Verification of sortase for protein conjugation by single-molecule force spectroscopy and molecular dynamics simulations

Fang Tian , Guoqiang Li , Bin Zheng , Yutong Liu , Shengchao Shi , Yibing Deng and Peng Zheng *
State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China. E-mail: pengz@nju.edu.cn

Received 27th January 2020 , Accepted 11th March 2020

First published on 11th March 2020


Sortase is one of the most widely used enzymes for covalent protein conjugation that links protein and protein/small molecules together in a site-specific way. It typically recognizes the “GGG” and “LPXTG” peptide sequences and conjugates them into an “LPXTGGG” linker. As a non-natural linker with several flexible glycine residues, it is unknown whether it affects the properties of the conjugated protein. To verify the use of sortase for protein–protein conjugation, we combined single-molecule force spectroscopy (SMFS) and molecular dynamics (MD) simulations to characterize sortase-conjugated polyprotein I27 with three different linkers. We found that the I27 with classic linkers “LPETGGG” and “LPETG” from sortase ligation were of normal stability. However, a protein with a longer artificial linker “LPETGGGG” showed a 15% lower unfolding force. MD simulations revealed that the 4G linker showed a high probability of a closed conformation, in which the adjacent monomer has transient protein–protein interaction. Thus, we verify the use of sortase for protein conjugation, and a longer linker with a higher glycine content should be used with caution.


Protein conjugation is a powerful methodology for both basic and applied research fields, including the study of protein mechanism and function, the construction of protein arrays for drug screening and proteomics, and protein-based drugs.1–4 Among different approaches, enzyme-mediated protein conjugation is of great interest because it allows for a site-specific and covalent peptide bond linkage between ligation units.5–9 For example, sortase, a transpeptidase known for decades, has been widely used for protein ligation, labeling, and immobilization.8,10 Sortase A recognizes specific residues on the protein terminus and eventually forms a seven amino-acid-length “LPXTGGG” linkage. However, such a non-natural and long linker with several flexible glycines may affect the structure and properties of the individual protein unit, leading to an unwanted “linker effect”.11–14

Recently, a paper reported the use of sortase for building polyprotein I27 with a GGGG linkage leading to much-reduced protein stability.15 Interestingly, another work using sortase with GGG as the linker for building polyprotein I27 showed a similar unfolding force to a normal protein.16 This raises concerns about the use of sortase for protein conjugation. To verify the use of sortase for protein–protein conjugation, we combined atomic force microscopy (AFM)-based SMFS, MD simulation, and protein engineering to characterize the stability of the protein unit in the sortase-mediated conjugated polyprotein I27 with three different linkers, “LPETG” (1G), “LPETGGG” (3G) and “LPETGGGG” (4G). AFM-based SMFS is a powerful way to manipulate protein mechanically and it measures the protein unfolding force.17–25 Together with MD simulations and theoretical methods, it characterizes protein stability and mechanics.26–34 Compared with other classic protein characterization methods, such as SDS-PAGE gel or mass spectroscopy, it measures the native protein in aqueous solution at room temperature. Moreover, it directly measures the unfolding force/stability of the protein and verifies the correct folding and structure of the protein.35,36 Thus, it is an alternative way to characterize ligated protein and provide complementary information for the conjugated protein under a native state.

mgSrtA, a sortase A variant with nine amino acid mutations, is used for building conjugated polyprotein I27 with different linkers.5,37 It recognizes both a classic N-terminal GGG sequence and a single G sequence with high ligation efficiency. Thus, it was used here for protein conjugation and to test the linker effect. The 27th immunoglobulin (Ig) domain of sarcomeric protein titin (I27) was chosen as the model protein. Titin is the largest naturally occurring protein molecule in the human body with hundreds of Ig domains and it was the first protein used for AFM-based SMFS protein unfolding experiments.17,18,38,39 Thus, it has been well characterized and is widely used as a marker protein for single-molecule studies. Previous measurements using the recombinantly expressed polyprotein I27 with an RS linker showed an average force of ≈200 pN with a contour length increment (ΔLc) of ≈28 nm upon unfolding.18

To construct sortase-mediated polyprotein (I27)N with different linkers for AFM measurement, a stepwise ligation and cleavage method using both mgSrtA and TEV protease was used.6,15 Accordingly, the protein Coh-Tev′-X-I27-LPETGG was constructed as the basic ligation unit. Tev′ stands for the peptide sequence ENLYFQ, which, with an additional glycine, is the complete TEV cleavage site. X stands for G, GGG, and GGGG. The different linkages between I27 in the polyprotein were achieved by adding different residue(s) X before the I27, leading to an “LPETX” linkage (Fig. 1). The AFM system measured the protein sample in a well-defined site-specific way.6,40 First, the protein unit was immobilized on a glycine-functionalized glass coverslip through its C terminal LPETGG by mgSrtA (Fig. 1, Step 1). Here, the Tev′ site served as temporary N-terminal protection. Then, TEV protease cleaved the protein and exposed the X at the N-terminus (Step 2, Fig. S1, ESI). As a result, mgSrtA was able to ligate another protein unit leading to a protein dimer with the linkage “LPETX”. This cycle can be repeated N times to allow for the construction of the polyprotein (I27)N. It is noted that the real polymerization degree is less than the number of cycles because the sortase hydrolyzes the linker itself. Typically, we repeated the cycles six times, and I27 dimers to tetramers were all obtained. For example, (I27)4 can be built as Coh-(I27-LPETX)4-Glass. Here, Coh (Cohesin) was used as the pulling handle for SMFS, because it forms a reversible Cohesin/Dockerin-Xmodule (Coh/XDoc) protein–protein interaction. Thus, a CBM-XDoc functionalized AFM tip can probe the polyprotein on the surface site specifically, and the CBM with a ΔLc of ≈55 nm was used as the single-molecule marker (Fig. 2A and Fig. S3, ESI). To compare the different constructs accurately, at least two constructs were measured using the same cantilever in the same experiment. The details of AFM measurement can be found in the ESI.


image file: d0cc00714e-f1.tif
Fig. 1 Schematic for building conjugated protein (I27)4 for AFM measurement. A protein ligation unit, Coh-Tev′-X-I27-LPETGG, was used. X stands for three different sequences. Firstly, the protein unit was enzymatically immobilized on a glycine-functionalized surface using mgSrtA. Then, it was cleaved by TEV protease, exposing the X. Thirdly, an additional unit was conjugated to the exposed immobilized protein. These cycles can be repeated four times with the construction of (I27)4. Finally, a CBM-XDoc functionalized AFM tip probed the polyprotein for measurement.

image file: d0cc00714e-f2.tif
Fig. 2 (A) Setup of the AFM unfolding experiment on sortase-mediated conjugated polyprotein with different linkages. The protein was covalently immobilized and probed specifically through a reversible Coh/XDoc interaction. (B) Representative force–extension curves from (I27)N with the linker “LPETG”, curve 1; “LPETGGG”, curve 2; “LPETGGGG”, curve 3 and “RS”, curve 4. Histograms of their corresponding unfolding force (C)–(F) and dimer conformation under MD simulations (G)–(J) are shown. A closed conformation with inter-domain interaction from hydrophobic residues is observed with a high probability for the 4G-construct.

First, the shortest linkage “LPETG” was tested for AFM measurement. Accordingly, the protein unit Coh-Tev′-G-I27-LPETGG was constructed. The stepwise protein conjugation protocol mentioned above was used, leading to a polyprotein Coh-(I27-LPETG)N-Glass. The force–extension curve obtained by stretching the polyprotein using single-molecule AFM showed the characteristic saw-tooth like peaks from the stepwise protein unfolding (Fig. 2B, curve 1). By fitting the elasticity of the curve using the worm-like chain model, unfolding events with a ΔLc of ≈28 nm were detected, which agreed well with the previous results from I27 unfolding. This result indicated the successful conjugation of I27 using sortase, and at least four I27s were linked. More importantly, the unfolding force for sortase-mediated polymerized I27 was 200 ± 39 pN (average + s.t., n = 364), which is also comparable with previous results. This result indicated no linker effect from the sortase-derived LPETG (1G) linker between protein monomers (Table 1).

Table 1 AFM results for conjugated I27 with different linkers
Linker ΔLc (nm) Force (pN) Number
LPETG (1G) 28.1 ± 0.7 200 ± 39 364
LPETGGG (3G) 28.7 ± 2.1 189 ± 35 286
LPETGGGG (4G) 28.6 ± 2.5 174 ± 31 299
RS control 28.6 ± 2.3 204 ± 30 144


Then, we tested the classic srtA-mediated linkage “LPETGGG” (3G), including three glycines between conjugated proteins. The protein unit Coh-Tev′-GGG-I27-LPETGG was built. And the polyprotein Coh-(I27-LPETGGG)N was constructed on the surface and measured using AFM. The same force–extension curve as before was observed (Fig. 2B, curve 2). Moreover, a slightly lower (15 pN, 7%) force of 189 ± 35 pN (n = 286) was obtained. These results prove that the classic LPETGGG linkage has a minimal effect on the conjugated protein.

Glycine is a flexible amino acid, and previous studies have suggested that a higher frequency of these flexible residues in the linker may cause a non-natural protein–protein interaction.11–14 It is also widely used to facilitate protein–protein interaction as the linker (GGS)n. To verify such a hypothesis, we tested an artificial linker, LPETGGGG, with four GGGG (4G). A protein unit, Coh-Tev′-GGGG-I27-LPETGG, was constructed accordingly. Similarly, AFM measurement showed that the protein was linked and I27 unfolding peaks were observed (Fig. 2B, curve 3). In contrast, the unfolding force was 174 ± 31 pN (n = 299). Compared with the unfolding force (204 pN) of the recombinantly expressed polyprotein,16 it was much lower (30 pN, 15%). To exclude other effects, such as the different protein immobilization methods, polyprotein length, and cantilever, we built polyprotein Coh-(I27-RS)4-LPETGG, recombinantly, and used the same method for AFM measurement. The unfolding force was 204 ± 30 pN, which was the same as that of previous results. Taken together, we believe that the use of sortase for protein conjugation with an LPETG or LPETGGG linkage is suitable and longer linkers, especially with higher glycine content, should be used with caution.

To further understand why the longer linker with more glycine residues leads to a different unfolding force of I27 in the conjugated protein, we performed MD simulations.41–44 The I27 dimer structures with four different linkers were constructed based on the crystal structure (PDB code: 1TIT). The details of the MD simulations are provided in the ESI.

After 100 ns of simulations, we compared the snapshots of four simulations (Fig. 2G–J). The I27 dimer with the linkers of LPETG, LPETGGG, and RS achieved an appropriate separation of connected proteins and reduced their interference with each other like an open state (Videos 1–3, ESI). Interestingly, the I27 dimers with the 4G linker appeared to intertwine around each other as a closed state. Indeed, during the simulations, individual I27s moved closer to each other step-by-step (Video 4, ESI). The closed state forms from the transient protein–protein interaction between several interdomain hydrophobic residues. Three different MD simulations were performed. Interestingly, Lys 37, Leu 65 and Thr 68 in the first I27 domain were always present for the interaction, while the residues involved in the other domain were not fixed (Fig. S4, ESI). The probability of open and closed conformations in all 100 ns MD simulations for the four linkers supports this difference (Table 2). The 4G-linked I27 gave rise to a more closed conformation (39.7 ± 7%, n = 3). And the analysis of the radius of gyration (Rg) also supports its more closed or compact conformation (Fig. S5, ESI). Thus, the observation of different probabilities of this closed conformation is the most significant difference between the four linkers.

Table 2 The probability of the two conformational states of the I27 dimer with different linkers in MD simulations
Linker Closed (%)
LPETG (1G) 6.1
LPETGGG (3G) 12.4
LPETGGGG (4G) 39.7
RS control 1.3


To further understand these observations, we performed steered molecular dynamics (SMD) simulations on the closed and open conformation of the I27 dimer linked by 3G and 4G, respectively. Each representative snapshot of the closed conformation from three MD simulations was selected as the starting state for SMD simulations. The results of the 4G-linked I27 showed that the I27 dimer unfolded in the same way as typical protein unfolding. The linker was straightened first, and then the protein was unfolded (Fig. 3 and Videos 5 and 6, ESI). It showed the highest force peak when the first β-strand was completely unfolded. Moreover, the simulated unfolding force of the closed conformation is lower than that of the open one (Fig. 3, 1650 pN vs. 2000 pN). Thus, the SMD simulations results also revealed that the closed conformation showed a lower mechanical stability. Nevertheless, the molecular/atomic mechanism for such an effect remains to be further explored.


image file: d0cc00714e-f3.tif
Fig. 3 Force–extension curves from SMD simulations of the closed (A) and open (B) conformation of the 4G-linked dimer. The simulated unfolding force of the closed conformation is lower than that of the open conformation.

In conclusion, AFM measurement and MD simulation verified the use of sortase for conjugating protein with a classic LPETGGG linker and LPETG linker. However, a longer LPETGGGG linker may induce a transient protein–protein interaction, and it should be used with caution.

This work was supported by the National Natural Science Foundation of China (Grant No. 21771103, and 21977047). The genes were ordered from GenScript Inc. The numerical calculations in this paper have been carried out on the computing facilities of the High Performance Computing Center (HPCC) of Nanjing University.

Conflicts of interest

There are no conflicts to declare.

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Footnote

Electronic supplementary information (ESI) available. See DOI: 10.1039/d0cc00714e

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