Normal mode analysis

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Revision as of 15:23, 25 August 2011 by Greil (talk | contribs)

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:

Figure 1.1: Mode 7 by WEBnm@: plot
Figure 1.2: Mode 7 by WEBnm@: vibrations
Figure 2.1: Mode 8 by WEBnm@: plot
Figure 2.2: Mode 8 by WEBnm@: vibrations
Figure 3.1: Mode 9 by WEBnm@: plot
Figure 3.2: Mode 9 by WEBnm@: vibrations
Figure 4.1: Mode 10 by WEBnm@: plot
Figure 4.2: Mode 10 by WEBnm@: vibrations
Figure 5.1: Mode 11 by WEBnm@: plot
Figure 5.2: Mode 11 by WEBnm@: vibrations
Figure 6.1: Mode 12 by WEBnm@: plot
Figure 6.2: Mode 12 by WEBnm@: vibrations


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:

Figure 7.1: Mode 7 by ElNemo: lateral view
Figure 7.2: Mode 7 by ElNemo: top view
Figure 7.3: Mode 7 by ElNemo: front view
Figure 8.1: Mode 8 by ElNemo: lateral view
Figure 8.2: Mode 8 by ElNemo: top view
Figure 8.3: Mode 8 by ElNemo: front view
Figure 9.1: Mode 9 by ElNemo: lateral view
Figure 9.2: Mode 9 by ElNemo: top view
Figure 9.3: Mode 9 by ElNemo: front view
Figure 10.1: Mode 10 by ElNemo: lateral view
Figure 10.2: Mode 10 by ElNemo: top view
Figure 10.3: Mode 10 by ElNemo: front view


Figure 11.1: Mode 11 by ElNemo: lateral view
Figure 11.2: Mode 11 by ElNemo: top view
Figure 11.3: Mode 11 by ElNemo: front view

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:

Figure 12: Mode 1 by ANM
Figure 13: Mode 2 by ANM
Figure 14: Mode 3 by ANM
Figure 15: Mode 4 by ANM
Figure 16: Mode 5 by ANM
Figure 17: Mode 6 by ANM


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

The oGNM is an online web-server that calculates the dynamics of PDB structures using an elastic network model which is called gaussian network model.

Webserver:

Input:

  • 1a6z

Params:

  • cutoff: 15 Å

Result:

Figure 18.1: Mode 1 by oGNM: plot
Figure 18.2: Mode 1 by oGNM: vibrations
Figure 19.1: Mode 2 by oGNM: plot
Figure 19.2: Mode 2 by oGNM: vibrations
Figure 20.1: Mode 3 by oGNM: plot
Figure 20.2: Mode 3 by oGNM: vibrations
Figure 21.1: Mode 4 by oGNM: plot
Figure 21.2: Mode 4 by oGNM: vibrations
Figure 22.1: Mode 5 by oGNM: plot
Figure 22.2: Mode 5 by oGNM: vibrations
Figure 23.1: Mode 6 by oGNM: plot
Figure 23.2: Mode 6 by oGNM: vibrations

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

NOMAD-Ref is an online web-server for normal mode calculations using the elastic network model.

Webserver:

Params:

  • distance weight: 3.0
  • cutoff: 15 Å

Result:

Figure 24: Mode 7 by NOMAD-Ref
Figure 25: Mode 8 by NOMAD-Ref
Figure 26: Mode 9 by NOMAD-Ref
Figure 27: Mode 10 by NOMAD-Ref
Figure 28: Mode 11 by NOMAD-Ref
Figure 29: Mode 12 by NOMAD-Ref


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:

The all-atom NMA using Gromacs is a normal mode calculation which uses force fiels and not elastic networks.

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
Figure 30: Mode 7 by Gromacs at 600K
Figure 31: Mode 8 by Gromacs at 600K
Figure 32: Mode 9 by Gromacs at 600K
Figure 33: Mode 10 by Gromacs at 600K
Figure 34: Mode 11 by Gromacs at 600K
Figure 35: Mode 12 by Gromacs at 600K
  • at 2000K
Figure 36: Mode 7 by Gromacs at 2000K
Figure 37: Mode 8 by Gromacs at 2000K
Figure 38: Mode 9 by Gromacs at 2000K
Figure 39: Mode 10 by Gromacs at 2000K
Figure 40: Mode 11 by Gromacs at 2000K
Figure 41: Mode 12 by Gromacs at 2000K
  • with Elastic Network
Figure 42: Mode 7 by NomadRef Elastic Network
Figure 43: Mode 8 by NomadRef Elastic Network
Figure 44: Mode 9 by NomadRef Elastic Network
Figure 45: Mode 10 by NomadRef Elastic Network
Figure 46: Mode 11 by NomadRef Elastic Network
Figure 47: Mode 12 by NomadRef 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.