Promode-oligomer: Database of normal mode analysis in dihedral angle space for a full-atom system of oligomeric proteins

Hiroshi Wako, Shigeru Endo

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035-2043, 2004), NMA was performed for a full-atom system using dihedral angles as independent variables, and we released the results (fluctuations of atoms, fluctuations of dihedral angles, correlations between atomic fluctuations, etc.). The vibrating oligomer is visualized by animation in an interactive molecular viewer for each of the 20 lowest-frequency normal modes. In addition, displacement vectors of constituent atoms for each normal mode were decomposed into two characteristic motions in individual subunits, i.e., internal and external (deformation and rigid-body movements of the individual subunits, respectively), and then the mutual movements of the subunits and the movement of atoms around the interface regions were investigated. These results released in ProMode-Oligomer are useful for characterizing oligomeric proteins from a dynamic point of view. The analyses are illustrated with immunoglobulin light- and heavy-chain variable domains bound to lysozyme and to a 12-residue peptide.

Original languageEnglish
Pages (from-to)9-19
Number of pages11
JournalOpen Bioinformatics Journal
Volume6
Issue number1
DOIs
Publication statusPublished - 2012

Fingerprint

Dihedral angle
Oligomers
Databases
Proteins
Atoms
Immunoglobulin Light Chains
Immunoglobulin Heavy Chains
Muramidase
Computational Biology
Bioinformatics
Animation
Peptides
Enzymes
Monomers

Keywords

  • External motion
  • Immunoglobulin
  • Internal motion
  • Lysozyme
  • Normal mode analysis
  • Oligomer

ASJC Scopus subject areas

  • Computer Science (miscellaneous)
  • Biomedical Engineering
  • Health Informatics

Cite this

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abstract = "The database ProMode-Oligomer (http://promode.socs.waseda.ac.jp/promode_oligomer) was constructed by collecting normal-mode-analysis (NMA) results for oligomeric proteins including protein-protein complexes. As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol. 20, pp. 2035-2043, 2004), NMA was performed for a full-atom system using dihedral angles as independent variables, and we released the results (fluctuations of atoms, fluctuations of dihedral angles, correlations between atomic fluctuations, etc.). The vibrating oligomer is visualized by animation in an interactive molecular viewer for each of the 20 lowest-frequency normal modes. In addition, displacement vectors of constituent atoms for each normal mode were decomposed into two characteristic motions in individual subunits, i.e., internal and external (deformation and rigid-body movements of the individual subunits, respectively), and then the mutual movements of the subunits and the movement of atoms around the interface regions were investigated. These results released in ProMode-Oligomer are useful for characterizing oligomeric proteins from a dynamic point of view. The analyses are illustrated with immunoglobulin light- and heavy-chain variable domains bound to lysozyme and to a 12-residue peptide.",
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