Normal mode analysis

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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.
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+C and B+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:

oGNM – 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

NOMAD-Ref

Webserver:

Params:

  • distance weight: 3.0
  • cutoff: 15 Å

Result:

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


Discussion:

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
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:

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