Difference between revisions of "I326T"
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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 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. |
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[[File:BCKDHA_mut7.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]] |
[[File:BCKDHA_mut7.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]] |
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| + | Looking at figure 1 it is not obvious why this mutation should be damaging, as it is not nearby the active center. The mutation does also not take place on the surface of the protein. So we have to take a look at the side chain properties to understand the damaging effect of this mutation. |
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=== Side chain properties === |
=== Side chain properties === |
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Figures 2 and 3 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. |
Figures 2 and 3 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. |
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Revision as of 19:12, 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.
Looking at figure 1 it is not obvious why this mutation should be damaging, as it is not nearby the active center. The mutation does also not take place on the surface of the protein. So we have to take a look at the side chain properties to understand the damaging effect of this mutation.
Side chain properties
Figures 2 and 3 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 mutation from isoleucine to threonine doesn't have an influence on the hydrogen bonding network, although the oxygen atom of threonine could serve as an additional hydrogen bond donor (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 | 432.94 | 31.94 |
| 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 | -4317.105618 | -1831.652863 |
| relative | 100% | 57% | 43% |
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 | 3214.03 | 2300 | 7364.47 | -13490.1 |
| Angle | 3738.44 | 310 | 698.943 | -1792.01 |
| Potential | 7.29e+06 | 6.9e+06 | 8.86e+07 | -4.38e+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 | 7.29e+06 | -19410100 |
| relative | 100% | 27% | 73% |
The calculated energy for the mutated structure is much smaller than for the wildtype structure.
Conclusion
return to Structure-based mutation analysis
