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.
Highlights
Protein folding and structure-function relationships are major challenges in molecular biology, biophysics, and other related fields
As in the ProMode database developed earlier for monomers and individual subunits of oligomers (Bioinformatics vol 20, pp. 2035–2043, 2004), normal mode analysis (NMA) was performed for a full-atom system using dihedral angles as independent variables, and we released the results
Iv) Inner products of internal and external displacement vectors of atoms defined in Eq 12, which are given in the temperature factor column of a Protein Data Bank (PDB)-format data file
Summary
Protein folding and structure-function relationships are major challenges in molecular biology, biophysics, and other related fields. The three-dimensional structural data deposited in the Protein Data Bank (PDB) have played an important role in researching these problems. Information extracted from the PDB contains mainly static structural features. It is generally recognized that both the dynamic and static aspects of protein structures are necessary to fully understand these problems. The only dynamics-related data provided in the PDB is temperature factor. This provides some information on the fluctuations of individual atoms, and reflects crystal disorder. Since temperature factor is not sufficient for most problems on protein dynamics, it is necessary to perform computer simulations, such as molecular dynamics and normal mode analysis (NMA), to acquire more information about its dynamics from the PDB data
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