Normal Mode Analysis BCKDHA

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Revision as of 10:05, 12 August 2011 by Demel (talk | contribs) (Background information)


Background information

WEBnm@ provides two different modes:

Single Analysis:

The Single Analysis calculates the lowest frequency normal modes of the given protein and offers different types of calculations to analyse the modes that were calculated. The force field used for the Normal Modes Calculations is the C-alpha force field It uses only the Calpha atoms of the protein which are assigned the masses of the whole residue they represent.
The different types of calculation are:

  • deformation energies of each mode
  • calculation of normalized squared atomic displacements (results are provided for each low frequency mode, either as raw data or as plots with displacement vs. residue number)
  • interactive visualization of the modes using vector field representation or vibrations

Comparative Analysis (beta version):

The Comparative Analysis calculates and compares the normal modes of a set of aligned protein structures. This tool is still under development. It also provides three types of calculations:

  • Deformation Energy profiles
  • Atomic Fluctuation profiles
  • Conformational Overlap Comparison


  • Single Analysis: structure file in the pdb format
  • Comparative Analysis: a file containing the sequence alignment of the proteins which should be compared and a protein structure file for each of the proteins. The alignment file needs to be written in the Fasta format, and the header line of each sequence should contain the name of the structure file as first field, and the chain in the last field.


Below are the values of the deformation energy for modes 7 to 20

Mode Index Deformation Energy
7 292.36
8 401.29
9 603.95
10 757.28
11 848.99
12 989.93
13 1745.19
14 2675.54
15 2999.49
16 3341.82
17 3572.19
18 3685.84
19 4103.34
20 4925.43

WEBnm@ visualised the normalized squared atomic displacements for the first five modes (modes 7 to 11). Figures 1-5 display the first five normal modes of our protein. Figure 6-10 show the square of the displacement of each C-alpha atom, normalized so that the sum over all residues is equal to 100. The highest values correspond to the most displaced regions. Cluster of peaks identify significantly big regions. Isolated peaks reflect local flexibility and are not relevant.

mode 7 mode 8 mode 9 mode 10 mode 11
Figure 1: normalized squared atomic displacement for mode 7
Figure 2: normalized squared atomic displacement for mode 8
Figure 3: normalized squared atomic displacement for mode 9
Figure 4: normalized squared atomic displacement for mode 10
Figure 5: normalized squared atomic displacement for mode 11
Figure 6: normalized squared atomic displacement for mode 7
Figure 7: normalized squared atomic displacement for mode 8
Figure 8: normalized squared atomic displacement for mode 9
Figure 9: normalized squared atomic displacement for mode 10
Figure 10: normalized squared atomic displacement for mode 11


The calculated normal modes of Webnma differ in the amplitude of movement. While modes 7 and 9-11 show the highest peak and therefore the most movement for residues 0-25, mode 8 has the highest peak for the last 40 residues in the sequence.

The normal modes calculated by Webnma show that the most displaced regions of the branched-chain alpha-keto acid dehydrogenase complex are the beginning and the end of the protein sequence. The two ends of the protein sequence which are also the outermost parts of the protein structure show some kind of hinge-movement. The protein motion could be described as an opening and closing complex.


Background information


The input for ElNemo is a protein structure in PDB format. From this PDB file only the residues that are encoded by ATOM are used in the calculations. The other residues are not taken into account. If there are other residues which should be used in the calculations they have to be encoded by ATOM. Additionally there are a lot of options which can be chosen.


  • properties of the first 100 lowest frequency modes (frequency, collectivity of atom movement, overlap of each mode with the observed conformational change (if two conformations are available) and its corresponding amplitude)
  • 3D animations from three orthogonal viewpoints in large and small sizes
  • Comparison of a normal mode perturbed structure and a second conformation in terms of RMSD and number of residues that are closer than 3Å can be done
  • cross plot where the analysis of distance fluctuations between all CA atoms is shown. Red (increasing) and blue dots (decreasing) indicate the residues for which the distance changes significantly in movement.


  • <ref></ref>
  • <ref>Karsten Suhre and Yves-Henri Sanejouand, ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement, Nucl. Acids Res, 2004</ref>


CA distance fluctuations for the six modes

mode 7 mode 8 mode 9 mode 10 mode 11
Figure 11: CA distance fluctuations for mode 7
Figure 12: CA distance fluctuations for mode 8
Figure 13: CA distance fluctuations for mode 9
Figure 14: CA distance fluctuations for mode 10
Figure 15: CA distance fluctuations for mode 11

ElNemo prepared different views from three orthologuous viewpoints with MolScript for each mode.

Mode 7:

Figure 16a: view 1 of mode 7
Figure 16b: view 2 of mode 7
Figure 16c: view 3 of mode 7

Mode 8:

Figure 17a: view 1 of mode 8
Figure 17b: view 2 of mode 8
Figure 17c: view 3 of mode 8

Mode 9:

Figure 18a: view 1 of mode 9
Figure 18b: view 2 of mode 9
Figure 18c: view 3 of mode 9

Mode 10:

Figure 19a: view 1 of mode 10
Figure 19b: view 2 of mode 10
Figure 19c: view 3 of mode 10

Mode 11:

Figure 20a: view 1 of mode 11
Figure 20b: view 2 of mode 11
Figure 20c: view 3 of mode 11

Anisotropic Network Model web server

oGNM – Gaussian network model

results here: [[1]]


The NOMAD <ref>[[2]]</ref> server provides a lot of information and options. The interface is quite user friendly as all available parameter choices are explained in detail and there is also the runtime listed for an example NMA, which can be used to estimate the runtime for our own jobs.

The following parameters can be set:

Number of modes to calculate
As specified in the task description we wanted to obtain 10 modes. NOMAD does six zero modes which are just translation and rotation. Therefore we set the number of modes to calculate to 16.
Distance weight parameter
This parameter is used to introduce a smoother cutoff value that in the original Tirion model. All distances are weightend by exp(-(d_ij/d)^2), where d is the distance weight parameter. As proposed by NOMAD a distance weight parameter of 3Å is well suited for CA-only models. As we are doing no all-atom calculation, the distance weight parameter was set to 3.0Å.
Cutoff to use for mode calculation
The cutoff describes which pairs of atomes are linked by a spring of universal length according to the Tirion model (Elastic Network Model). The cutoff was set to 15Å.
Average Rmsd in output trajectories
For the average RMSD the default value (3.0) was used.
Method to use
    • Automatic
    • Full matrix solver
    • Sparse matrix solver
Here we used the default option, the automatic mode.

The output contains one PDB file and one plot per mode. The plot contains the rmsd per residue, which can be interpreted as the amplitude of movement and which is controlled by the average rmsd of trajectory (input parameter).

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”…

mode 1 mode 2 mode 3 mode 4 mode 5
NOMAD normal mode 1
NOMAD normal mode 2
NOMAD normal mode 3
NOMAD normal 4
NOMAD normal 5
Amplitude of movement as rmsd per residue for mode 1
Amplitude of movement as rmsd per residue for mode 2
Amplitude of movement as rmsd per residue for mode 3
Amplitude of movement as rmsd per residue for mode 4
Amplitude of movement as rmsd per residue for mode 5
Elastic network for mode 1
Elastic network for mode 2
Elastic network for mode 3
Elastic network for mode 4
Elastic network for mode 5

All-atom NMA using Gromacs on the NOMAD-Ref server

In order to do the all-atom NMA we needed an appropriate small molecule that contained not more than 2000 atoms. This small protien was found by searching for "all atom nma". We found a paper <ref>Hetunandan Kamisetty, Eric P. Xing and Christopher J. Langmead: Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation[[3]]</ref>. They used the structure of a hen egg-white lysozyme for an all atom NMA. So we did all the calculations for the corresponding PDB entry 2lyz.

First, we needed to prepare our PDB file. The PDB file for 2LYZ protein contains 1001 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.

600 K

The following movies show the all-atom NMA for 2LYZ at 600K

mode 1 mode 2 mode 3
All atom normal mode 1 at 600K
All atom normal mode 2 at 600K
All atom normal mode 3 at 600K

2000 K

The following movies show the all-atom NMA for 2LYZ at 2000K

mode 1 mode 2 mode 3
All atom normal mode 1 at 2000K
All atom normal mode 2 at 2000K
All atom normal mode 3 at 2000K

Comparison to an Elastic Network

Frage: je berechnung eines elastic networks für mode 7, 8 und 9 oder berechnugn eines el networks für "normale" pdb und dann überlagerung mit den modes?

Ich habe jetzt mal für jeden mode (7,8,9) das vorher berechnete network einfach überlagert.

mode 1 mode 2 mode 3
Elastic network and mode 1
Elastic network and mode 2
Elastic network and mode 3

Advantages and Disadvantages from NMA and MD


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