Normal mode analysis
Contents
Introduction
NMA (normal mode analysis) is a time-independent apprach to simulate low-frequency motions and vibrations of protein. These simulation are all based on the harmonic approximation and therefore ignore the influence of the solvent. The proteins are seen as models made out of springs and point masses, which are connected and represent the interatomic forces. Simulation done this way are very easy to do, but are no more than a slight insight into the protein flexibility.
WEBnm@
WEBnm@ is a webserver based application that allows computation and low-frequency analysis of normal nodes of proteins. This computation is fully automated and only different types of results are presented to the user.
Webserver:
Input:
- 1a6z - all chains
Result:
Discussion:
All animated gifs have to be created the hard way, frame after frame, because WEBnm@ does not allow the concurrent saving of more than one frame.
The Normalized Squared Atomic Displacements (nsad) plots show the vibrations according to the amino acid position. The peaks are almost always at the betasheets of chains A and C.
Except for mode 11 there is no special movement inside the alpha helix of chains A and C. The movement is almost everytime between the chains or inside/around the beta strands of chain B and D. This behaviour is also visible by analyzing the plots; the regions of low movement are always around the chains A and C with their corresponding alpha helices and the high movement regions lies within the beta strands of chain B and D.
The movement/vibrations can be described mostly as repulsive or flattening, stretching and twisting.
There seems to be some strange behaviour at figure 4.2 mode 10; it is slighty twitching and we do not know why. Maybe it is because of a wrong frame or some other aspect of visual glitches, we will check that again, if there is time.
ElNemo
ElNémo is a webserver based to work with the Elastic Network Model. It calculates and analyses low-frequency normal modes of proteins.
Webserver:
Input:
- 1a6z
Result:
Discussion:
For all generated models the vibrations are shown in three different perspectives.
The Movement/Vibrations are very similar to these obtained by WEBnm@. There is almost no movement inside the alpha helices of chain A and C and much movement inside and outside the the beta strands of chain B and D. Vibrations between chains can also be observed but these are mostly between A+B and C+D because they form a subunit.
Anisotropic Network Model web server
The Anisotropic Network Model web server uses the fast approach anisotropic network model (elastic network) to calculate the global modes.
Webserver:
Params:
- distance weight: 3
Result:
Discussion:
All models created by ANM have something in common: The flexible parts are the outer betasheets and the unflexible or rigid parts are the alphahelices inside the protein. The movements are therefore mostly the same, the outer parts move in some directions and the inner parts stand still or are moved coercively.
Figure 12 shows movement of betasheets from back to front and thus slightly rotating the inside of the protein between the A and C chain.
In figure 13 the other betasheets are going up and so the inner is moved a bit down as a follow-up reaction.
Figure 14 is a nice one, because there is rotation inside the chains A and C. The connection between the alphahelices and betasheets is moved to the top while the chains B and D are moved to the bottom, thus letting the protein wobble.
The mutual vibration of the outer beta sheets (up and down) of figure 15 create a shaking inside the protein. But the alphahelices are not moved, they are still fixed but only tipped to left an right.
The outer parts are again in mutual vibration. This time they are pulled to the center of the protein at the front and at the back at same time. That induces a turning of the alphahelices in the middle of the protein as seen in figure 16.
The last figure 17 shows the outer parts being lifted up and the whole protein looks compressed.
oGNM – Gaussian network model
Webserver:
Input:
- 1a6z
Params:
- cutoff: 15 Å
Result:
Discussion:
For all figures the plot of chain A and C and B and D is always identical, because they are the same chains only placed in opposite direction. A high value of the y-axis codes a high flexibility for that amino acid position, these parts are marked as red. The unflexible parts are colored in blue.
Figure 18.1 shows clearly the unflexible alphahelices of chains A and C which are getting more and more flexible as the position advances the betasheets. These are the most flexible part of the protein alongside the betasheets of chains B and D, which are according to the plot not that flexible. This observeration is confirmed by the figure 18.2.
Figure 19.1 is somewhat special, because it illustrates that alphahelices of chains A and C are not only flexible parts but slightly more flexible as the betasheets of chains B and D. This is spectacular because all other models tend to define the alphahelices as rigid parts. Figure 19.2 shows this aspect as the alphahelices are slightly red but the betasheets of chains B and D are full blue.
Figure 20.1 shows a very mixed up model. Only the outer parts of the betasheets are defined as flexible all other parts are more or less static parts.
Figure 21.1 is similar to figure 18.1 excluding the mobility of the betasheets of chains A and C. These are almost fixed and therefore achieve more blue coloring.
Figure 22.1 is again a very quirky model because the mobility of the outer betasheets is reduced to almost nothing but the flexibilty of the betasheets of chains B and D is greatly raised.
Figure 23.1 is similar to figure 19.1 but more restrictive in the mobility of the betasheets. There is no more flexibility at chain B and D but therefore a very versatile core inside the protein consisting of the alphahelices of chains A and C.
NOMAD-Ref
Webserver:
Params:
- distance weight: 3.0
- cutoff: 15 Å
Result:
Discussion:
Figure 24 shows movement between both of the subunits of 1A6Z. There are no other vibrations inside any of the chains, only rotation between both complexes.
Figure 25 visualizes the the flexible betasheets of the chains A and C. These are shifted saw-like with the betasheets of chains B and D.
The whole protein is stretched at figure 26. It is clearly visible, that the betasheets are much more flexible than the alpha helices which seems to work as springs, trying to keep the protein in a closely packed state.
In figure 27 there is a rotation between the complexes of chains A+B and C+D and also again some stretching inside the betasheets of chains B and D. The movement is somewhat similar to Figure 26.
Figure 28 is also a rotation between the complexes but also inside the complexes. They are rotated at the connection of the alphahelices to the betasheets of chains A and C.
Figure 29 is almost identical to Figure 28.
All-atom NMA using Gromacs on the NOMAD-Ref server
Webserver:
Params:
- temperature: 600K and 2000K
- pdb ID: 1BPT
Information: We used the given protein 1BPT because our HFE protein (1A6Z) has around 6080 ATOM lines and is therefore too big (limit is 2000 ATOM lines).
Result:
- at 600K
- at 2000K
- with Elastic Network
Discussion:
As one can see, there is no big difference between the movements at 600K and 2000K. The only difference is the range of the vibrations; at 2000K it is slighty more than at 600K which leads to the conclusion that the movements do not really depend on the temperature.
The Elastic Network movements are mostly stretching of the beta sheets or rotations around the center of the protein which are clearly visible. The movements of the elastic network are much stronger than these of Gromacs.
But summing up, the movements of the Gromacs models and the elastic network models are somehow similar. Because of this fact, we think the modelling of the movement is correct and it could be the real vibration of 1BPT.
