M82L

Structure-based Mutation Analysis

SCWRL

scwrl wt energy?

Side chain properties

Figure 2: Structure of methionine on position 82 in the wildtype protein

Figure 3: Structure of Leucine on position 82 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 methionine on pos 82 in the wild type structure

Figure 5: Hydrogen Bonds for leucine on pos 82 in the mutated type structure

Comparing the figures 2 and 3 for the wildtype and the mutated amino acid on position 82, no change in the hydrogen bonding network can be observed. This is due to the similar physiochemical properties of these two amino acids. No atom which could serve as additional hydrogen-bond donor or acceptor was introduced or removed.

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	437.88	36.88
relative	100%	109%	9%

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	-4253.174790	-1767.722015
relative	100%	58%	42%

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

gromacs Energy comparison

Energy	Average	Err.Est	RMSD	Tot-Drift (kJ/mol)
Bond	2518.71	1700	6337.97	-10023.3
Angle	3642.41	270	638.624	-1479.34
Potential	5.16e+06	5.1e+06	7.47e+07	-3.13e+07