Structure-based mutation analysis GLA
- 1 Introduction
- 2 Methods
- 3 Results
- 3.1 Structure Selection
- 3.2 Visual Examination of the Mutations
- 3.3 Energy Comparison
- 3.4 Individual Evaluation of the Mutations
- 3.5 Gromacs
- 4 References
In this task we analyse the structure of our protein to find out what effects the point mutations have. Therefore we created mutated structures and compared them to the wild-type protein. Several tools based on different methods have been used to achieve that aim. We used the mutations that we have chosen in the previous task.
In the first step of this task we had to find available protein structures for our protein and to decide which one would be the best for our detailed analysis. We set several cut-offs to exclude improper structures. The following tools have been used to perform the energy calulations. They were used as described in the task description.
SCWRL was initially developed by Dunbrack et al. in 1997. We use SCWRL4<ref name=dunb>G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack, Jr. Improved prediction of protein side-chain conformations with SCWRL4. Proteins (2009)</ref> which was published in 2009. The program takes a PDB file and a sequence file as input. By usage of a rotamer library, collision detection, and a residue interaction graph the optimal side-chain conformation is calculated, based on the backbone and the mutated sequence given in the input files. The output is a PDB file containing the conformation and the total minimal energy of the graph in STDOUT.
FoldX was developed by Serrano et al. in 2002<ref name=serr>Guerois R, Nielsen JE, Serrano L., Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutation. Journal of Molecular Biology (2002)</ref>. We used version FoldX 3.0 beta 4. The program provides the calculation of determination of energy effects of point mutations. It provides different run modes, but basically it takes a PDB file as input calculates several single energies(e.g. Van der Waals, Electrostatics, ...) and returns the single energies together with the total energy as output.
Before this tool from the virtual box was used we had to remove the hydrogens and waters from the PDB file with the script repairPDB. Afterwards we were able to compare the energies differences between the wildtype and the mutated protein.
GROMACS is mostly a package to perform molecular dynamics, but it also provides energy calculations.
For the mutations we used the forcefield AMBER03 and for the wildtype AMBER03, AMBERGS and CHARMM27.
Additionally to the energy calculation task we did a runtime analysis with values from nsteps=10 to nsteps=1500. The results are shown in the results section of this task.
According to the task description we created an MDP file with the following content:
title = PBSA minimization in vacuum cpp = /usr/bin/cpp define = -DFLEXIBLE -DPOSRES implicit_solvent = GBSA integrator = steep emtol = 1.0 nsteps = 500 nstenergy = 1 energygrps = System ns_type = grid coulombtype = cut-off rcoulomb = 1.0 rvdw = 1.0 constraints = none pbc = no
|Keyword||Describtion<ref name=manual>Gromacs Manual</ref>|
|title||Name of Project|
|cpp||Location of c-preprocessor|
|define||Defines to pass to the preprocessor; |
-DFLEXIBLE:include flexible water in stead of rigid water into your topology;
-DPOSRES: include posre.itp into your topology, used for position restraints
|implicit_solvent||Simulation with implicit solvent using the Generalized Born formalism|
|integrator||Steepest descent algorithm for energy minimization|
|nsteps||Maximum number of steps to integrate or minimize|
|emtol||Rhe minimization is converged when the maximum force is smaller than this value|
|nstenergy||Frequency to write energies to energy file|
|energygrps||Group(s) to write to energy file|
|ns_type||Type of neighbor searching|
|pbc||Remove the periodicity (make molecule whole again)|
|coulombtype||Type of coulomb energy|
|rcoulomb||Distance for the Coulomb cut-off|
|rvdw||distance for the LJ or Buckingham cut-off|
|constraints||Which constraints should be used|
Within the GROMACS work step we used the script fetchpdb. It checks if the given input is a valid PDB entry. If the check was successful it downloads the PDB file, extracts it and removes the packed version.
There are several structure files available for our protein:
|PDB ID||Resolution [Å]||ph-Value||R-Factor||Coverage [%]||Missing Residues|
We set two cutoffs to decide which structures are excluded:
- ph-value: < 6.5
- resolution: > 2.7
After we applied the cutoffs to our set of structures three were left (exclusion factors are colored red in the table). One of them was slightly better than the other ones so we decided to use 3HG3 (worse values are colored gray in the table). Additionally 3GH3 has the best overall resolution and R-factor (colored green). As the missing residues are very similar for all structures they are not further taken into account.
Visual Examination of the Mutations
Figure 1 shows the protein α-galactosidase A and the residues which will be mutated. In the following sections, we compare the side chain conformation of the mutated residues and discuss the influence of the mutation. Aspects will be, inter alia, loss of polar interactions and clashes with other residues.
SCWRL was used to model the side chain conformation of the mutated residue and we use the term tool-based to describe this side chain conformation. The side chain conformation which was done according to this tutorial is referred to as manual side chain conformation.
M42T (Mutation 1)
Figures 2 to 4 show the side chain conformation of the residue 42 in α-galactosidase A. The only difference between the manual and the tool-based side chain conformation is a variation in the conformation of the hydroxyl group of threonine (see figure 3 and 4). The tool-based side chain conformation does not lead to any clashes with the surrounding residues.
The wildtype M42 has two hydrogen bonds with E87 and Y88. Since these hydrogen bonds are formed by the carboxylgroup of the backbone, they are also abundant in the mutation, but T42 also forms a hydrogen bond with G85.
A part of T42 is exposed to the surface (see figure 5B). This is no problem, since threonine is slightly hydrophilic. But the mutation introduces a small hole into the surface of GLA (see figure 5A and 5B).
S65T (Mutation 2)
The side chain conformations of the wildtype and the mutated residues are shown in figure 6 to 8. The hydroxyl and methyl group of threonine point towards totally different direction in the tool-based conformation (see figure 6 and 8), but there are no clashes with other residues. The wildtype S65 forms five hydrogen bonds with surrounding residues (C63, K67, L68, F69). The mutated residue T65 forms also five hydrogen bonds, but one of them is with E66 instead of K67.
Serine is hydrophilic and the residue is exposed on the surface, but threonine is also a hydrophilic residue. There is no remarkable change of the surface of the protein.
I117S (Mutation 3)
Since the tool-based side chain conformation of the mutated residue (see figure 11) is pretty similar to the side chain conformation of the wildtype (see figure 9), there are no clashes in the mutated structure. The angle of the hydroxyl group is slightly different in the manual side chain conformation (see figure 10).
The hydroxyl group in the backbone of I117 forms two hydrogen bonds with L120 and A121. These bonds are also abundant in the mutated structure. Serine is a hydrophilic amino acid, but this is no problem, because it is part of the surface. Overall there is no remarkable difference in the surface of the protein due to the mutation.
A143T (Mutation 4)
This is the only mutation which is close to the active site of the protein (see figure 12). The general orientation of the side chain is very similar between the wildtype, manual and tool confirmation (see figure 13, 14 and 15). The hydroxyl group of threonine leads to an increase of the space requirements with the tool-based side chain conformation. Hence there is a clash between the hydroxyl group of T143 and the residue D93 (see figure 16).
A143 forms two hydrogen bonds with the carboxyl group of its backbone to D92 and T141. These hydrogen bonds are also formed by T143, but a third hydrogen bond is established between the oxygen of the hydroxyl group of T143 and D92.
T143 is part of the surface, so it is no problem that this position becomes hydrophilic. The mutation changes the surface and since this mutation is nearby the active site, this will probably have an influence on the work rate of the protein (see figure 17). The entry to the active site becomes more narrow due to the mutation. Hence it will be less likely or even impossible that the ligand binds in the active site.
H186R (Mutation 5)
Figures 13 to 15 show the side chain conformations of the residue. The general orientation of the side chain is similar. Because of this, the residue points towards the exterior of the protein. There is small collision with the residue D153 which is located in alpha-helix nearby (see figure 16).
H186 forms three hydrogen bonds with its backbone to D182, L189 and A190, which are also formed by the mutated residue R186. Both amino acids, histidine and arginine, are hydrophobic even though the position itself is exposed on the surface. The change on the surface is not noteworthy.
P205T (Mutation 6)
Since the structure of proline is a special case, the comparison of the side chain conformation is not trivial. Threonine has a higher space requirement than proline. The difference between the manual and tool-based side chain conformation is a variation of one angle in the side chain. There are two small collisions with surrounding residues (I219 and N228) due to the higher space requirements of threonine (see figure 25).
P205 forms two hydrogen bond with M208 and W209. The bond with M208 is also formed by T205, but the hydrogen bond to W209 is lost. Therefor a hydrogen bond to N228 is established. The substitution of proline to threonine does not have any influence on the surface of the protein.
D244H (Mutation 7)
The side chain of the wildtype has a very flat angle to the alpha-helix (see figure 26), whereas the manual and tool-based side chain conformations show an almost orthogonal orientation (see figure 27 and 28). Hence there are no collisions with other residues. The manual and tool-based conformations are also very similar to each other.
D244 forms four hydrogen bonds. The carboxyl group of the side chain forms two bonds with arginine at position 356. The remaining two bonds are formed by the backbone of D244 with K240 and F248. These two hydrogen bonds are also established by the mutated residue H244 and the side chain forms a third bond S247.
This position is exposed on the surface of the protein and aspartic acid and histidine are hydrophilic amino acids. The orthogonal angle of histidine to the alpha-helix adds a bulge and a small hole to the surface of the protein (see figure 29).
Q283P (Mutation 8)
Figures 30 to 32 show the side chain conformation at position 283. The manual and the tool-based side chain conformation are very similar (see figure 31 and 32). This is probably due to the fact that proline is a very rigid amino acid. Glutamine has much higher space requirements. Hence the substitution to proline does not lead to a collision with other residues.
The hydroxyl group of the side chain of Q238 forms two hydrogen bonds with M267 and V268. The backbone establishs another four hydrogen bonds with Q278, Q279, L286 and W287. These four residues are located in the same alpha-helix. The mutated residue P283 forms only two of these four hydrogen bonds with L286 and W287. This might result in partial loss of the alpha-helix which is no surprise, since proline is considered to be a helix breaker<ref name=proline_helix>Gunasekaran et al., "Stereochemical punctuation marks in protein structures: glycine and proline containing helix stop signals.". J Mol Biol. 1998 Feb 6. PubMed</ref>.
Q283 is part of the core, so the substitution does not change the surface.
Q321E (Mutation 9)
Since the structures of glutamine and glutamic acid are so similar, the side chain conformation shows almost no differences (see figure 33, 34 and 35). There is only one angle in the side chain which is slightly different that does not lead to a collision with other residues.
The oxygen in the side chain of Q321 forms a hydrogen bond with T39, the amine forms two hydrogen bonds with P40 and N320. The backbone of Q321 establishs a hydrogen bond with I317 which is also formed by the mutation E321. The side chain of the mutation E321 only establishs one hydrogen bond with T39. So there are two bonds missing due to the mutation.
Even though this position is exposed on the surface, there are no remarkable changes due to the substitution.
R363C (Mutation 10)
The side chain confirmations of this position are shown in figures 36 to 38. The conformation between the manual and the tool-based ones is very similar. Arginine has a much higher space requirment, hence there is no collusion with other residues due to the substitution to cysteine.
The side chain of R363 forms five hydrogen bonds with D335, N336 and N355. These bonds are all lost due to the substitution to cysteine. The backbone of R363 establishs another two hydrogen bonds with I407 which are preserved in the mutation C363. So overall there is a loss of five hydrogen bonds.
Arginine is a hydrophilic amino acid and R363 is exposed on the surface. The substitution to the hydrophobic amino acid cysteine could be a problem. The mutation also introduces a big hole in the surface (see figure 39).
The results of the energy comparison are presented in the table below. Due to the fact that the result of minimise for mutation 8 clearly differed from the other results, the run was repeated with the outcome from the first run as input. Thus, there is the number 8.2 in the table.
|Number||AA-Position||Amino acid change||SCWRL4||FoldX||Minimise||Gromacs|
|1||42||Met -> Thr||343.25||157.29||-178.22||-20324.41||-156.82||-90528.4||-779.3|
|2||65||Ser -> Thr||327.798||152.87||-173.8||-20339.34||-141.89||-90481.9||-825.8|
|3||117||Ile -> Ser||333.027||157.97||-178.9||-20353.47||-127.76||-90654||-653.7|
|4||143||Ala -> Thr||333.944||154.40||-175.33||-20339.32||-141.91||-90541||-766.7|
|5||186||His -> Arg||323.717||154.57||-175.5||-20321.32||-159.91||-91011.7||-296|
|6||205||Pro -> Thr||340.619||155.96||-176.89||-20345.87||-135.36||-90782.2||-524.8|
|7||244||Asp -> His||333.594||152.08||-173.01||-20393.12||-88.11||-90232.9||-1074.8|
|8||283||Gln -> Pro||332.631||159.91||-180.84||-8027.71||-12453.52||-87316||-3991.7|
|9||321||Gln -> Glu||332.853||160.95||-181.88||-20246.98||-234.25||-90090.3||-1217.4|
|10||363||Arg -> Cys||330.56||150.50||-171.43||-20295.77||-185.46||-89721.8||-1585.9|
There is no mutation that stands out with a very high or very low energy. Every energy difference ranges from approximately -170 to -185. Hence it is very tough to make a clear distinction between neutral and non-neutral mutations.
The results of Minimise cover a much wider range than the results of FoldX. This is mainly due to the result of mutation 8 which shows a significantly lower result than the others. Mutation 9 and 10 should also be mentioned as mutations with a very high difference to the wildtype. Mutation 7 has the lowest difference and the other mutations are somewhere in between.
Mutation 5 is the mutation with the lowest difference to the wildtype. Once again, mutation 8 has the highest difference. The next least stable structures are the ones of mutation 10, 9 and 7. Mutation 5 has the lowest difference
Individual Evaluation of the Mutations
We evaluate the results of the visual examination and the energy comparison in the following sections individual for each mutation and try to predict the influence of the mutation on the protein.
M42T (Mutation 1)
The structural influence of the substitution from methionine to threonine at this position can be reduced to the change of the surface in this case, since this is the only aspect in which a remarkable difference occurs. Another aspect is the loss of disulfide bonds due to the mutation which could lead to a loss of stability of the protein. Since the energy comparison does not indicate such a strong influence. This is backed up by the annotation of the UniProt entry which does not contain a disulfid bond at this position.
S65T (Mutation 2)
The side chain conformation of the mutated residue is slightly different, but there a no clashes with other residues and the hydrogen bonds are preserved or substituted, respectively.
I117S (Mutation 3)
The substitution of isoleucine to serine does not lead to a remarkable change in any of the visual examined aspects.
A143T (Mutation 4)
This mutation has a huge influecne on the structure of the protein. There are two aspects that show a remarkable change. The mutations leads to a clash with another residue. But the major aspect is the change of the surface of the protein. Since this mutation is nearby the active site, the ligand is unlikely to be able to bind at the active site and this will probably have a strong influence on the functionality of the protein. The energy comparison does not show such a strong tendency to a non-neutral mutation, but the observed changes do not lead neccessarily to a change of the energy. Nevertheless, this mutation is very likely to be a non-neutral mutation.
Prediction: a non-neutral mutation.
H186R (Mutation 5)
Even though the substitution to arginine leads to clash with another residue at this position, the energy values does not indicate an extraordinary result in relation to the other mutations. Quite the contrary, the value of Gromacs is one of the lowest.
P205T (Mutation 6)
Even though the substitution of proline to threonine leads to collisions with two other residues, the energy comparison does not indicate a less stable protein in relation to the energies of the other mutations. This mutation has the third or second lowest difference in the results of Minimise or Gromacs, respectively. Since the energy comparison indicates a neutral mutation and the collisions are very slight, we assume that this mutation is neutral.
Prediction: a neutral mutation.
D244H (Mutation 7)
Q283P (Mutation 8)
Q321E (Mutation 9)
R363C (Mutation 10)
This section shows the results of Gromacs in more detail.
|Force Field||Average||Error Estimat||RMSD||Tot-Drift (kJ/mol)|
|Force Field||Average||Error Estimat||RMSD||Tot/Drift|