Y438N

Structure-based Mutation Analysis

Mapping onto crystal structure

Figure 1 shows the protein structure with highlighted amino acids. The mutation position is colored violet, the thiamine pyrophosphate binding sites are orange, and metal binding sites are yellow.

Figure 1: Structure of BCKDHA with highlighted amino acids

Figure 2: Surface of BCKDHA with highlighted amino acids

Figure 1 and 2 show that this mutation takes places on the surface of the protein but not nearby any active site. So we have to investigate the biophysical properties of the wildtype and the mutated amino acids to understand the effect of the mutation.

Side chain properties

Figures 3 and 4 show the superposition of the mutated amino acid with the wildtype. The pictures showing the wildtype structure display the unmutated residue in bold and vice versa.

Figure 3: Structure of tyrosine on position 82 in the wildtype protein

Figure 4: Structure of asparagine on position 82 in the mutated protein

This mutation also changes the amino acid completely. A big aromatic, hydrophobic residue is substituted by a small polar one. These differences are likely to affect the protein's function.

Hydrogen Bonding network

Hydrogen bonds are interactions between an hydrogen atom and an electronegative atom. Electronegative atoms which often take part in hydrogen bonds are oxygen, nitrogen and fluorine (not present in amino acid side chains). They serve as a hydrogen bond acceptor, whereas a hydrogen bond donor is a electronegative atom bonded to a hydrogen atom. Hydrogen bonds are essential for the three-dimensional structures of proteins. They play a important role in the formation of helices and beta-sheets and cause proteins to fold into a specific structure.

Showing hydrogen bonds with Pymol: A -> find -> polar contacts -> within selection The respective amino acids were colored by element, s.t. oxygen is red, nitrogen is blue, hydrogen is white and sulfur is yellow.

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 5: Hydrogen Bonds for tyrosine on pos 438 in the wild type structure

Figure 6: Hydrogen Bonds for asparagine on pos 438 in the mutated type structure

The hydrogen bond donor property of the amino acid on position 438 is maintained but the bond seems to be different between the sidechains now (Compare Figure 5 and 6). This substitution also disturbs the hydrogen bonding network of our protein.

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	431.56	30.56
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	-4339.778964	-1854.326209
relative	100%	57%	43%

The mutated structure has an energy that is much smaller than the wildtype. As the energy of the wildtype is about twice of energy of the mutated protein, the effect of this mutation is severe. The big difference in energies leads to the assumption that the stability of the protein is strongly affected.

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	3141.2	2300	-nan	-13216.1
Angle	3672.66	290	-nan	-1550.04
Potential	8.33e+06	8.1e+06	-nan	-4.94e+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	5.16e+06	-18370100
relative	100%	19%	81%

The calculated energy for the mutated structure is much smaller than for the wildtype structure. This observation agrees with the results from the minimise calculation. Here the energy is even smaller for the mutated structure, which supports the damaging effect of this mutation on the protein's function even more.

Conclusion

All energy calculations show a significant divergence from the wildtype-structure energy which indicate that the mutation led to an instable protein. These calculations agree with the observations made based on the biophysical properties of the amino acids and the local hydrogen bonding network. The biophyiscal properties changed drastically and different hydrogen bonds were formed. This could be the reason for the instability of the mutated protein structure.

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