A class of exact dynamical solutions in the elastic rod model of DNA with implications for the theory of fluctuations in the torsional motion of plasmids

1996 ◽  
Vol 105 (6) ◽  
pp. 2517-2526 ◽  
Author(s):  
Irwin Tobias ◽  
Bernard D. Coleman ◽  
Marzio Lembo
Keyword(s):  
Torsional Motion ◽  
Elastic Rod ◽  
Rod Model ◽  
Elastic Rod Model

scholarly journals Asymmetric elastic rod model for DNA

2009 ◽  
Vol 80 (1) ◽  
Author(s):  
B. Eslami-Mossallam ◽  
M. R. Ejtehadi
Keyword(s):  
Elastic Rod ◽  
Rod Model ◽  
Elastic Rod Model

Elastic Rod Model of a DNA Loop in theLacOperon

1999 ◽  
Vol 83 (23) ◽  
pp. 4900-4903 ◽  
Author(s):  
Alexander Balaeff ◽  
L. Mahadevan ◽  
Klaus Schulten
Keyword(s):  
Elastic Rod ◽  
Dna Loop ◽  
Rod Model ◽  
Elastic Rod Model

scholarly journals KOBRA: a fluctuating elastic rod model for slender biological macromolecules

Soft Matter ◽  
2020 ◽  
Vol 16 (32) ◽  
pp. 7544-7555
Author(s):  
Robert Welch ◽  
Sarah A. Harris ◽  
Oliver G. Harlen ◽  
Daniel J. Read
Keyword(s):  
Coarse Grained ◽  
Biological Macromolecules ◽  
Elastic Rod ◽  
Rod Model ◽  
Elastic Rod Model

KOBRA is a coarse-grained algorithm for parameterising and simulating slender proteins using Kirchoff rods.

An Elastic Rod Representation for the LacI-DNA Loop Complex

2011 ◽  
Author(s):  
Todd D. Lillian
Keyword(s):  
Gene Regulation ◽  
Large Range ◽  
Protein Flexibility ◽  
Lac Repressor ◽  
Elastic Rod ◽  
Repressor Protein ◽  
Dna Loop ◽  
Rod Model ◽  
Elastic Rod Model

The well-recognized Lac repressor protein (LacI) regulates transcription by bending DNA into a loop. In addition to the known role of DNA flexibility, there is accumulating evidence suggesting that the flexibility of LacI also plays a role in this gene regulation. Here we extend our elastic rod model for DNA (previously used to model DNA only) to represent LacI. Specifically, we represent sites of concentrated flexibility in the protein with flexible elastic rod domains; and we represent relatively rigid domains of the protein with stiff elastic rod domains. Our analysis shows the sensitivity of looping energetics to the degree of flexibility within the protein over a large range of DNA lengths. In addition, we show that the predicted energetically dominant binding topology (A) remains upon introducing protein flexibility.

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