Normal Mode Analysis Hemochromatosis

Hemochromatosis>>Task 9: Normal mode analysis

Short task description

Detailed description: Normal mode analysis

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

General

<figtable id="comparison">

Table 1: HFE's structure from 1a6zC (green) superimposed with a different conformation from 1de4A (red). Each figure shows the comparison from a different angle.

</figtable>

We used the PDB structures 1a6z and 1de4 for our NMA. 1a6z represents HFE bound with Beta-2-Microglobulin only and 1de4 contains the whole TFR-HFE-B2M complex. We extracted HFE's conformations from these structures (chain C from 1a6z and chain A from 1de4). Both files contain the same 272 residues (26-297 within HFE's sequence). A comparison between the two showed that there are only minor differences in the conformation (cf. <xr id="comparison"/>) and almost all of them are within loop regions. TM-Score calculated an RMSD of only 1.602 and a TM-Score of 0.9607 for them.

For the NMA we used WEBnm@ and ElNemo. Both webservers use the C-alpha atoms only for the normal mode calculations and thus could theoretically compute 816 (3N, N = 272) normal modes, though the first 6 are irrelevant as they represent the three simple translations and rotations of the whole protein. In addition to the normal modes they provide also features to compare normal mode motions with other conformations of the same protein or correlation analysis of different normal modes.

WEBnm@

The deformation energy scores computed by WEBnm@ are shown in <xr id="webnma_energy"/>. The first 6 modes (7-12) could be put into three groups: Mode 7-9 which have a very small score, 10 and 11 which have about double the score of 8/9, and Mode 12 which again doubles Mode 10's score. This suggests that the first three combine big motions while the latter three exhibit more and more smaller parts that move separately.

<figtable id="webnma_energy">

Table 2: Energy scores calculated by WEBnm@ for the normal modes 7-20 of 1a6zC.

Mode number	Energy score	Mode number	Energy score
7	416.65	14	4673.81
8	841.18	15	5862.82
9	849.58	16	6800.91
10	1436.11	17	8236.15
11	1899.61	18	7878.34
12	2981.09	19	8104.36
13	4518.38	20	9899.01

</figtable>

Modes

<figtable id="webnma_modes7to12">

Table X: TODO.

	Mode 7	Mode 8	Mode 9	Mode 10	Mode 11	Mode 12
	Mode 7 (front)	Mode 8 (front)	Mode 9 (front)	Mode 10 (front)	Mode 11 (front)	Mode 12 (front)

</figtable>

Correlation

<figure id="correlation">

Figure: TODO.

</figure>

Overlap

<figtable id="overlap">

Table X: TODO.

</figtable>

Atomic fluctuations

<figtable id="webnma_fluctuations">

Table X: TODO.

</figtable>

ElNemo

Modes

<figtable id="elnemo_modes7to12">

Table X: TODO.

	Mode 7	Mode 8	Mode 9	Mode 10	Mode 11	Mode 12
	Mode 7 (front)	Mode 8 (front)	Mode 9 (front)	Mode 10 (front)	Mode 11 (front)	Mode 12 (front)

</figtable>

Overlap

References

<references/>