experiments will be done to understand the differences.
Gradient Experiment
After exploring the basic character, i.e., the ability to crosslink, of our reactants, we would like to further explore the advantageous conditions for our polymerization, such as pH gradient, temperature gradient, and concentration gradient of monomers.
Fig. 2. Design the gradient experiment of pH, temperature and concentration
First experiment is concerned with pH gradient. Given that our Spy Network in practical application would face water environment with pH nearly neutral, and our proteins have their own optimum pH of functioning, we decide to make pH gradient of 6.3/7.3/8.3. Typical monomers 3A-SUP and 3B would firstly dissolve in TBS at certain pH values, then they were put to react at mentioned pH gradient. The reaction would be conducted at 25℃, with duration of 2 hours. Samples would be extracted every 30min to make clear the variation tendency of monomers. After the reaction, SDS-PAGE would be conducted and the gels would be scanned and analyzed by the software Lane 1D. Thus the relationship between time and the content of 3B and 3A would be found out. Three parallel groups were set to realize quantitative analysis.
左边是柱状图，显示不同pH下3B在不同时间点时的剩余量；右边需放上GIF文件，以显示不同pH下质量分布随时间之变化。
Fig. 3. pH Gradient Experiment Left: the surplus content of 3B at different pH. Right: The mass distribution of oligomers at different pH.
From the results of analyzing SDS-PAGE gels showing above, we clearly observed the changing law of 3B and the mass distribution of polymer homologs. Appropriately lower pH would lead to faster consumption of monomers, while our time scale should be smaller in order to show the condensation polymerization nature.
Second is concerned with temperature. According to the common environmental temperature, three typical values, 16℃, 25℃, 37℃ were introduced in our temperature experiment. Similar to pH Gradient Experiment, typical monomers 3A-SUP and 3B would firstly dissolve in TBS at pH=7.3, then they were put to react at mentioned temperature gradient. The reaction would be conducted at pH=7.3, with the duration of 2 hours. The subsequent steps were same to that of pH Gradient Experiment.
左边是柱状图，显示不同温度下3B在不同时间点时的剩余量；右边需放上GIF文件，以显示不同温度下质量分布随时间之变化。
Fig. 4. Temperature Gradient Experiment Left: the surplus content of 3B at different temperature. [Error Bar 的表述] Right: The mass distribution of oligomers at different temperature.
The analysis of SDS-PAGE gel clearly showed the variation tendency of the surplus content of 3B as a function of time, and of the mass distribution of homologs. According to the result, we could conclude that higher temperature would lead to the faster consumption of monomer, and at designated time scale we didn???t see any change in the change of weight distribution of polymer homologs. We supposed that it should be easier to form loops (intramolecular reactions) at such low concentration, and the time scale is too large to show the variation. Though the rate of polymerization should be described by the consumption rate of functional groups, we decide to use the consumption rate of monomers to simply describe the tendency.
Third is concerned with concentration. At low concentration would cross-linkage not polymerize, but oligomerize (The difference between these two reactions can be described by crosslinking density, the former is large, while the latter is rather small.), according to the basic knowledge of Polymer Science. From this point of view, if we hope to promote the mass, strength and contact area of polymers, we have to mix our monomers at high concentration. Thus, understand the relationship between the concentration and the variation of mass distribution of polymers is quite essential.
左边是胶图，右边是凝胶分析图。只用标出疑似产物即可。
Fig. 5. The mass distribution of oligomers of concentration gradient experiment at different concentration Left: SDS-PAGE gel, Right: Gel analysis.
The analysis of SDS-PAGE gel showed that more hyper-branched products with heavier molecular weight appeared with the increase of concentration, which, could also lead to the prediction that the average weight would be larger if higher concentration of monomers were mixed together.
References
1. Rodolphe Barrangou, Christophe Fremaux, H??l??ne Deveau, et al. CRISPR provides acquired resistance against viruses. Science, 2007, 315: 1709-1712.
2. Deltcheva E, Chylinski K, Sharma CM, et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011;471:602???7.
3. Martin Jinek, Krzysztof Chylinski, Ines Fonfara, et al. A Programmable Dual-RNA???Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science, 2012, 337: 816-821.
Sequence and Features