Part:BBa_K5398001

TRn5

This part codes for the biosynthetic proteins with five tandem repeats of the squid-inspired building block (TRn5). In our project, we used TRn5 as a component of self-healing materials for underwater soft robots after damage. In this year's experiments, we employed different strategies for TRn5 protein production and purification and examined its self-healing ability.

Usage and Biology

Squid ring teeth (SRT) proteins have high elastic modulus and toughness due to their special sequence. Thus, squid-inspired high-strength proteins were synthesized by recent researchers, which shows excellent healing properties (2-23 MPa strength after 1 s of healing). Such healing performance creates new opportunities for bioinspired materials design, especially in self-healing materials for soft robotics and personal protective equipment.

Biosynthetic proteins are composed of tandem repetitions (TRn) of the squid-inspired building block. Driven by their segmented amino acid sequences, TRn self-assemble into supramolecular β-sheet-stabilized networks (Fig. 1). It's proved that there exists a positive correlation between the number of repeat units and self-healing properties of squid-inspired proteins, which means the more repeat units the proteins have, the better self-healing properties it will be.

In our project, we used TRn5 as a component of special materials to realize self-healing.

Fig. 1 | The sequence and structure of squid-inspired biosynthetic proteins.

Characterization

In order to obtain proteins with self-healing properties, we carried out dry and wet experiments of TRn5.

For the dry experiment, we predicted the structure of TRn5 using AlphaFold3. We found the TRn5 predicted by AlphaFold (Fig. 2) had five β-sheet and were connected by flexible chains, as we expected. This provided solid foundation for our next experiment.

Fig. 2 | TRn5 predicted by AlphaFold3.

For the wet experiment, we used the pET-29a(+) vector to express TRn5. We tried different strategies for TRn5 protein production and purification and tested its function.

Cloning strategy and results

In our project, we first synthesized pET-11b-TRn5 plasmid and attemped to express it in E.coli BL21 (DE3) using LB medium. However, it didn't express our targeting protein TRn5. So, to continue our project, we constructed pET-29a(+)-TRn5 plasmid to express TRn5 (Fig. 3a).

• PCR amplification of TRn5 and pET-29a(+) vector respectively. This PCR produced the pET-29a(+)-TRn5 parts ready for In-fusion Cloning (Fig. 3b,c).


Fig. 3 | The plasmid map of pET-29a(+)-TRn5 and 1% agarose gel electrophoresis of the PCR amplified pET-29a(+)-TRn5 parts.

a. The plasmid map of pET-29a(+)-TRn5. b. 1% agarose gel electrophoresis of the PCR amplified TRn5 (K5398001) (527 bp). c. 1% agarose gel electrophoresis of the PCR amplified pET-29a(+) vector (5170 bp).

• In-fusion Cloning of purified PCR amplified TRn5 and the pET-29a(+) vector parts for the efficient construction of the TRn5 coding sequence under the transcriptional control of the T7lac promoter. The recombinant plasmid was transferred into E.coli DH5α.
• Verification of target recombinant plamid. Colony PCR was used to screen for clones with inserts of the desired sizes and Sanger sequencing confirmed the lengths and compositions of the clones after plasmid isolation, from which we concluded that the pET-29a(+)-TRn5 was conducted plasmid successfully (Fig. 4).


Fig. 4 | Verification of recombinant plasmid pET-29a(+)-TRn5.

a. 1% agarose gel electrophoresis of colony PCR of using T7 and T7 ter primers. b. The result of sequencing the TRn5 of the recombinant plasmid.

Protein expression

We expressed the protein in E.coli BL21 (DE3) using LB medium. After incubation at 23℃ for 16 h and 37℃ for 5 h respectively, we found that most TRn5 (17.58 kDa) existed in precipitate as stated in previous research and the TRn5 expression level at two temperatures had little difference (Fig. 5).



Fig. 5 | SDS-PAGE of expression products of TRn5.

Lane 1: marker; Lanes 2-4: whole-cell lysate, supernatant and pellet from uninduced cells at 23℃, respectively; Lanes 5-7: whole-cell lysate, supernatant and pellet from induced cells at 23℃, respectively; Lanes 8-10: whole-cell lysate, supernatant and pellet from uninduced cells at 37℃, respectively; Lanes 11-13: whole-cell lysate, supernatant and pellet from induced cells at 37℃, respectively.

Then, we denatured TRn5 with 8 M urea overnight and renatured it by dialysis, which proved great protein losses as shown in SDS-PAGE. As a result, when we purified TRn5 by Immobilized Metal Affinity Chromatography (IMAC), the TRn5 expression level was too low to verify (Fig. 6).



Fig. 6 | SDS-PAGE of expression products of TRn5 purified by IMAC.

Lane 1: marker; Lanes 2-11, induced cell samples at 23℃; Lane 2: pellet; Lane 3: sample washed with denaturing buffer with 8 M urea; Lane 4: sample after dialysis overnight; Lane 5: sample after being bound to Ni-NTA resin; Lane 6: sample eluted with 20 mM Tris-HCl; Lane 7-11: samples eluted with 20, 50, 150, 300 and 500 mM imidazoles.

In order to optimize the expression of TRn5, we conducted a comprehensive review of the existing literature, revealing that the presence of Histidine facilitates the effortless dissolution of TRn5 in 5% acetic acid. Consequently, we implemented a novel protocol for the purification of TRn5. Upon solubilization in 5% acetic acid, a distinct and clear band of TRn5 was observed (Fig. 7).



Fig. 7 | SDS-PAGE of expression products of TRn5 using a new protocol.

Lane 1: marker; Lanes 2-4: whole-cell lysate, supernatant and pellet from induced cells at 37℃, respectively; Lane 5: sample washed with 5% acetic acid.

Self-healing test

We obtained protein samples of TRn5 by freezedrying 24 h (Fig. 8). The final yield was about 150.4 mg/L bacterial culture. Next, we dissolved protein samples in 5% acetic acid to reach 20 mg/μL, cast them into square models and dried them at 70℃ for 3 h to obtain protein films.



Fig. 8 | The protein samples freeze-dried by a lyophilizer.

To examine the property of self-healing of TRn5, we punctured a TRn5 protein film to create a hole defect by a needle (Fig. 9a). After putting the punctured film at room temperature for 12 h, we clearly saw the hole defect healing (Fig. 9b). So it was proved that these kind of film made of TRn5 has self-healing properties.



Fig. 9 | Self-healing of TRn5 protein films after puncture damage.

a. A hole defect was left by a needle through the film. b. Puncture damage was healed.

More information about the project for which the part was created: SAMUS (NAU-CHINA 2024).

Sequence and Features




Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]

Reference

[1] JUNG H, PENA-FRANCESCH A, SAADAT A, et al. Molecular tandem repeat strategy for elucidating mechanical properties of high-strength proteins[J]. PNAS, 2016, 113(23): 6478-6483.

[2] PENA-FRANCESCH A, JUNG H, DEMIREL M C, et al. Biosynthetic self-healing materials for soft machines [J]. Nat. Mater., 2020, 19(11): 1230-1235.

[3] PENA-FRANCESCH A, FLOREZ S, JUNG H, et al. Materials Fabrication from Native and Recombinant Thermoplastic Squid Proteins[J]. Adv. Funct., 2014, 24(47): 7401-7409.

[4] GUERETTE P A, HOON S, SEOW Y, et al. Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science[J]. Nat. Biotechnol., 2013, 31(10): 908-915.

[5] DING D, GUERETTE P A, HOON S, et al. Biomimetic Production of Silk-Like Recombinant Squid Sucker Ring Teeth Proteins[J]. Biomacromolecules, 2014, 15(9): 3278-3289.