Modeling protein-DNA complexes with tangles

被引：9

作者：

Darcy, Isabel K. ^{[1
]}

机构：

[1] Univ Iowa, Dept Math, Iowa City, IA 52242 USA

来源：

COMPUTERS & MATHEMATICS WITH APPLICATIONS | 2008年 / 55卷 / 05期

基金：

美国国家卫生研究院;

关键词：

tangle; topoisomerase; recombinase; DNA knot; unknotting number;

D O I：

10.1016/j.camwa.2006.12.099

中图分类号：

O29 [应用数学];

学科分类号：

070104 ;

摘要：

The mathematics of tangles has been applied to model protein-DNA binding. A tangle consists of strings properly embedded in a 3-dimensional ball. The protein complex can be thought of as a 3D ball while the DNA segments bound by the protein complex can be thought of as strings embedded within the ball. This simple model can be used to determine the topology of protein-bound DNA. We review some tangle models and related software for modeling recombinase and topoisomerase action. (c) 2008 Published by Elsevier Ltd.

引用

页码：924 / 937

页数：14

共 50 条

[21] TFmodeller: comparative modelling of protein-DNA complexes
Contreras-Moreira, Bruno
Branger, Pierre-Alain
Collado-Vides, Julio
BIOINFORMATICS, 2007, 23 (13) : 1694 - 1696
[22] FOOTPRINTING PROTEIN-DNA COMPLEXES IN-VIVO
SASSEDWIGHT, S
GRALLA, JD
METHODS IN ENZYMOLOGY, 1991, 208 : 146 - 168
[23] Multiscale method for simulating protein-DNA complexes
Villa, E
Balaeff, A
Mahadevan, L
Schulten, K
MULTISCALE MODELING & SIMULATION, 2004, 2 (04): : 527 - 553
[24] INSIGHTS INTO DNA HELICAL TRANSITIONS FOUND IN PROTEIN-DNA COMPLEXES
Colasanti, Andrew V.
Li, Yun
Singh, Gautam
Lu, Xiang-Jun
Olson, Wilma K.
BIOMOLECULAR FORMS AND FUNCTIONS: A CELEBRATION OF 50 YEARS OF THE RAMACHANDRAN MAP, 2013, : 230 - 246
[25] Anomalous migration of DNA and protein-DNA complexes in gel.
Mohanty, U
Spasic, A
Mohanty, J
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2002, 223 : C88 - C88
[26] Modeling protein-DNA interactions at electrified interfaces
Williams, Keeshan
Levicky, Rastislav
ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 2012, 244
[27] INFLUENCE OF PROTEIN-DNA COMPLEXES ON STABILITY OF ADJOINING DNA REGIONS
WARTELL, RM
BIOPHYSICAL JOURNAL, 1977, 17 (02) : A61 - A61
[28] Imaging of DNA and Protein-DNA Complexes with Atomic Force Microscopy
Lyubchenko, Yuri L.
Shlyakhtenko, Luda S.
CRITICAL REVIEWS IN EUKARYOTIC GENE EXPRESSION, 2016, 26 (01): : 63 - 96
[29] AFM for analysis of structure and dynamics of DNA and protein-DNA complexes
Lyubchenko, Yuri L.
Shlyakhtenko, Luda S.
METHODS, 2009, 47 (03) : 206 - 213
[30] SPECIFICITY OF NON-HISTONE PROTEIN-DNA COMPLEXES
不详
NATURE, 1971, 233 (5319) : 374 - +

← 1 2 3 4 5 →