Fabry:Normal mode analysis
Fabry Disease » Normal mode analysis
For further information on the execution, please refer to our Journal
Introduction
<figure id="fig:bindSite">
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Maybe one of the first questions that can be asked in this task is, why we use low-frequency normal modes. This is explained in the paper of Marc Delarue and Philippe Dumas<ref>Marc Delarue and Philippe Dumas On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models, Proc. Natl. Acad. Sci. (USA), 101, 6957-6962 (2004)</ref>, where they claim, that "many of the structural transitions (...) can be explained by just a few of the lowest-frequency normal modes". The normal modes can be used to generate the general motion of a system by superposition them. Thus we could in principle infer from our analysis in this task how the alpha-galactosidase A, which we examine hydrolyses the terminal alpha-galactosyl moiety of its substrate<ref>Normal mode http://en.wikipedia.org/wiki/Normal_mode, July 5th, 2012</ref>.
We decided to use the structures 3HG2 and 3HG3, which represent the human α-Galactosidase catalytic mechanism with empty active site and substrate bound, respectively (see <xr id="fig:bindSite"/>). From this, we hope to getter an insight into the mechanism and a possibility to compare normal modes and the behaviour of the molecule.
Possible normal modes:
The structure 3HG2 has 781 C-alpha atoms in its pdb file, thus 781*3 - 6 = 2337 normal modes could be calculated in principle for this structure without any cutoff by elNémo. Since the structure has a total of 6765 atoms, 20289 NMs could be calculated by WEBnm@.
The structure 3HG3 has 793 C-alpha atoms in its pdb file, thus 793*3 - 6 = 2373 normal modes could be calculated in principle for this structure without any cutoff by elNémo. Since the structure has a total of 7537 atoms, 22605 NMs could be calculated by WEBnm@.
WEBnm@
WEBnm@ <ref>Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref> claim to administer simple and automated computation of low-frequency normal modes for proteins as well as their analysis in order to clarify if it is beneficial to perform a complete study on the protein in question.
The server calculates Normal Modes with the help of the MMTK package <ref>Hinsen K, The Molecular Modelling Toolkit: a new approach to molecular simulations, J Comput Chem, 21:79-85, 2000</ref>, which is an Open Source program library for molecular simulation applications. A C-alpha force field <ref>Hinsen K, Petrescu AJ, Dellerue S, Bellissent-Funel MC, Kneller GR, Harmonicity in slow protein dynamics, Chemical Physics, 261:25-37, 2000</ref> is used and only these C-alpha atoms are used, but with a weight assigned that corresponds to the masses of the whole residue they represent.
The server provides a bunch of analysis tools and all results can be downloaded without any problems. The tools are:
- deformation energies of each mode
- eigenvalues
- calculation of normalized squared atomic displacements
- calculation of normalized squared fluctuations
- interactive visualization of the modes using vector field representation or vibrations
- correlation matrix
Deformation energies and eigenvalues
<figtable id="tab:eigen">
</figure></figure>
| <figure id="fig:eigen3HG2"> |
| <figure id="fig:eigen3HG3"> |
</figtable>
<figure id="fig:avEn">
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In <xr id="fig:eigen3HG2"/> and <xr id="fig:eigen3HG3"/> the Eigenvalues for the first 50 modes for both examined structures are plotted. The increase of the values shows a decrease of amplitude of motion in the modes, since there is an invers relationship between the Eigenvalues and the amplitude. Hence, mode 7 has the highest amplitude.
Since the eigenvalues correspond to the frequencies and a low frequency tends to describe a global movement of the protein our assumption is confirmed, that the lower modes express global movement, while higher modes rather show many smaller local movements. <ref>Normal Mode (Harmonic) Analysis http://cmm.cit.nih.gov/intro_simulation/node26.html, August 14th, 2012</ref>
Average Energies
In figure <xr id="fig:avEn"/> the average deformation energies of the lowest 14 modes of both catalytic mechanism are compared. For most modes the energies of the modes for 3HG2 are bigger than those for 3HG3. This means, that the amplitude of the motion is in general slighty lower in 3HG2 than in 3HG3 (see also Deformation Energies Table for the values of the average energies).
Mode Visualization
In this section, we want to visually inspect the motion of the protein in the 6 smallest modes that were identified by WEBnm@.
For a description of the modes of the molecules 3HG2 and 3HG3 see <xr id="tab:webnma_3hg2" /> and <xr id="tab:webnma_3hg3"/>, respectively. Modes 7 through 9 are similar for both molecules and mode 11 of 3HG2 corresponds to mode 10 in 3HG3. Although mode 7 of 3HG2 moves outwards, while mode 7 of 3HG3 moves inwards, making them moving in opposite directions. Of course, all similar modes can be explained in both states of the α-galactosidase catalytic mechanism, especially, mode 11/10, where one active site is in the process of releasing the substrate and one is binding it. Left is to compare both modes 12, where 3HG2's looks like closing in on the substrate that is to be bound, while 3HG3's mode 12 could be the beginning of releasing the hydrolized sugar.
For the modes 3HG2 10 and 3HG3 11 we do not have an explanation, why they could explain the function of our protein.
Concluding, it can be said, that the protein α-Galactosidase is rather rigid in most parts, except for the residues that connect chain A and B and the big and small part of each chain.
<figtable id="tab:webnma_3hg2">
In this table the 6 modes are shown, that were calculated by WEBnm@. Depicted is the structure 3HG2, which represents the Human α-galactosidase catalytic mechanism with empty active site in cyan and the substrate binding site at position 203 to 207 highlighted in red.
 Again in WEBnm@ mode 9 it seems that mostly the region that connects chain A and B is rigid (cf. mode 7 and 8), now bending both upper parts of the molecule to the left and both lower parts to the right. This may be explained by "shoving" the sugar into the active site, which is located in the front of the picture, while releasing the sugar that has been hydrolized in the active site in the back of the picture (which cannot be seen). | ||
 WEBnm@ mode 10 : Here all four parts of the protein (both upper parts of the chains and both lower parts of it) seems to bend towards the center of the groove and while doing so turning to the left, where a little more parts than only the bridge between the chains need to be flexible. We cannot think of an explanation for this kind of movement, but again being involved in bringing the sugar inside the active site. |
 The WEBnm@ mode 11 looks like an opening or closing motion if only either the front part or the back part of the dimer (the bigger part of the right chain and the smaller part of the left chain or vice versa) is considered. Looking at the whole molecule, we see that both upper parts move to the right and both lower parts move to the left, which gives the impression of turning an imaginary bound molecule in the groove between the chains. In this movement again the part that binds both chains together has to be non-rigid, but also the part that lies between the bigger part, which contains the substrate binding site, and the smaller part has to be elastic. |
 In WEBnm@ mode 12 the molecule seems again to make some kind of a closing motion, where the central part of the dimer (the part that connects both chains) is pushed downwards, bringing all four parts (big and small part of both chains) to close up towards the middle. This could again be due to having to hold on to a sugar that has to be bound to the active site in order to be cleaved. To do so, again mainly the connecting part has to be flexible. In addition, some parts of the chains have to bend, to really close up the opening. |
</figtable>
<figtable id="tab:webnma_3hg3"> In this table the 6 modes are shown, that were calculated by WEBnm@. Depicted is the structure 3HG3, which represents the Human α-galactosidase catalytic mechanism with bound substrate (green, α-D-Galactose with bound α-D-Glucose) in cyan and the substrate binding site at position 203 to 207 highlighted in red.
 WEBnm@ mode 7shows a shearing motion in the groove between chain A and B, which might relate to the function of the galactosidase, namely the hydrolysis of terminal α-D-galactose. It can be observed, that the binding groove moves around the substrate. Here almost the whole protein stays rigid, while the small part linking both chains moves. |
 In WEBnm@ mode 8 the two monomeres of the structure make an opening movement, thus enlargening the groove between them and exposing the binding pockets for the substrate and the active site. Again there is not much flexibility, but in the linking part of the dimer. The movement makes it possible for the substrate to enter the binding site, which becomes exposed. |
 Again in WEBnm@ mode 9 it seems that mostly the region that connects chain A and B is rigid (cf. mode 7 and 8), now bending both upper parts of the molecule to the left and both lower parts to the right. It can be observed that the binding pocket closes in on the sugar and the smaller part of the left chain helps fixating the substrate, while the sugar that has been hydrolized in the active site in the back of the picture (which cannot be seen) is released |
 The WEBnm@ mode 10 looks like an opening or closing motion if only either the front part or the back part of the dimer (the bigger part of the right chain and the smaller part of the left chain or vice versa) is considered. Looking at the whole molecule, it seems that the active site in the front releases the substrate, while the active site in the back is in the process of binding a new sugar that has to be hydrolized. In this movement again the part that binds both chains together has to be non-rigid, but also the part that lies between the bigger part, which contains the substrate binding site, and the smaller part has to be elastic. |
 WEBnm@ mode 11 is the first mode, that is different from all the other modes examined so far. It gives the impression of a breathing or relaxing a spring. The whole dimer expands towards the outside by stretching many bonds throughout the molecule. In this motion the active site moves away from the substrate. |
 In WEBnm@ mode 12 the front part of the dimer (small part of the left chain and big part of the right chain) moves away from the back part, resulting in a small rotation of each of the active sites around their substrate. Again, both the connecting part between both chains and between the bigger and the smaller part has to be elastic. |
</figtable>
Motion
Atomic Displacement Analysis
<figure id="fig:atomDisplacement3HG2">
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<figure id="fig:atomDisplacement3HG3">
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In <xr id="fig:atomDisplacement3HG2"/> and <xr id="fig:atomDisplacement3HG3"/> the square of the atomic displacements of the C alphas of the examined structures are shown. These are normalized in a way, such that the sum over all residues is equal to 100. With these plots we can find out, which regions are displaced most, i.e. which move the most; this is shown by the highest values. It is recommended to look for clustered peaks, which identify significantly big regions. Local flexibility (a single peak) is of less importance.
In both figures, chain A and B are colored different. From this we can see, that although in <xr id="tab:webnma_3hg2"/> and <xr id="tab:webnma_3hg3"/> the motion of both chains in a mode looks alike, but in general it is not perfectly equal or even differs a lot. A good example for a significant variation is mode 7 of the structure 3HG2 (see <xr id="fig:atomDisplacement3HG2"/>, upper left). While the first part of both chains (approximately until position 200) behaves similiar, except for a different amplitude, the second half differs with chain B showing much more movement. This action can be oberserved in <xr id="tab:webnma_3hg2"/> only after a very close inspection.
For the dimer it seems to be easier to act different when no substrate is bound, since the atomic displacements of the chains in the modes of 3HG3 seem to be much more alike than those of 3HG2.
All in all, the substrate binding site itself (residue 203 to 207) seems to be rather ridgid, except for maybe mode 10 in 3HG3, while the ends of both chains (the last 50 residues) are fairly flexible. This can best be seen in both modes 12.
Fluctuations
<figure id="fig:fluctuation_3HG2">
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<figure id="fig:fluctuation_3HG3">
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Fluctuation is the sum of the atomic displacements of each C alpha atom in each non-trivial mode weighted by the inverse of their corresponding eigenvalues. These are normalized in a way, such that the sum over all residues is equal to 100. The fluctuations of the structures 3HG2 and 3HG3 are shown in <xr id="fig:fluctuation_3HG2"/> and <xr id="fig:fluctuation_3HG3"/>, respectively.
The plots support our previous assumption, that the chains of the substrate bound structure 3HG3 act much more similiar than those of the structure with an empty active site, since the overlap is almost perfect in the left plot of <xr id="fig:fluctuation_3HG3"/>.
Again we can observe that the binding site is an rigid island among two moderate flexible regions, which probably are responsible for opening and closing the binding pocket and the needed movement for the breake down of the bound sugar.
Towards the end of the chain more motion can be observed, which is needed for the independant movement of both chains.
Correlation Matrix
<figtable id="tab:corrMatr">
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| <figure id="fig:corrMatr3HG2"> |
| <figure id="fig:corrMatr3HG3"> |
</figtable>
In the plots in <xr id="tab:corrMatr"/> both correlation matrices of 3HG2 and 3HG3 are shown. Over all, the plots look very similar, showing a positive correlation of the first part of both chain A and B to each other and also of both second halves to each other. And a negative correlation of the first half of chain A to the secon half of chain B and vice versa. The chains among themselves are rather strong positively correlated along the less strict diagonal and in the second half of the chain and negatively correlated in the rest. This underlines our statement (see section Mode Visualization) that the protein is quite rigid, with only the connecting parts being flexible and also that as well both chains move away from each other or towards each other, as the two halves of each chain itself can move independently.
The only difference between the plot of 3HG2 and 3HG3 is the strength of the correlations, where the colors in the second plot are darker, indicating a stronger correlation and therefore a higher amplitude which we have already seen in section Average Energies.
Overlap Analysis
General error. A trouble ticket has already been send on 04.07.2012 11:22
ElNémo
ElNémo <ref>K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004. </ref> <ref>K. Suhre & Y.H. Sanejouand, On the potential of normal mode analysis for solving difficult molecular replacement problems. Acta Cryst. D vol.60, p796-799, 2004 © International Union of Crystallography. </ref> is the web-interface to the "Elastic Network Model", which is a tool to compute the low frequency normal modes of a protein. It performs several analyses, including
- an overall normal mode analysis taking into account frequency, collectivity of atom movement, overlap of each mode with the observed conformational change (if two conformations provided) and the corresponding amplitude
- an individual normal mode analysis with animations and RMSD for each mode
- an Analysis of distance fluctuations between all CA atoms (cross plot)
- a B-factor analysis
- a comparison of a normal mode perturbed structure and a second conformations in terms of RMSD and number of residues that are closer than 3 Angstrom
Additionally you can compute combined models from two modes. Also the server claims that there is a way to download all the results at once, which only produced errors in our case.
We decided to examine the 6 lowest modes that ElNémo provides to obtain a result that is comparable to the 6 modes by WEBnm@.
B-factor analysis
3HG2: Correlation= 0.651 for 781 C-alpha atoms.
3HG3: Correlation= 0.779 for 793 C-alpha atoms.
Both correlations are according to the developers in a normal range.w
NOTE: We wanted to extract the per-residue B-factors of both structures after rerunning the NMA, but there seems to be another error at the elNémo server that now does not accept any of our (previously accepted) pdb-files.
Mode Visualization
In this section, we want to visually inspect the motion of the protein in the 6 lowest frequency modes were identified by ElNémo. For a description of the modes of the molecules 3HG2 and 3HG3 see <xr id="tab:elnemo_3hg2"/> and <xr id="tab:elnemo_3hg3"/>, respectively.
In comparison, we see a large overlap of the modes of 3HG2 and 3HG3. Mode 7 of 3HG2 combines modes 7 and 8 of 3HG3 in it, while mode 8(3HG2) is the opposite movement to mode 8(3HG3). The same applies for both modes 10, where one moves to the right, the other one to the left. Both modes 9 are the exact same. Mode 11(3HG2) is similar to mode 12(3HG3), except for the additional independant site in the latter one. The left mode of 3HG3 (mode 11) is similar to the modes 10, but again there is one part that moves independantly from the others. The only mode that cannot be observed in both conformations is mode 12(3HG2), but it might be that it is similar to a higher frequency mode in 3HG3.
<figtable id="tab:elnemo_3hg2"> This table shows the 6 lowest modes, that were calculated by ElNémo. Depicted is the structure 3HG2, which represents the Human α-galactosidase catalytic mechanism with empty active site in cyan and the substrate binding site at position 203 to 207 highlighted in red.
 ElNémo mode 7 shows a closing motion that is combined with a shearing movement in the groove between chain A and B, thus the axis of it is diagonal. This motion might relate to the function of the galactosidase, namely the hydrolysis of terminal α-D-galactose. Here almost the whole protein stays rigid, while the small part linking both chains moves. |
 Again in ElNémo mode 9 it seems that mostly the region that connects chain A and B is rigid (cf. mode 7 and 8), now bending both upper parts of the molecule to the right and both lower parts to the left. This may be explained by "shoving" the sugar into the active site, which is located in the back of the picture (and thus cannot be seen), while releasing the sugar that has been hydrolized in the active site in the front of the picture. | |
 The ElNémo mode 10 looks like an opening or closing motion if only either the front part or the back part of the dimer (the bigger part of the right chain and the smaller part of the left chain or vice versa) is considered. Looking at the whole molecule, we see that both upper parts move to the left and both lower parts move to the right, which gives the impression of turning an imaginary bound molecule in the groove between the chains. In this movement again the part that binds both chains together has to be non-rigid, but also the part that lies between the bigger part, which contains the substrate binding site, and the smaller part has to be elastic. |
 ElNémo mode 11 is the first mode, that is different from all the other modes examined so far. It gives the impression of breathing or of relaxing a spring. The whole dimer expands towards the outside by stretching many bonds throughout the molecule. In this motion the active site moves away from the center, thus opens for the substrate that is to be bound. |
 In ElNémo mode 12 the front part of the dimer (small part of the left chain and big part of the right chain) moves towards the back part, while the back part itself turns towards the center. This results in a closing movement, but around an axis that is orthogonal to the one in mode 8. Again, both the connecting part between the chains and between the bigger and the smaller part of each chain has to be elastic. |
</figtable>
<figtable id="tab:elnemo_3hg3"> This table shows the 6 lowest modes, that were calculated by ElNémo. Depicted is the structure 3HG3, which represents the Human α-galactosidase catalytic mechanism with bound substrate (green, α-D-Galactose with bound α-D-Glucose) in cyan and the substrate binding site at position 203 to 207 highlighted in red.
 ElNémo mode 7 shows a shearing motion in the groove between chain A and B, which might relate to the function of the galactosidase, namely the hydrolysis of terminal α-D-galactose. It can be observed, that the binding groove moves around the substrate that is bound to the active site. Here almost the whole protein stays rigid, while the small part linking both chains moves. |
 Again in ElNémo mode 9 it seems that mostly the region that connects chain A and B is rigid (cf. mode 7 and 8), now bending both upper parts of the molecule to the right and both lower parts to the left. This may be explained by "shoving" the sugar into the active site, which is located in the back of the picture (and thus cannot be seen), while releasing the sugar that has been hydrolized in the active site in the front of the picture. | |
 The ElNémo mode 10 looks like an opening or closing motion if only either the front part or the back part of the dimer (the bigger part of the right chain and the smaller part of the left chain or vice versa) is considered. Looking at the whole molecule, we see that both upper parts move to the right and both lower parts move to the left, which gives the impression of turning an imaginary bound molecule in the groove between the chains. In this movement again the part that binds both chains together has to be non-rigid, but also the part that lies between the bigger part, which contains the substrate binding site, and the smaller part has to be elastic. |
 ElNémo mode 11 is the most assymetric mode. Here three parts, that is both bigger parts and the smaller part of the left chain, move to the left, while the smaller part of the right chain moves away from them. This can again be explained by processing the sugar in the active site in the front while releasing the sugar in the active site in the back. As in most other modes of 3HG3, the linking residues between the chains and both part of each chain have to be flexible. |
 ElNémo mode 12 is again different from the majority of the other modes. It gives the impression of breathing or of relaxing a spring. The whole dimer expands towards the outside by stretching many bonds throughout the molecule. In this motion the active site moves away from the center, thus opens for the substrate that is to be released. Here an additional movement comes into account, that makes this mode a little more assymetric than e.g. ElNémo mode 11 from 3HG2. The smaller part turns downwards while stretching towards the center. |
</figtable>
Distance variation
<figure id="fig:FABRY_caStrain3HG2">
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<figure id="fig:FABRY_caStrain3HG3">
</figure>
The distance variation plots in <xr id="fig:FABRY_caStrain3HG2"/> and <xr id="fig:FABRY_caStrain3HG3"/> show the distance variation between successive pairs of CA atoms in the two extreme conformations that were computed for each mode (DQMIN/DQMAX). This can be interpreted as the internal movement or flexibility. In the modes 7 and 8 of both structures there is not much variation, like we expected. In the modes 9, the variation is very similar, except that chain A in 3HG2 corresponds to chain B in 3HG3 and vice versa. From the vizual inspection before we have not expected this. Therefore we think we could have made a mistake in identifying chain A and B in the pictures in the earlier section, but on the other hand see also section Distance fluctuations, where the results from earlier are underlined. The same applies for modes 10 and in 11 of 3HG2 and accordingly 10 and 12 of 3HG3.
Besides from that there is moderate difference in the amplitude and, as expected, fairly long stretches without significant peaks indicating rigid regions interupted by some flexible residues. Usually, a change of behaviour can be observed after about two thirds of each chains' sequence (around position 260). This confirms our finding from section Distance variation, where we saw the flexible link between the chains (around position 257 to 267) and a smaller part of the chain (position 268 to end) behaving different than the rest.
Distance fluctuations
<figtable id="tab:elnemo_fluct_3hg2"> ...
</figtable>
<figtable id="tab:elnemo_fluct_3hg2"> ...
</figtable>
This matrix displays the maximum distance fluctuations between all pairs of CA atoms and between the two extreme conformations that were computed for this mode (DQMIN/DQMAX). Distance increases are plotted in blue and decreases in red for the strongest 10% of the residue pair distance changes. Every pixel corresponds to a single residue. Grey lines are drawn every 10 residues, yellow lines every 100 residues (counting from the upper left corner).
Comparison
Domains
CATH
Divides each chain into two domains, Aldolase class I from position 32 to 324 and from 325 to 421 a Golgi alpha-mannosidase II, which is a "mainly beta" domain thus containing only loops and beta-sheets in our protein. TODO: Can be seen?
SCOP
No result could be obtained from this ressource.
Pfam
No additional information could be found on Pfam.
References
<references/>
