Difference between revisions of "M82L"
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== Structure-based Mutation Analysis == |
== Structure-based Mutation Analysis == |
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=== Mapping onto crystal structure === |
=== Mapping onto crystal structure === |
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− | ===SCWRL === |
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− | scwrl wt energy? |
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+ | === Side chain properties === |
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− | ==== Side chain properties ==== |
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− | + | === Hydrogen Bonding network === |
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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 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. |
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The calculated energy for the mutated structure is much smaller than for the wildtype structure. |
The calculated energy for the mutated structure is much smaller than for the wildtype structure. |
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+ | === Conclusion === |
Revision as of 11:12, 11 August 2011
Contents
Structure-based Mutation Analysis
Mapping onto crystal structure
Side chain properties
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.
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
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 | 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 |
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 | -21540100 |
relative | 100% | 19% | 81% |
The calculated energy for the mutated structure is much smaller than for the wildtype structure.