Normal mode analysis of oligomeric proteins: Reduction of the memory requirement by consideration of rigid geometry and molecular symmetry

1994 ◽  
Vol 15 (8) ◽  
pp. 820-837 ◽  
Author(s):  
Jean-fran�ois Gibrat ◽  
Jean Garnier ◽  
Nobuhiro G?
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Molecular Symmetry ◽  
Memory Requirement ◽  
Oligomeric Proteins

scholarly journals ProMode-Oligomer: Database of Normal Mode Analysis in Dihedral Angle Space for a Full-Atom System of Oligomeric Proteins

2012 ◽  
Vol 6 (1) ◽  
pp. 9-19 ◽  
Author(s):  
Hiroshi Wako ◽  
Shigeru Endo
Keyword(s):  
Normal Mode ◽  
Protein Complexes ◽  
Normal Mode Analysis ◽  
Normal Modes ◽  
Point Of View ◽  
Mode Analysis ◽  
Dihedral Angles ◽  
Oligomeric Proteins ◽  
Displacement Vectors ◽  
Atom System

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.

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

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.

scholarly journals Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer

2020 ◽  
Vol 153 (21) ◽  
pp. 215103
Author(s):  
Alexander Klinger ◽  
Dominik Lindorfer ◽  
Frank Müh ◽  
Thomas Renger
Keyword(s):  
Energy Transfer ◽  
Spectral Density ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis

scholarly journals Normal-mode analysis for scalar fields in BTZ black-hole background

2009 ◽  
Vol 60 (2) ◽  
pp. 169-173 ◽  
Author(s):  
Sayan K. Chakrabarti ◽  
Pulak Ranjan Giri ◽  
Kumar S. Gupta
Keyword(s):  
Black Hole ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Scalar Fields ◽  
Mode Analysis ◽  
Btz Black Hole ◽  
Black Hole Background

scholarly journals Rapid Characterization of Allosteric Networks with Ensemble Normal Mode Analysis

2016 ◽  
Vol 120 (33) ◽  
pp. 8276-8288 ◽  
Author(s):  
Xin-Qiu Yao ◽  
Lars Skjærven ◽  
Barry J. Grant
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Rapid Characterization

Normal Mode Analysis of Trp RNA Binding Attenuation Protein: Structure and Collective Motions

2011 ◽  
Vol 51 (9) ◽  
pp. 2361-2371 ◽  
Author(s):  
Guang Hu ◽  
Servaas Michielssens ◽  
Samuel L. C. Moors ◽  
Arnout Ceulemans
Keyword(s):  
Protein Structure ◽  
Normal Mode ◽  
Rna Binding ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Collective Motions

Large-Debye-distance effects in a homogeneous plasma

1989 ◽  
Vol 41 (3) ◽  
pp. 493-516 ◽  
Author(s):  
Jan Scheffel ◽  
Bo Lehnert
Keyword(s):  
Normal Mode ◽  
Numerical Solutions ◽  
Normal Mode Analysis ◽  
Distribution Functions ◽  
Mode Analysis ◽  
Larmor Radius ◽  
Order Unity ◽  
Phase Velocities ◽  
Standard Normal ◽  
Velocity Distribution Functions

The classical phenomenon of electron plasma oscillations has been investigated from new aspects. The applicability of standard normal-mode analysis of plasma perturbations has been judged from comparisons with exact numerical solutions to the linearized initial-value problem. We consider both Maxwellian and non-Maxwellian velocity distributions. Emphasis is on perturbations for which αλD is of order unity, where α is the wavenumber and λD the Debye distance. The corresponding large-Debye-distance (LDD) damping is found to substantially dominate over Landau damping. This limits the applicability of normal-mode analysis of non-Maxwellian distributions. The physics of LDD damping and its close connection to large-Larmor-radius (LLR) damping is discussed. A major discovery concerns perturbations of plasmas with non-Maxwellian, bump-in-tail, velocity distribution functions f0(ω). For sufficiently large αλD (of order unity) the plasma responds by damping perturbations that are initially unstable in the Landau sense, i.e. with phase velocities initially in the interval where df0/dw > 0. It is found that the plasma responds through shifting the phase velocity above the upper velocity limit of this interval. This is shown to be due to a resonance with the drifting electrons of the bump, and explains the Penrose criterion.

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