Normal mode analysis

TODO

WORKY!

Discussion per section.
information about method per section
re-reference all pictures
add all references/quotes

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:

• http://apps.cbu.uib.no/webnma/home

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:

• http://www.igs.cnrs-mrs.fr/elnemo/start.html

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:

• http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi

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:

• http://ignm.ccbb.pitt.edu/GNM_Online_Calculation-t.htm

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:

• http://lorentz.dynstr.pasteur.fr/nma/submission.php

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:

• http://lorentz.dynstr.pasteur.fr/gromacs/nma_submission.php

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.