Normal mode analysis

TODO

WORKY!

re-check all pictures
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.

Task?

For each server, analyze at least the lowest five normal modes.

• What information do the different servers provide?
• Which regions of your protein are most flexible, most stable?
• When you visualize the modes (provided by server or using for example PyMol or VMD), try to describe what movements you observe? Hinge-movement, “breathing”…
• Can you observe notable differences between the normal modes calculated by different servers?
• Out of the servers, chose one or two favorites and discuss the results of these in more detail. Why do you like these?
• When your MD simulations are finished, compare the lowest-frequency normal modes with your MD simulation using visualization software, e.g. PyMol or VMD. Can you observe different movements or similar dynamics? If possible, compare an overlay of the lowest-frequency modes to your MD simulation. You can superimpose the normal modes for example in VMD.
• What are the advantages and disadvantages of NMA compared to MD?

Parameters

• If possible, use a cutoff for C_α atom pairs of 15 Å.
• Calculate the 10 lowest-frequency normal modes (the six zero modes have to be considered for a few applications).
• In most cases you can upload the original .pdb file from the Protein Data Bank. In some cases, however, you can upload only the structure itself (ATOM lines of the .pdb file).

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@: nsad

Figure 1.2: Mode 7 by WEBnm@: vibrations

Figure 2.1: Mode 8 by WEBnm@: nsad

Figure 2.2: Mode 8 by WEBnm@: vibrations

Figure 3.1: Mode 9 by WEBnm@: nsad

Figure 3.2: Mode 9 by WEBnm@: vibrations

Figure 4.1: Mode 10 by WEBnm@: nsad

Figure 4.2: Mode 10 by WEBnm@: vibrations

Figure 5.1: Mode 11 by WEBnm@: nsad

Figure 5.2: Mode 11 by WEBnm@: vibrations

Figure 6.1: Mode 12 by WEBnm@: nsad

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 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:

• 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, which are 4080 too much.

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

File:1bpt2000k mode 7 0.gif Figure 36: Mode 7 by Gromacs at 2000K

File:1bpt2000k mode 8 0.gif Figure 37: Mode 8 by Gromacs at 2000K

File:1bpt2000k mode 9 0.gif Figure 38: Mode 9 by Gromacs at 2000K

File:1bpt2000k mode 10 0.gif Figure 39: Mode 10 by Gromacs at 2000K

File:1bpt2000k mode 11 0.gif Figure 40: Mode 11 by Gromacs at 2000K

File:1bpt2000k mode 12 0.gif 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: