Normal Mode Analysis BCKDHA

NOMAD-Ref

The NOMAD <ref>[[1]]</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
File:BCKDHA NOMAD mode7.png NOMAD normal mode 1	File:BCKDHA NOMAD mode8.png NOMAD normal mode 2	File:BCKDHA NOMAD mode9.png NOMAD normal mode 3	File:BCKDHA NOMAD mode10.png NOMAD normal 4	File:BCKDHA NOMAD mode11.png 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

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

In order to do the all-atom NMA we needed to prepare our PDB file. The PDB file for 1BPT protein contains 1629 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.

References

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