View source for Q125E

== 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.
[[File:BCKDHA_mut2_wt.png|thumb|center| Figure 1:  Structure of BCKDHA with highlighted amino acids]]

=== 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:Wildtype2_BCKDHAMinimise.png|thumb|Figure 2: Structure of glutamineon position 125 in the wildtype protein]]
|[[File:Mutation2_BCKDHAMinimise.png|thumb|Figure 3: Structure of glutamic acid on position 125 in the mutated protein]]
|}

=== 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.


{|class="centered"
|[[File:BCKDHA_Wt80.png|thumb|150px|Figure 4: Hydrogen Bonds for glutamine on pos 125 in the wild type structure]]
|[[File:BCKDHA_Mut80.png|thumb|150px|Figure 5: Hydrogen Bonds for glutamic acid on pos 125 in the mutated type structure]]
|}
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:

{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
!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:

{|border="1" style="border-spacing:0" align="center" cellpadding="3" cellspacing="3"
!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.

{|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"
!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:

{|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||5.23e+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_BCKDHA| Structure-based mutation analysis]]