Difference between revisions of "M82L"

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== Structure-based Mutation Analysis ==
 
== Structure-based Mutation Analysis ==
 
=== Mapping onto crystal structure ===
 
=== 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.
===SCWRL ===
 
  +
[[File:BCKDHA_mut1.png|thumb|center| Figure 1: Structure of BCKDHA with highlighted amino acids]]
scwrl wt energy?
 
   
  +
The substitution of methionine on position 82 with leucine does not hinder ligand binding in the protein's active center. Therefore there must be other reasons why this mutation might be harmful for the protein's function.
  +
  +
=== 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.
  +
  +
  +
{|class="centered"
  +
|[[File:Wildtype1_BCKDHAMinimise.png|thumb|Figure 2: Structure of methionine on position 82 in the wildtype protein]]
  +
|[[File:Mutation1_BCKDHAMinimise.png|thumb|Figure 3: Structure of Leucine on position 82 in the mutated protein]]
  +
|}
  +
  +
Comparing figure 2 and 3 the structures of considerated amino acids are quite similar. Both amino acids are hydrophobic, but methionine contains a sulfur-atom which is then lost after the mutation. This could have an effect on 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.
   
== 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.
 
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.
   
   
 
{|class="centered"
 
{|class="centered"
|[[File:BCKDHA_Wt37.png|thumb|150px|Figure 2: Hydrogen Bonds for methionine on pos 82 in the wild type structure]]
+
|[[File:BCKDHA_Wt37.png|thumb|150px|Figure 4: Hydrogen Bonds for methionine on pos 82 in the wild type structure]]
|[[File:BCKDHA_Mut37.png|thumb|150px|Figure 3: Hydrogen Bonds for leucine on pos 82 in the mutated type structure]]
+
|[[File:BCKDHA_Mut37.png|thumb|150px|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.
 
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===
 
===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:
  +
 
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
 
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
  +
!Energy
 
!wildtype energy
 
!wildtype energy
 
!total energy of mutated protein
 
!total energy of mutated protein
 
!difference
 
!difference
 
|-
 
|-
|401.00||437.88||36.88
+
|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===
 
===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:
  +
 
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
 
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
  +
!Energy
 
!wildtype energy
 
!wildtype energy
 
!total energy of mutated protein
 
!total energy of mutated protein
 
!difference
 
!difference
 
|-
 
|-
| -2485.452755||-4253.174790||-1767.722015
+
|absolute|| -2485.452755||-4253.174790||-1767.722015
  +
|-
  +
|relative|| 100%||58%||42%
 
|}
 
|}
  +
  +
The mutated structure has an energy which is only about half of the energy of the wildtype structure. This is an extreme change in energy which might be accompanied by the instability of the mutated protein.
   
 
===gromacs Energy comparison===
 
===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.
  +
  +
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
  +
!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.
   
 
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
 
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
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|Potential || 5.16e+06 ||5.1e+06||7.47e+07||-3.13e+07
 
|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:
  +
  +
{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
  +
!Energy
  +
!wildtype energy
  +
!total energy of mutated protein
  +
!difference
  +
|-
  +
|absolute|| 2.67001e+07||5.16e+06||-21540100
  +
|-
  +
|relative|| 100%||19%||81%
  +
|}
  +
  +
The energy difference calculated by Gromacs is even higher than the calculations by minimise. These enormous energy changes are due to totally different protein structures, caused by the mutation of one amino acid. This mutation lowers the protein's energy and might therefore be to destabilizing and affect the protein's function.
  +
  +
=== Conclusion ===
  +
All energy calculations show a significant divergence of the mutated protein structure from the wildtype-structure which indicate that this mutation leads to an instable protein. These calculations could be affirmed as the biophysical properties of the corresponding amino acids are quite similar and the hydrogen bonding network didn't change.

Latest revision as of 20:01, 11 August 2011

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

The substitution of methionine on position 82 with leucine does not hinder ligand binding in the protein's active center. Therefore there must be other reasons why this mutation might be harmful for the protein's function.

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.


Figure 2: Structure of methionine on position 82 in the wildtype protein
Figure 3: Structure of Leucine on position 82 in the mutated protein

Comparing figure 2 and 3 the structures of considerated amino acids are quite similar. Both amino acids are hydrophobic, but methionine contains a sulfur-atom which is then lost after the mutation. This could have an effect on 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 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 which is only about half of the energy of the wildtype structure. This is an extreme change in energy which might be accompanied by the instability of the mutated protein.

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 energy difference calculated by Gromacs is even higher than the calculations by minimise. These enormous energy changes are due to totally different protein structures, caused by the mutation of one amino acid. This mutation lowers the protein's energy and might therefore be to destabilizing and affect the protein's function.

Conclusion

All energy calculations show a significant divergence of the mutated protein structure from the wildtype-structure which indicate that this mutation leads to an instable protein. These calculations could be affirmed as the biophysical properties of the corresponding amino acids are quite similar and the hydrogen bonding network didn't change.