Normal mode analysis GLA

^{by Benjamin Drexler and Fabian Grandke}

Methods

The following sections give a brief explanation about the methods and information about their usage.

WEBnm@

The normal mode analysis webserver WEBnm@ was published by Siv Midtun Hollup, Gisle Salensminde and Nathalie Reuter in 2005<ref name=webnma>Siv Midtun Hollup, Gisle Salensminde and Nathalie Reuter. "WEBnm@: a web application for normal mode analyses of proteins". BMC Bioinformatics 2005, 6:52. PubMed</ref>. It allows the calculation of the normal modes and offers serveral types of analyses, i.e. deformation energy, animation of the vibration, atomic squared displacements and vector field analysis.

Usage

• Webserver: http://apps.cbu.uib.no/webnma/home
• Input
  • PDB structure (ID or file)
  • Specification of chains
• Output
  • Animation of vibration
  • Deformation energy
  • Squared atomic displacements

ElNemo

Karsten Suhre and Yves-Henri Sanejouand published the webserver ElNemo in 2004<ref name=elnemo>Karsten Suhre and Yves-Henri Sanejouand. "ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement". Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W610-4. PubMed</ref>. It is used for the calculation of normal modes and is able to process very large proteins due to a building block approximation. This is, several residues are grouped into a single super residue.

Usage

• Webserver: http://www.igs.cnrs-mrs.fr/elnemo/start.html
• Input
  • PDB structure (file or pasted sequence)
  • Number of modes to calculate (the trivial modes 1 to 6 are excluded in this number)
  • Range of perturbation (DQMIN, DQMAX and DQSTEP)
  • Cutoff used to dentify elastic interactions
• Output
  • Animation of the vibration
  • Distance fluctations between the C-alpha atoms
  • Mean square displacement of all C-alpha atoms

Anisotropic Network Model

Anisotropic network model (ANM) is an elastic network and was introduced by Doruker et al. and Atilgan et al. in 2000<ref name=anm_doruker>Doruker P, Atilgan AR, Bahar I. "Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.". Proteins. 2000 Aug 15;40(3):512-24. PubMed</ref><ref name=anm_atilgan>Atilgan AR, Durell SR, Jernigan RL, Demirel MC, Keskin O, Bahar I. "Anisotropy of fluctuation dynamics of proteins with an elastic network model.". Biophys J. 2001 Jan;80(1):505-15. PubMed</ref>. The ANM webserver is used to calculate the global modes and was published by Eyal et al. in 2006<ref name=anm_eyal>Eyal E, Yang LW, Bahar I. "Anisotropic network model: systematic evaluation and a new web interface.". Bioinformatics. 2006 Nov 1;22(21):2619-27. Epub 2006 Aug 23. PubMed</ref>. The nodes are represented by the C-alpha atoms and the calculation is based on the spring force constant γ.

Usage

• Webserver: http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi
• Input
  • PDB structure (ID or file)
  • Cutoff for interactions
  • Distance weight for interactions
• Output
  • Animation of the vibration
  • Fluctuation profiles
  • Inter-residue distance fluctuations
  • Deformation energies

Results & Discussion

α-galactosidase A

Mode 7

WEBnm@	ElNemo	ANM	oGNM	NOMAD Ref

The results of the webservers display a high degree of consensus in the mode 7. Especially the beta strands on the right side show a strong movement in the down direction. This movement can also be expressed as a twist movement which is the strongest in the results of ANM and ElNemo. It seems like that there is also a fluctuation of a large part on the left side which could be driven by the twist movement on the right side. These obversations in the animations can also be seen in the presentation of oGNM that highlights the beta strands on the right side and also indicates some sort of flexibility on the left side.

Mode 8

WEBnm@	ElNemo	ANM	oGNM	NOMAD Ref

Mode 9

WEBnm@	ElNemo	ANM	oGNM	NOMAD Ref

Mode 10

WEBnm@	ElNemo	ANM	oGNM	NOMAD Ref

Mode 11

WEBnm@	ElNemo	ANM	oGNM	NOMAD Ref

Mode 12

WEBnm@	ElNemo	ANM	oGNM	NOMAD Ref

Animations

WEBnm@

ElNemo

Anisotropic Network Model

oGNM

NOMAD-Ref

References

<references/>