Difference between revisions of "Q125E"
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| − | As one can see from figure 1, the mutation of glutamine on position 125 to glutamic acid does not interfere with any active site. But looking at figure 2 it is clear that this mutation changes an amino acid on the surface of the protein. |
+ | As one can see from figure 1, the mutation of glutamine on position 125 to glutamic acid does not interfere with any active site. But looking at figure 2 it is clear that this mutation changes an amino acid on the surface of the protein. This could be problematic if the biochemical properties of the mutated amino acid would not agree with the biophysical environmental conditions of the protein's surface. Therefore we have to take a look at the side chain properties. |
=== Side chain properties === |
=== Side chain properties === |
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Revision as of 18:46, 11 August 2011
Contents
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.
As one can see from figure 1, the mutation of glutamine on position 125 to glutamic acid does not interfere with any active site. But looking at figure 2 it is clear that this mutation changes an amino acid on the surface of the protein. This could be problematic if the biochemical properties of the mutated amino acid would not agree with the biophysical environmental conditions of the protein's surface. Therefore we have to take a look at the side chain properties.
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.
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.
The substitution from glutamine to glutamic acid changes the side chain properties completely. A NH2 group is substituted by a negatively charged oxygen. The NH2 which served in the wildtype structure as a hydrogen bond acceptor (see Figure 4) is not present any more, so the hydrogen bonding network changed for this substitution (compare Figure 4 and 5).
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 | 431.77 | 30.77 |
| 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 | -4080.989512 | -1595.536757 |
| relative | 100% | 60% | 40% |
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 | 2519.85 | 1700 | 6351.32 | -10027.5 |
| Angle | 3626.21 | 260 | 618.433 | -1418.24 |
| Potential | 5.23e+06 | 5.2e+06 | 7.5e+07 | -3.17e+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 | 5.23e+06 | --21470100 |
| relative | 100% | 19% | 81% |
The calculated energy for the mutated structure is much smaller than for the wildtype structure.
Conclusion
return to Structure-based mutation analysis
