Normal Mode Analysis of Glucocerebrosidase

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@

TODO: EDIT Image 5

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: 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

References

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