G249S

Structure-based Mutation Analysis

Side chain properties

Figure 2: Structure of glycine on position 249 in the wildtype protein

Figure 3: Structure of serine on position 249 in the mutated protein

Hydrogen Bonding network

The following figures show the hydrogen bonds between the wildtype residue and its environment compared to the formation of hydrogen bonds when the corresponding residue is mutated.

Figure 4: Hydrogen Bonds for glycine 249 in the wild type structure

Figure 5: Hydrogen Bonds for serine on pos 249 in the mutated type structure

Introducing a serine on position 249 leads to the formation of several additional hydrogen bonds (see Figure 5). Two of the newly established bonds are due to the new hydroxy group which is very likely to participate in hydrogen bonds. Another additional hydrogen bond is formed using the nitrogen atom as a hydrogen bond acceptor.

foldX Energy Comparison

We used the foldX tool to compare the energy of the wildtype protein and the mutated structure. The following table shows the calculated energy values as well as the percentage of difference, to compare the energy calculations with other tools:

Energy	wildtype energy	total energy of mutated protein	difference
absolute	401.00	432.22	31.22
relative	100%	107%	7%

The total energy of the mutated structure is a little bit higher than the energy of the wildtype protein structure. As protein energies should be low for a stable protein, the increasing energy leads to the assumption that this mutation might be damaging for the protein structure.

minimise Energy Comparison

Next we used the minimise tool to compare the energy of the wildtype protein and the mutated structure. The following table shows the calculated energy values as well as the percentage of difference, to compare the energy calculations with other tools:

Energy	wildtype energy	total energy of mutated protein	difference
absolute	-2485.452755	-4280.043000	-1794.590245
relative	100%	58%	42%

The mutated structure has an energy that is much smaller than the wildtype

gromacs Energy comparison

The Gromacs energy comparison was conducted using the AMBER03 force field. The following table shows the calculated energies for the wildtype protein structure.

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	3072.83	2200	-nan	-13100.2
Angle	3616.97	230	-nan	-1295.57
Potential	2.67001e+07	2.6e+07	-nan	-1.60382e+08

Here are the results for the mutated protein structure.

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2775.97	2000	6761.45	-11375.2
Angle	3682.24	300	670.885	-1625.24
Potential	5.96e+06	5.0e+06	8.02e+07	-3.61e+07

As we want to compare the Gromacs energies with the other tools, we calculate the ratio of difference considering the potential energy:

Energy	wildtype energy	total energy of mutated protein	difference
absolute	2.67001e+07	5.96e+06	-20740100
relative	100%	22%	78%

The calculated energy for the mutated structure is much smaller than for the wildtype structure.

Conclusion

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