Task 9: Normal Mode Analysis

There are several forces acting within a protein. Most of these forces have one or more equilibrium states. In reality the protein is flexible. That means, that the atoms of the system swing around these equilibrium states. These swinging around the equilibrium states can be approximated by the harmonic approximation. The forces can then be replaced by a less complex system of springs. With this model it is possible to calculate large motions of the protein by Normal Mode Analysis.

In opposite to Molecular Dynamics this is very fast and it is not a simulation it is a calculation of possible simple and large motions.

In this task we want to try several servers, which calculate normal mode analysis. A detailed description of the task can be found here. For most runs we used the structure 1J8U for our protein PAH. In the case of the all-atom NMA we used a smaller protein to test the server and this kind of approach.

1 Webnma
- 1.1 Results
  - 1.1.1 Plots of atomic displacement
  - 1.1.2 Visualization of Normal Modes
2 ElNemo
- 2.1 Results
  - 2.1.1 Visualization of Normal Modes
3 Anisotropic Network Model web server
- 3.1 Results
  - 3.1.1 Visualization of Normal Modes
4 oGNM – Gaussian network model
5 NOMAD-Ref
6 All-atom NMA using Gromacs on the NOMAD-Ref server

Webnma

The server WEBnm@ uses only the C-alpha atoms to calculate the normal modes. The calculations are performed using the Molecular Modelling Toolkit with the C-alpha force field.

The used input format is very easy (see below).

Results

The server offers different statistics and visualizations to the performed NMA calculation.

An atomic displacement analysis plots the displacement of each C-alpha atom, therefore one can inspect the parts of the protein, which are the most displaced for each mode. These plots are shown for PAH below.
Mode visualization and vector field analysis. The vector field representation of the modes shows the directions and (relative) amplitude of the displacements undergone by different parts of the protein as vectors. The visualization and the vector field analysis can be downloaded as vmd-files. But these files seem to be broken. The mode visualizations of PAH are shown below.