Analysis of nucleosome structures based on molecular dynamics

Debby D. Wang; Hong Yan

doi:10.1109/ICSMC.2011.6084132

Analysis of nucleosome structures based on molecular dynamics

Debby D. Wang, Hong Yan

Department of Electrical Engineering

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

Abstract

In this paper, we present a method to analyze the molecular structure and dynamics of nucleosomes, which are the basic unit in eukaryotic cells. In nucleosomal DNA chains, periodic dinucleotides are key patterns in protein-DNA interactions. This paper aims at revealing the significances of these periodic dinucleotides in the nucleosomal DNA motions. Normal mode analysis (NMA) is used to detect significant structural deformations of nucleosomal DNA. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently. © 2011 IEEE.

Original language	English
Title of host publication	Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics
Pages	3078-3083
DOIs	https://doi.org/10.1109/ICSMC.2011.6084132
Publication status	Published - 2011
Event	2011 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2011 - Anchorage, AK, United States Duration: 9 Oct 2011 → 12 Oct 2011

Publication series

Name
ISSN (Print)	1062-922X

Conference

Conference	2011 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2011
Place	United States
City	Anchorage, AK
Period	9/10/11 → 12/10/11

Research Keywords

DNA and protein motions
Normal Mode Analysis (NMA)
Nucleosome
Periodic dinucleotides

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title = "Analysis of nucleosome structures based on molecular dynamics",

abstract = "In this paper, we present a method to analyze the molecular structure and dynamics of nucleosomes, which are the basic unit in eukaryotic cells. In nucleosomal DNA chains, periodic dinucleotides are key patterns in protein-DNA interactions. This paper aims at revealing the significances of these periodic dinucleotides in the nucleosomal DNA motions. Normal mode analysis (NMA) is used to detect significant structural deformations of nucleosomal DNA. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently. {\textcopyright} 2011 IEEE.",

keywords = "DNA and protein motions, Normal Mode Analysis (NMA), Nucleosome, Periodic dinucleotides",

author = "Wang, {Debby D.} and Hong Yan",

year = "2011",

doi = "10.1109/ICSMC.2011.6084132",

language = "English",

isbn = "9781457706523",

pages = "3078--3083",

booktitle = "Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics",

note = "2011 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2011 ; Conference date: 09-10-2011 Through 12-10-2011",

}

TY - GEN

T1 - Analysis of nucleosome structures based on molecular dynamics

AU - Wang, Debby D.

AU - Yan, Hong

PY - 2011

Y1 - 2011

N2 - In this paper, we present a method to analyze the molecular structure and dynamics of nucleosomes, which are the basic unit in eukaryotic cells. In nucleosomal DNA chains, periodic dinucleotides are key patterns in protein-DNA interactions. This paper aims at revealing the significances of these periodic dinucleotides in the nucleosomal DNA motions. Normal mode analysis (NMA) is used to detect significant structural deformations of nucleosomal DNA. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently. © 2011 IEEE.

AB - In this paper, we present a method to analyze the molecular structure and dynamics of nucleosomes, which are the basic unit in eukaryotic cells. In nucleosomal DNA chains, periodic dinucleotides are key patterns in protein-DNA interactions. This paper aims at revealing the significances of these periodic dinucleotides in the nucleosomal DNA motions. Normal mode analysis (NMA) is used to detect significant structural deformations of nucleosomal DNA. We have found that periodic dinucleotides are usually located at the peaks or valleys of DNA and protein motions, revealing they dominate the nucleosome dynamics. Also, a specific dinucleotide pattern CA/TG appears most frequently. © 2011 IEEE.

KW - DNA and protein motions

KW - Normal Mode Analysis (NMA)

KW - Nucleosome

KW - Periodic dinucleotides

UR - http://www.scopus.com/inward/record.url?scp=83755163715&partnerID=8YFLogxK

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-83755163715&origin=recordpage

U2 - 10.1109/ICSMC.2011.6084132

DO - 10.1109/ICSMC.2011.6084132

M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 9781457706523

SP - 3078

EP - 3083

BT - Conference Proceedings - IEEE International Conference on Systems, Man and Cybernetics

T2 - 2011 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2011

Y2 - 9 October 2011 through 12 October 2011

ER -

Analysis of nucleosome structures based on molecular dynamics

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