Difference between revisions of "Normal Mode Analysis of Glucocerebrosidase"

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| [[File:anm_glucocerebrosidase_bfmode6.png |thumb|center|150px|'''Figure 36: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode7.png |thumb|center|150px|'''Figure 37: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode8.png |thumb|center|150px|'''Figure 38: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode9.png |thumb|center|150px|'''Figure 39: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode10.png |thumb|center|150px|'''Figure 40: B-factors/mode fluctuations''']] ||
 
| [[File:anm_glucocerebrosidase_bfmode6.png |thumb|center|150px|'''Figure 36: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode7.png |thumb|center|150px|'''Figure 37: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode8.png |thumb|center|150px|'''Figure 38: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode9.png |thumb|center|150px|'''Figure 39: B-factors/mode fluctuations''']] || [[File:anm_glucocerebrosidase_bfmode10.png |thumb|center|150px|'''Figure 40: B-factors/mode fluctuations''']] ||
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{| border="1" style="text-align:center; border-spacing:0" cellpadding="2" cellspacing="3" align = "center"
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|colspan="4"|'''Cα anisotropic temperature factors as ellipsoids'''
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|colspan="2"|'''purely computational'''||colspan="2"|'''refined by experimental b-factors'''
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|Rastep||Povscript||Rastep||Povscript
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|[[File:anm_glucocerebrosidase_temp11.png |thumb|center|150px|'''Figure 41''']]||[[File:anm_glucocerebrosidase_temp12.png |thumb|center|150px|'''Figure 42''']]||[[File:anm_glucocerebrosidase_temp21.png |thumb|center|150px|'''Figure 43''']]||[[File:anm_glucocerebrosidase_temp22.png |thumb|center|150px|'''Figure 44''']]
 
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Revision as of 10:41, 16 July 2011

Introduction

Elastic and Gaussian Network Models

WEBnm@

WEBnm@ is a web-server which provides automated computation and analysis of low-frequency normal modes of proteins. For an input structure file in PDB format, the normal modes are calculated and a series of automated calculations (normalized squared atomic displacements, vector field representation and an animation of the first six vibrational modes). Additional to the single analysis (calculating lowest frequency normal modes for one protein), the server offers a comperative analysis. In this analysis, the normal modes of a set of aligned sequences are calculated and compared. This feature is still under development. <ref>Hollup SM, Sælensminde G, Reuter N. WEBnm@: a web application for normal mode analysis of proteins BMC Bioinformatics. 2005 Mar 11;6(1):52 </ref>

Usage

  • Webserver: http://apps.cbu.uib.no/webnma/home
  • Input:
    • Single Analysis: structure file in PDB format
    • Comparative Analysis: structure files in PDB format and sequence files in fasta format


Results

Figure 1 to 5 show the first five vibrational modes (modes 7 to 11) calculated with WEBnm@ for the structure of glucocerebrosidase (2NTO). On the left side of each figure the vectors are shown, whereas the movement is illustrated to the right.


Figure 1: Normal Mode 7 calculated with WEBnm@
Figure 2: Normal Mode 8 calculated with WEBnm@
Figure 3: Normal Mode 9 calculated with WEBnm@
Figure 4: Normal Mode 10 calculated with WEBnm@
Figure 5: Normal Mode 11 calculated with WEBnm@



Discussion

ElNémo

ElNémo is a web-server based on the Elastic Network Model. The tool computes, visualizes and analyses low-frequency normal modes of large macro-molecules. Any size of proteins can be treated as ElNémo uses a 'rotation-translation-block' approximation. <ref>K. Suhre & Y.H. Sanejouand, ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research, 32, W610-W614, 2004. </ref>

Usage

  • Webserver: http://www.igs.cnrs-mrs.fr/elnemo/start.html
  • Input:
      • structure file in PDB format
      • supplementary options for NMA calculation (number of normal modes to be calculated, minimum and maximum perturbation and stepsize between DQMIN and DQMAX)
      • options for computing the eigenmodes (NRBL and cutoff to identify elastic interactions)

Results

Figure 6 to 9 show for each of the five first vibrational normal modes calculated with ElNémo three different perspectives.

Figure 6: Normal Mode 7 calculated with ElNémo
Figure 7: Normal Mode 8 calculated with ElNémo
Figure 8: Normal Mode 9 calculated with ElNémo
Figure 9: Normal Mode 10 calculated with ElNémo
Figure 10: Normal Mode 11 calculated with ElNémo


Discussion

Anisotropic Network Model

The ANM Webserver provides NMA Analysis with the anisotropic network model (ANM) which is an elastic network (EN) introduced in 2000. It is a very fast method which predicts the global modes. The ANM adopts a uniform force constant γ to all springs and nodes are refered as the Cα atoms.<ref>Anisotropic network model: systematic evaluation and a new web interface, Eyal E, Yang LW, Bahar I. Bioinformatics. 22, 2619-2627, (2006)</ref>

Usage

Results

Mode 1 Mode 2 Mode 3 Mode 4 Mode 5
Figure 11: Normal Mode 1 calculated with ANM
Figure 12: Normal Mode 2 calculated with ANM
Figure 13: Normal Mode 3 calculated with ANM
Figure 14: Normal Mode 4 calculated with ANM
Figure 15: Normal Mode 5 calculated with ANM
Inter Distance Analysis
Figure 16a: Distance Matrix

Figure 16b: Deformation Energy

Overall energy: 27824.672768448
Figure 17a: Distance Matrix

Figure 17b: Deformation Energy

Overall energy: 42344.496142536
Figure 18a: Distance Matrix

Figure 18b: Deformation Energy

Overall energy: 43818.992771088
Figure 19a: Distance Matrix

Figure 19b: Deformation Energy

Overall energy: 85235.1119198879
Figure 20a: Distance Matrix

Figure 20b: Deformation Energy

Overall energy: 90925.846279128
B-factors/mode fluctuations
Figure 21: B-factors/mode fluctuations
Figure 22: B-factors/mode fluctuations
Figure 23: B-factors/mode fluctuations
Figure 24: B-factors/mode fluctuations
Figure 25: B-factors/mode fluctuations
Mode 6 Mode 7 Mode 8 Mode 9 Mode 10
Figure 26: Normal Mode 6 calculated with ANM
Figure 27: Normal Mode 7 calculated with ANM
Figure 28: Normal Mode 8 calculated with ANM
Figure 29: Normal Mode 9 calculated with ANM
Figure 30: Normal Mode 10 calculated with ANM
Inter Distance Analysis
Figure 31a: Distance Matrix

Figure 31b: Deformation Energy

Overall energy: 107191.169783064
Figure 32a: Distance Matrix

Figure 32b: Deformation Energy

Overall energy: 112430.078797944
Figure 33a: Distance Matrix

Figure 33b: Deformation Energy

Overall energy: 138939.176046648
Figure 34a: Distance Matrix

Figure 34b: Deformation Energy

Overall energy: 156195.358655472
Figure 35a: Distance Matrix

Figure 35b: Deformation Energy

Overall energy: 154660.33882932
B-factors/mode fluctuations
Figure 36: B-factors/mode fluctuations
Figure 37: B-factors/mode fluctuations
Figure 38: B-factors/mode fluctuations
Figure 39: B-factors/mode fluctuations
Figure 40: B-factors/mode fluctuations


Cα anisotropic temperature factors as ellipsoids
purely computational refined by experimental b-factors
Rastep Povscript Rastep Povscript
Figure 41
Figure 42
Figure 43
Figure 44

Discussion

oGNM

NOMAD-Ref

Discussion

All-atom NMA

Comparison NMA / MD

References

<references/>

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