Part:BBa_K5322014

SOD Pro1

Background

Mutagenesis of specific bases in proteins has proven to be invaluable in probing the contribution of individual amino acid side chains to protein properties. The ability of alanine scanning mutagenesis to provide key biological insights has been demonstrated by early examples, and combinatorial alanine scanning combines the convenience of combinatorial libraries with the insights of site-directed scanning mutagenesis. In recent years, methods based on sequence coevolution analysis have shown great potential in enzyme engineering, which can reveal the interactions between amino acid residues and provide a theoretical basis for the modification of enzyme function and structure.

Methods and Results

So we learned virtual amino acid mutation, used FoldX to perform virtual amino acid mutation based on interaction force on a protein-ligand complex, sorted in descending order according to the relevant change in Gibbs free energy of protein folding (ΔG), identified 28 key amino acids in the active site and amino acid mutation targets that can improve affinity, and tried to improve SOD enzyme activity.

Figure 2-1 28 pairs of mutation sites for virtual amino acid mutation based on interaction forces

We used the scanner to output the final SCI scores of mutations, sorted them in descending order according to the SCI score, and identified the five key amino acids far away from the active site and the amino acid mutation targets that can improve stability, trying to improve the SOD enzyme activity. The SCI index (Sequence Co-evolution Index) is an indicator used in the enzyme activity engineering method based on sequence co-evolution analysis. It is used to evaluate the potential impact of the co-evolution relationship of the enzyme mutation site on the enzyme activity. The calculation of the SCI index takes into account the number and strength of the co-evolutionary relationships between the mutation site and other sites, as well as the distribution of these relationships in the enzyme sequence. The SCI index increases as the frequency of the mutant amino acid pair in the multiple sequence alignment (MSA) increases relative to the wild-type (WT) amino acid pair. Simply put, if a mutation site has a strong co-evolutionary relationship with many other sites in the enzyme sequence, and this relationship is prevalent in the sequence, then the SCI index of this site will be high, indicating that the mutation at this site may have a greater effect on the enzyme activity.

Figure 2-2 Five pairs of mutation targets for virtual amino acid mutation based on thermal stability and sci

Figure 2-3 33 pairs of mutation targets

Functional Expression

An inducible SOD-1 expression plasmid was constructed by single-point mutation of SOD-1.The 10th base is mutated from glycine to alanine，marked by Number 2.We took 2 mL of the overnight induced bacterial culture and used the Beyotime™ bacterial active protein extraction reagent to extract the protein. SOD activity was measured using the Beyotime™ SOD activity detection kit.

Figure 3-1 Protein standard curve

The activity of SOD was measured using the Bio-Tech™ SOD enzyme activity kit and A450 was measured using a microplate reader.

Figure 3-1Calculation formula of SOD inhibition rate and enzyme activity

Definition of SOD Enzyme Activity Units: In the aforementioned xanthine oxidase coupled reaction system, when the inhibition percentage reaches 50%, the enzyme activity in the reaction system is defined as one enzyme activity unit (unit). The original data are shown in the table below, and the inhibition rate of SOD Pro1 is 67.4%, and the enzyme activity is 2.0672 U.

Figure 3-3Data of the Inhibition rate and enzyme activity

Figure 3-4Comparison of inhibition rate and enzyme activity

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
  INCOMPATIBLE WITH RFC[25]

  Illegal AgeI site found at 412
  
• 1000
  COMPATIBLE WITH RFC[1000]