Transcriptional cooperativity in molecular dynamics based on normal mode analysis

Author

Wang, Debby D. ; Yan, Hong ; Be, Qiang

Author_Institution

Dept. of Electron. Eng., City Univ. of Hong Kong, Kowloon, China

Volume

3

fYear

2012

fDate

15-17 July 2012

Firstpage

1001

Lastpage

1006

Abstract

Transcriptional regulation is an important component in genetics, with transcriptional factors (TFs) and regulatory DNA regions involved in. In this paper, we observe cooperativity between two significant TFs Oct-1 and Sox-2 at their enhancer DNA binding sites in collective motions. Normal mode analysis (NMA) is carried out to simulate the motions of two POU/HMG/DNA complexes, with molecular dynamics (MD) results used as a comparison. We have discovered several types of cooperative interactions between the two TFs in these obtained motions.

Keywords

DNA; biology computing; genetics; molecular biophysics; molecular dynamics method; NMA; POU-HMG-DNA complexes; Sox-2; TFs Oct-l; collective motions; enhancer DNA binding sites; genetics; molecular dynamics method; normal mode analysis; regulatory DNA regions; transcriptional cooperativity; transcriptional factors; transcriptional regulation; Abstracts; DNA; Dynamics; Proteins; Embryonic Sstem Cells; Normal Mode Analysis; Protein Cooperativity; Transcriptional Factors;

fLanguage

English

Publisher

ieee

Conference_Titel

Machine Learning and Cybernetics (ICMLC), 2012 International Conference on

Conference_Location

Xian

ISSN

2160-133X

Print_ISBN

978-1-4673-1484-8

Type

conf

DOI

10.1109/ICMLC.2012.6359491

Filename

6359491