Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis

2011 ◽  
Vol 159 (2-3) ◽  
pp. 257-266 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo
2012 ◽  
Vol 6 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo

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.


2008 ◽  
Vol 95 (6) ◽  
pp. 2895-2908 ◽  
Author(s):  
Atsushi Matsumoto ◽  
Tetsuji Kamata ◽  
Junichi Takagi ◽  
Kenji Iwasaki ◽  
Kei Yura

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.


2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger

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