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| − | <p style="text-align:center"><b>Fig. 22 Ramachandran plot of wild-type MnP at distinct temperature.</b> <i>In our simulation, the shrinking area (white part) represents the disruption of the secondary structure.</i></p> | + | <p style="text-align:center"><b>Fig. 22 Dynamic Ramachandran plot of wild-type MnP at distinct temperature.</b> <i>In our simulation, the shrinking area (white part) represents the disruption of the secondary structure.</i></p> |
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Revision as of 21:07, 21 October 2021
his-tag-SpyTag-MnP
Manganese Peroxidase (MnP) is a highly glycosylated lignin peroxidase with heme. This is the version with SpyTag. In order to constructed our multi-enzyme complex, we introduced the SpyTag/SpyCatcher system. We added SpyTag to the N-terminus of each protein through 10 × ELP, which is a oligopeptide linker that does not affect the function of the protein it attaches to, as described in the literature. So this part can be combined with dCas9-SpyCatcher through covalent isopeptide action[1], thereby being immobilized on dsDNA. His-tag was added to purify the protein. We used BBa_K3853051 to construct the expression system to express and purify the protein.
Modeled 3D-Structure of SpyTag-MnP created through alphafold2.
Biology
Manganese peroxidase (MnP) is a highly glycosylated, heme-containing[2] lignin peroxidase produced by the white-rot fungus Phanerochaete chrysosporium. MnP catalyzes the hydrogen peroxide-dependent oxidation of Mn2+ to Mn3+, which is released from the enzyme in complex with oxalate, enabling the oxalate-Mn3+ complex to serve as a diffusible redox mediator capable of oxidizing lignin or other refractory chemicals[2,3] (Fig. 1).
The SpyCatcher/SpyTag system is a bio-coupling technology connected by isopeptide bonds, which is derived from the modification of immunoglobulin like collagen adhesin domain (CnaB2)[4]. The two can spontaneously form isopeptide bond and bond stably[5].
Fig. 1 Catalytic cycle of manganese peroxidase.
Usage
The SpyTag was fused to the N-terminus of MnP. The fusion protein could combined with dCas9-SpyCatcher (which is producted by BBa_K3853055 ) for multi-enzyme complex assembly. we obtained the composite part BBa_K3853051(Fig. 2) and transformed the constructed plasmid into Pichia pastoris GS115 to verify its expression. The positive clones were cultivated.
Fig. 2 Gene circuit of SpyTag-MnP.
For MnP itself, fusion with SpyTag will not affect its function, which means that SpyTag-MnP can still exert the powerful ability of degrade pollutants like MnP. In our project, SpyTag-MnP was selected due to its polyethylene (PE) degradation ability and assemblability. It can exert PE degradation ability in the presence of Tween 80 and H2O2, and significant changes on PE films can be observed within 10 days. For SpyTag-MnP itself, assembled with dCas9-SpyCather will not affect its function neither, which means that it could be assembled on double-stranded DNA together with other auxiliary enzymes like H2O2 producing enzyme and hydrophobin. This indicates that we could adjust the spatial distance and ratio of each enzyme by altering the sequence of double-stranded DNA and corresponding single guide RNA. Besides, SpyTag-MnP and its assembly have high organic solvent stability, which is conducive to its industrial application. Both SpyTag-MnP and its assembly could work normally under the condition of pH 5-6 and lower than 37℃. In order to broaden the application of SpyTag-MnP in industry, we had gained some reliable data through molecular modeling and the potential mutants with better stability and activity were obtained. It is of great significance for further research.
Characterization
1. Identification
After receiving the pPIC9K plasmid carrying BBa_K3853008, it was linearized and electrotransformed into Pichia pastoris strain GS115. Colony PCR (using primer α-factor and 3'AOX1) was used to verify whether the plasmid was successfully transferred into the yeast genome. The experimental results were shown in Fig. 3, and the corresponding band underwent sequencing verification (see File 1).
Fig. 3 Gel electrophoresis result of colony PCR to detect the insertion of BBa_K3853008 into Pichia pastoris strain GS115. Control refers to the wild-type Pichia pastoris strain GS115 without electrotransformation. A target band around 1325 bp should appear to indicate a successful construction, which was shown as marked.
2. Proof of the expression
We used AOX1 promoter to express SpyTag-MnP in Pichia pastoris strain GS115 in our composite part BBa_K3853051. Then we used sulfate salting out method to get purified SpyTag-MnP. We set a series of concentration gradients of ammonium sulfate solution to determine the best salting-out concentration and our target bands were observed through SDS-PAGE (Fig. 4).
For assaying the mRNA expression of SpyTag-MnP, qRT-PCRs were performed. We did data analysis using a variation of the Livak method. To determine the relative expression of SpyTag-MnP vs. reference gene ACT1, total RNA was prepared from an equal volum of yeast solution. In Fig. 5, SpyTag-MnP reached its peak to a fold difference of 0.21 after 2% methanol inducing for 72 h, and kept stable after 48 h. The CT values for the SpyTag-MnP and the reference gene ACT1 were then used to calculate the fold difference with the following equation:
Fig. 4 SDS-PAGE analysis of SpyTag-MnP after ammonium sulfide salting out. Lane 1: SpyTag-MnP salting out with 40% (NH4)2SO4 ; Lane 2: SpyTag-MnP salting out with 50% (NH4)2SO4 ; Lane 3: SpyTag-MnP salting out with 60% (NH4)2SO4 ; Lane 4: SpyTag-MnP salting out with 70% (NH4)2SO4 . Control refers to the supernatant of wild-type Pichia pastoris strain GS115 without plasmid transfer. We finally chose 60% ammonium sulfate as our salting out concentration.
Fig. 5 qRT-PCR results of SpyTag-MnP using the relative quantitative method. Microbial samples were taken every 24 hours and ACT1 was applied as the reference gene. This result indicated that the SpyTag-MnP expression reached the maximum after 72 h of fermentation in buffered complex methanol medium (BMMY) medium.
3. MnP activity
MnP activity of SpyTag-MnP was measured by monitoring the oxidation of 2,6-dimethyloxyphenol (2,6-DMP) at 469 nm[6]. H2O2 concentration were determined using ε240 = 43.6 M-1 cm-1. The reaction mixtures contained 0.4 mM MnSO4, 50 mM sodium malonate (pH 4.5), and 1 mM 2, 6-DMP. For a 96-well plate, 140 μl of the above reaction mixtures and 20 μl enzyme solution were mixed uniformly in advance and then 40 μl 0.1 mM H2O2 were added to initiate reaction. The concentration of 2, 6-DMP's oxidation products, 2, 2', 6, 6'-tetramethoxydibenzo-1, 1'-diquinone, were determined using ε469 = 49.6 mM-1 cm-1. One unit (U) of MnP activity is defined as the amount of enzyme required to convert 1 μM 2, 6-DMP to 2, 2', 6, 6'-tetramethoxydibenzo-1, 1'-diquinone in 1 minute.
As shown in Fig. 6A, the absorbance of the reaction system with SpyTag-MnP continued to rise within 1 min, while the absorbance of the control group (without enzyme) did not change. Through UV-visible spectrum of the reaction system after 1 min, the characteristic absorption at 469 nm was observed (Fig. 6B). Besides, SpyTag-MnP showed the same characteristic as MnP and the enzyme activity of the former exhibited a slightly higher profile than the latter, which means that SpyTag-MnP retained the functions of the original MnP and had the potential to surpass the latter (Fig. 6).
Fig. 6 The detection of 2, 2', 6, 6'-tetramethoxydibenzo-1, 1'-diquinone. Control group refers to the reaction system without enzyme. A: The absorbance change at 469 nm in the reaction system within 1 min. B: UV-visible spectrum of the reaction system after 1 min.
4. Thermolstability of SpyTag-MnP
To evaluate whether SpyTag-MnP had sufficient thermal stability to support our application, the purified SpyTag-MnP were incubated in 20 mM sodium malonate buffer (pH 5.5)[7] with 100 mM NaCl at different temperature for 6 h and the residual enzyme activity were measured and calculated every 2 h. The relative enzyme activity under different temperatures were calculated with the following equation:
As shown in Fig. 7, relative enzyme activity of SpyTag-MnP under different incubation temperature displayed distinct characteristics. The enzyme remained steady when the temperature was below 37℃. However, when the temperature exceeded 50℃, a sharp decline of enzyme activity within 2 h could be observed, and it gradually decreased in the following 4 hours. This result indicated that SpyTag-MnP should better be used lower than 37℃.
Fig. 7 Effect of temperature on the stability of SpyTag-MnP. The initial MnP activity before incubation was set as 100%.
5. pH stability of SpyTag-MnP
To evaluate whether SpyTag-MnP had sufficient pH stability to support our application, the purified SpyTag-MnP were incubated in 20 mM sodium malonate buffer with 100 mM NaCl under pH 3-7 for 12 h at room temperature[7]. The relative enzyme activity at different pH conditions were calculated with the following equation:
As shown in Fig. 8, SpyTag-MnP played a poorer performance at low pH range (pH 3-4) and showed higher stability at high pH range (pH 5-6), which indicated that SpyTag-MnP would perform better under higher pH conditions (pH 5-6).
Fig. 8 Effect of pH on the stability of SpyTag-MnP after 12 h incubation. The initial MnP activity before incubation was set as 100%.
6. Organic Solvents Stability of SpyTag-MnP
To evaluate whether SpyTag-MnP could be used in organic solvents, we conducted an organic solvents stability test on SpyTag-MnP. The purified SpyTag-MnP were incubated in methanol and ethanol (10-30%) for 12 h at the room temperature[7], respectively. The incubation process was held in 20 mM sodium malonate buffer (pH 5.5) with 100 mM NaCl and the residual enzyme activity were measured and calculated after 12 h. The relative enzyme activity of different organic solvent at distinct concentrations were calculated with the following equation:
As shown in Fig. 9, SpyTag-MnP played a good performance in almost all concentration gradient we set both in methanol and ethanol. However, when the concentration of ethanol reached to 30%, its stability declined. This result may reflect that SpyTag-MnP could withstand low-concentration organic solvent environments, while functioning normally. This was conducive to the industrial application of SpyTag-MnP, as both methanol and ethanol were solvents commonly used in industry.
Fig. 9 Effect of different concentrations of different organic solvents on the stability of SpyTag-MnP after 12 h incubation. The MnP activity without adding any organic solvent was set to 100% as the control.
7. Ability of polyethylene degradation
To analysis the polyethylene degradation ability of SpyTag-MnP, corresponding experiments were designed. We cut the PE film from polyethylene gloves to a size of 0.5 cm × 0.5 cm, washed it with 75% ethanol , and dried at 37°C for 2 h. All PE films were divided into two groups: one group were immersed in the degradation system (200 μl), containing 50 mM sodium malonate (pH 6.0), 0.2 mM MnSO4, 0.1 mM H2O2, 150 mM NaCl, 0.1% Tween 80 and 1 U SpyTag-MnP[8], while the other group didn't treated. Then, the two groups were incubated in a shaker at 37°C and 200 rpm for 10 days. After 10 days, all the PE films were washed with 1% SDS, 0.1 M NaOH, ddH2O and 75% ethanol successively.
We next used multiple techniques to further verify the PE degradation ability of SpyTag-MnP. First, we used Fourier Transform Infrared (FTIR) imaging to analyze the changes of surface chemical components and functional groups. In SpyTag-MnP treated PE, FTIR spectra showed two distinct peaks (Fig. 10). One peak was observed in the vicinity of 1636 cm−1, indicating carbonyl bonds (-C=O-), while the other peak was observed at a wave number of 3400 cm−1 and was attributed to hydroxyl groups[9] (Fig. 10). Overall, compared with the untreated PE, our FTIR spectra data suggested an oxidation reaction of PE films happened in SpyTag-MnP treated PE, including the formation of hydroxyl groups and carbonyl bonds.
We then monitored the surface structure changes of the two groups by Scanning Electron Microscopy (SEM). As shown in Fig. 11, obvious fragments appeared in SpyTag-MnP treated PE, while the untreated PE seemed to have no change.
We eventually analyzed molecular weight distribution (MWD) changes using High Temperature Gel Permeation Chromatography (HT-GPC). We found the MWD of SpyTag-MnP treated PE film showed molecular weights decreasing from 298046 Da to 249588 Da (Fig. 12C, D). And not only the peak molecular weight response value had decreased, but the proportion of hydrocarbon chain with a molecular weight of less than 10000 Da had declined from 1.37% to 0.70% after SpyTag-MnP treated (Fig. 12A, B).
In summary, our SpyTag-MnP has good PE degradation ability.
Fig. 10 FTIR analysis of untreated PE films and PE films treated by SpyTag-MnP after 10 days incubation.
Fig. 11 SEM observation of untreated PE films and PE films treated by SpyTag-MnP after 10 days incubation. A-D: SEM observation of PE films treated by SpyTag-MnP after 10 days incubation. E-H: SEM observation of untreated PE films after 10 days.
Fig. 12 HT-GPC analysis of untreated PE films and PE films treated by SpyTag-MnP after 10 days incubation. A: HT-GPC spectrum of untreated PE. B: HT-GPC spectrum of SpyTag-MnP treated PE. C: HT-GPC calculus curve graph of untreated PE. D: HT-GPC calculus curve graph of SpyTag-MnP treated PE.
8. Assemblability of SpyTag-MnP
For assembling the dCas9-SpyCather/SpyTag-MnP complex, SpyTag-MnP was mixed with dCas9-SpyCather in a ratio of 1 : 1 and allowed to conjugate for 1 h at 37℃[10]. As shown in Fig. 13, the band of the complex appeared, which was higher than that of dCas9-SpyCather and the original SpyTag-MnP band had disappeared. Then we compared the difference in MnP activity between SpyTag-MnP and the complex, and, as shown in Fig. 14, there was no significant change. This result suggested that the assembly of SpyTag-MnP and dCas9-SpyCather will not affect the enzyme activity.
Fig. 13 SDS-PAGE showing the conjugation of SpyTag-MnP to dCas9-SpyCatcher. Lane 1: SpyTag-MnP (0.3 μM); Lane 2: dCas9-SpyCatcher (0.3 μM); Lane 3: SpyTag-MnP (0.3 μM) mixed with dCas9-SpyCatcher (0.3 μM). Upon mixing the two components, the upward shift in the band corresponding to dCas9-SpyCatcher as well as the disappearance of the band corresponding to SpyTag-MnP were observed, indicating successful conjugation. Note that the conjugation is unaffected by the SDS-PAGE conditions due to covalent isopeptide bond formation.
Fig. 14 Comparison of MnP activity between SpyTag-MnP and dCas9-SpyCather/SpyTag-MnP complex. Complex refers to the dCas9-SpyCather/SpyTag-MnP complex. p > 0.05.
9. Thermostability of dCas9-SpyCather/SpyTag-MnP complex
We used the above method to test whether assembly would affect thrermal stability of SpyTag-MnP and as shown in Fig. 15, the relative enzyme activity of the complex would decline gradually after 6 h incubation in all temperture we set. However, compared with unassembled SpyTag-MnP, it shown an improve of thermostability at mild temperture (below 60 ℃) (Fig. 16).
Fig. 15 Thermal stability of dCas9-SpyCather/SpyTag-MnP complex. The initial MnP activity before incubation was set as 100%.
Fig. 16 Effect of temperature on the stability of the complex and SpyTag-MnP after 6 h incubation. The initial MnP activity before incubation was set as 100%. The complex refers to dCas9-SpyCather/SpyTag-MnP complex. *P < 0.05, **P < 0.01.
10. pH stability of dCas9-SpyCather/SpyTag-MnP complex
We used the mentioned method to test whether assembly would affect pH stability of SpyTag-MnP and as shown in Fig. 17, it didn't perform well at low pH range (pH 3-5) as both the complex and SpyTag-MnP had precipitated (Fig. 17), which probably because the 100 mM NaCl was not enough for the complex as its molecular weight became about 5 times than the unassembled SpyTag-MnP. However, it would perform better at high pH range (pH 6-7), although its relative enzyme activity was lower than SpyTag-MnP at pH 7.
Fig. 17 Effect of pH on the stability of the complex and SpyTag-MnP after 12 h incubation. The initial MnP activity before incubation was set as 100%. The complex refers to dCas9-SpyCather/SpyTag-MnP complex. *P < 0.05.
11. Organic solvents stability of dCas9-SpyCather/SpyTag-MnP complex
As for organic solvent stability, we would be happy to say that our assembly could tolerate methanol and ethanol while concentration was less than 30% (Fig. 18). This may mean that our assemblies would more adaptable to industrial environments. Besides, its organic solvent stability was significantly higher than the unassembled SpyTag-MnP (Fig. 18).
Fig. 18 Effect of different concentrations of different organic solvents on the stability of the complex and SpyTag-MnP after 12 h incubation. The MnP activity without adding any organic solvent was set to 100% as the control. The complex refers to dCas9-SpyCather/SpyTag-MnP complex. A: The effect of different concentrations of methanol on MnP activity. B: The effect of different concentrations of ethanol on MnP activity. *P < 0.05, ***P < 0.001.
Molecular Modeling
Introduction
In synthetic biology, theoretical models are often used to gain insights, predict and improve experiments. In our project, the relative enzyme activity of dCas9-SpyCather/SpyTag-MnP complex varied greatly over time at different temperatures, resulting in a lower working temperature (lower than 37°C) (Fig. 14). In this case, molecular modeling was applied to predict possible mutants to improve stability and activity for broaden the application of SpyTag-MnP in industry. Here the version of SpyTag-MnP without SpyTag (PDB entry: 3M5Q) was used for molecular modeling as it has a known high-precision 3D structure (0.93 Å)[11] and the improvement of its stability has the potential to improve the complex.
Molecular dynamics
1. RMSD Analysis
To evaluate the temperature effect on the structure stability of wild-type MnP, root-mean-square deviation (RMSD) was applied using Gromacs[12] as RMSD is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed proteins. Higher RMSD value means poorer the stability of protein backbone is. As shown in Fig. 19, the value stabilized at a time of 5000 ps and fluctuated around the value of 0.25 nm while at 298.15 K. Both the curve of 313.15 K and 338.15 K remained steady at a time of 7000 ps and fluctuated around 0.4 nm, which indicated the temperature has the strong effect on the wild-type MnP's backbone structure as when temperature rose to 400 K, it severely damaged.
Fig. 19 RMSD curve of wild-type MnP at distinct temperature. Such curve is about the average RMSD of every residue over time, which reflect the influence of temperature on the overall stability of the whole protein.
2. RMSF Analysis verified by B-factor
Judging the major amino acid residues that affected by the temperature, root mean square fluctuation (RMSF) of wild-type MnP was also evaluated to measure of the deviation between the position of amino acid residue and some reference position under each condition. As shown in Fig. 20, the fluctuations (RMSF) of most residues appeared insignificant compared to the N-, C-terminus and the residues close to residue 70, 180, 230, 310 and 340. Typically the N- and C-terminus tend to fluctuate more intensively due to the lack of stabilizing structures. The prominent fluctuations in the other five positions indicated that the temperature had a significant impact on it, which was confirmed by B-factor plot created by the R package Bio3D[13] (Fig. 21). The insignificant changes in the position of the amino acid residues at positions 70 and 310 may be due to the fact that the B-factor plot was obtained at 298.15 K (Fig. 21).
Fig. 20 RMSF curve of wild-type MnP at distinct temperature. Such curve is about the average deviation of every amino acid residue compared to reference position under each condition, which could reflect the major unstabled amino acid residues under distinct condition.
Fig. 21 B-factor plot of wild-type MnP at 298.15 K. Such plot reflects the thermal stability of each amino acid residues of the wild-type MnP, which could confirm the results of Fig. 20.
3. Assess the effect of temperature on the secondary structure of wild-type MnP
To evaluate the variation of the secondary structure under distinct temperature, Ramachandran plot was applied as it is a typical way to visualize energetically allowed regions for backbone dihedral angles ψ against φ of amino acid residues in protein structure. The white area shown in the dynamic Ramachandran plot we obtained shrank with the increase of temperature (Fig. 22), which represented the disruption of wild-type MnP’s structure[14]. [14].
Besides, as shown in Fig. 23, when the temperature rose from 298.15 K to 400 K, the secondary structure of most amino acid residue was severely damaged, as most amino acid residues were difficult to have a fixed secondary structure.
Fig. 22 Dynamic Ramachandran plot of wild-type MnP at distinct temperature. In our simulation, the shrinking area (white part) represents the disruption of the secondary structure.
Fig. 23 The distribution of secondary structure of wild-type MnP over time at distinct temperature.
4. Radius of Gyration Analysis
Gyrates reflects the variation of the radius of gyration of wild-type MnP over time. The radius of gyration (Rg) is a physical quantity that describes the compactness of the protein structure. The smaller the value, the greater the compactness. As shown in Fig. 24, only when temperature rose above 400 K, a rise could be observed before 10000 ps and it remained steady subsequently like the other three temperature. In this case, temperature seemed to have little effect on the compactness of wild-type MnP.
Fig. 24 Radius of gyration curve of wild-type MnP at distinct temperature. Such curve reflect the compactness of the protein structure and the smaller the value, the greater the compactness.
5. Hydrogen Bond Analysis
Hydrogen bond is a very important non-covalent structural force, and an important factor affecting protein stability. To evaluate the effect of temperature on the number of wild-type MnP's hydrogen bonds, corresponding simulation was carried out. As shown in Fig. 25, the temperature seemed to have little effect on the number of hydrogen bonds while the temperature was below 120 ℃.
Fig. 25 Hydrogen Bonds curve of wild-type MnP at distinct temperature.
6. SASA Analysis
Solvent accessibility surface area (SASA), for enzymes, it reflects the possibility of substrates entering the enzyme cavity to some extent. While evaluating the effect of temperature on SASA of wild-type MnP, we found that the value of SASA shown a initial trend of rising before experiencing a fall (Fig. 26). If the value of SASA is larger, it is more conducive to the related docking of the ligand, however, the excessive of SASA may also cause the loss of binging energy of the substrates, as our results shown that it performed better in low temperature (Fig. 27).
Fig. 26 SASA curve of wild-type MnP at distinct temperature. Larger the value of SASA, the more hydrophilic the protein is.
Fig. 27 The plot of MnP activity of wild-type MnP over temperature. The MnP activity was detected after incubating at distinct temperature for 2 h.
7. RMSPH Analysis
RMSPH is the RMSD in different pH environment simulated using leaprc. constph force field. Our RMSPH curve revealed that different pH values (pH 3~7) had relatively low impact on the whole protein structure (Fig. 27). However, due to the small time scale of the simulation, the results may be a little inaccuracy and this result didn't mean that pH will not affect the MnP activity of wild-type MnP.
Fig. 28 RMSPH curve about wild-type MnP at distinct pH condition. Such curve is about the average RMSD of every residue over time, which reflect the influence of pH on the overall stability of the whole protein.
Single Point Mutation
Based on the results of molecular dynamics mentioned above, we adopt a semi-rational design method to carry out directed evolution of wild-type MnP expecting to improve the enzyme activity and stability.
1. Mutant Library Construct
We chose 19 amino acid residues based on the result of RMSF and B-factor, 361 (19 × 19 = 361) results with free energy change (ΔΔG) data were constructed by FoldX software (see File 2). Considering the effect of ectopic dominance (the spatial position of amino acid residues after mutation is different from that before mutation), we wrote PLMC module to calculated MnP homologous sequence and the results were essentially proportional to the results of FoldX[15] (Fig. 29).
Besides, the results of 361 mutants were ranked according to ΔΔG, and the top ten mutants (see Table 1) were selected to be constructed in Pichia pastoris strain GS115. Mutant 1# (BBa_K3853013), 2# (BBa_K3853014), 5# (BBa_K3853015), 6#(BBa_K3853016), 7# (BBa_K3853017) and 8# (BBa_K3853018) were successfully constructed, among which mutant 2# (BBa_K3853014) was compared exhibited improved thermal stability over wild-type MnP (Fig. 30).
Fig. 29 MnP PLMC module analysis and the distance matrix of amino acid residues.
Table. 1 Mutation sites of ten mutants with the smallest ΔΔG according to computational simulation.
Fig. 30 Effect of temperature on the stability of BBa_K3853014 and MnP after 6 h incubation. The initial MnP activity before incubation was set as 100%. Mutant 2# refers to BBa_K3853014. *P < 0.05, **P < 0.01.
2. Deep Learning & Machine Learning
With Turi Create applied, we trained the data calculated by FoldX with negative free energy using three kinds of models (Support Vector Machines (SVM), K-Nearest Neighbour (KNN), and Random Forest[16], respectively) and got the predicted “scaled_effect” of wild-type MnP[17] (Fig. 31). We evaluated the deep learning results of the three models through spearman coefficients, and the results were accordingly 0.86, 0.88, and 0.92, which proved the deep learning results were reliable.
Fig. 31 Scaled_effect of deep learning. The scatter points in the figure are composed of the first principal component of PCA and the second principal component of PCA. Variant effect’s color reflects the confidence of scaled_effect. Scaled_effect of wild-type MnP was the training result to determine which mutations were helpful to improve the structural stability.
3. Rosetta analysis
As the data obtained by FoldX lacked the accuracy to a certain extent, we used Rosetta[18, 19] to correct the mutation free energy of mutation points. Through Rosetta based on the above-mentioned deep learning results, the 4 amino acids (35E, 39E, 177R, 179D) around the Mn2+ ion binding site were evaluated for mutagenicity and the range of ΔΔG as shown in the Table. 2. As shown in Table. 2, less structural stability changes would be observed while mutating 177R into A, H, L, M, T and Y (179D was unable to mutate according to the result).
Table. 2 Calculated amino acid residue sets at available mutation sites under different ΔΔG values.
Modeling Conclusion
According to the molecular modeling results shown above, we got all the properties of wild-type MnP, which would be potential to improve the properties of not only wild-type MnP but also SpyTag-MnP and the dCas9-SpyCather/SpyTag-MnP complex. The mutant library and the result of Rosetta analysis would be useful to improve thermostability and MnP activity, respectively.
References
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[10] Lim, S., Kim, J., Kim, Y., Xu, D. & Clark, D. S. CRISPR/Cas-directed programmable assembly of multi-enzyme complexes. Chem Commun (Camb) 56, 4950-4953, doi:10.1039/d0cc01174f (2020).
[11] Sundaramoorthy, M., Gold, M. H. & Poulos, T. L. Ultrahigh (0.93A) resolution structure of manganese peroxidase from Phanerochaete chrysosporium: implications for the catalytic mechanism. J Inorg Biochem 104, 683-690, doi:10.1016/j.jinorgbio.2010.02.011 (2010).
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[13] Sutherland, G. R. & Aust, S. D. The effects of calcium on the thermal stability and activity of manganese peroxidase. Arch Biochem Biophys 332, 128-134 (1996).
[14] Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J Mol Graph 14 (1996).
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[16] Negi, S. S., Goldblum, R. M., Braun, W. & Midoro-Horiuti, T. Design of peptides with high affinity binding to a monoclonal antibody as a basis for immunotherapy. Peptides 145, 170628 (2021).
[17] Goldman, M. & Pruitt, L. Comparison of the effects of gamma radiation and low temperature hydrogen peroxide gas plasma sterilization on the molecular structure, fatigue resistance, and wear behavior of UHMWPE. J Biomed Mater Res 40, 378-384 (1998).
[18] Fleishman, S. J. et al. RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS One 6, e20161 (2011).
[19] Rohl, C. A., Strauss, C. E. M., Misura, K. M. S. & Baker, D. Protein structure prediction using Rosetta. Methods Enzymol 383, 66-93 (2004).
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]