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

scholarly journals Transcriptional Protein-Protein Cooperativity in POU/HMG/DNA Complexes Revealed by Normal Mode Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-10 ◽  
Author(s):  
Debby D. Wang ◽  
Hong Yan
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Embryonic Stem ◽  
Interaction Mechanism ◽  
Mode Analysis ◽  
Biological Processes ◽  
Dna Complexes ◽  
Median Correlation ◽  
Collective Motions ◽  
Statistical Studies

Biomolecular cooperativity is of great scientific interest due to its role in biological processes. Two transcription factors (TFs), Oct-4 and Sox-2, are crucial in transcriptional regulation of embryonic stem cells. In this paper, we analyze how Oct-1 (a similar POU factor) and Sox-2, interact cooperatively at their enhancer binding sites in collective motions. Normal mode analysis (NMA) is implemented to study the collective motions of two complexes with each involving these TFs and an enhancer. The special structure of Oct proteins is analyzed comprehensively, after which each Oct/Sox group is reassembled into two protein pairs. We subsequently propose a segmentation idea to extract the most correlated segments in each pair, using correlations of motion magnitude curves. The median analysis on these correlation values shows the intimacy of subunit POUS (Oct-1) and Sox-2. Using those larger-than-median correlation values, we conduct statistical studies and propose several protein-protein cooperative modes (SandD) coupled with their subtypes. Additional filters are applied and similar results are obtained. A supplementary study on the rotation angle curves reaches an agreement with these modes. Overall, these proposed cooperative modes provide useful information for us to understand the complicated interaction mechanism in the POU/HMG/DNA complexes.

Normal mode analysis of the horseradish peroxidase collective motions: Correlation with spectroscopically observed heme distortions

Biopolymers ◽  
2006 ◽  
Vol 82 (4) ◽  
pp. 425-429 ◽  
Author(s):  
Monique Laberge ◽  
Istvan Kovesi ◽  
Takashi Yonetani ◽  
Judit Fidy
Keyword(s):  
Horseradish Peroxidase ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Collective Motions

scholarly journals Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease

2010 ◽  
Vol 12 (12) ◽  
pp. 2850 ◽  
Author(s):  
Paulo Ricardo Batista ◽  
Charles Herbert Robert ◽  
Jean-Didier Maréchal ◽  
Meriam Ben Hamida-Rebaï ◽  
Pedro Geraldo Pascutti ◽  
...  
Keyword(s):  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Collective Motions ◽  
Analysis Application ◽  
Multiple Minima ◽  
Hiv 1

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.

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