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.

Webnma

Der server WEBnm@ uses only the C-alpha atoms to calculate the normal modes.

Results

Plots of atomic displacement

Mode 7

Mode 8

Mode 9

Mode 10

Mode 11

Visualization of Normal Modes

Mode 7

Mode 8

Mode 9

Mode 10

Mode 11

ElNemo

Results

Low Collectivity of Mode 4:

Visualization of Normal Modes

Mode 7

Mode 8

Mode 9

Mode 10

Mode 11

Anisotropic Network Model web server

Results

Visualization of Normal Modes

Mode 1

Mode 2

Mode 3

Mode 4

Mode 5