Issue 6, 2012
From the journal:

Physical Chemistry Chemical Physics

The natural DNA bending angle in the lac repressor headpiece–O1 operator complex is determined by protein–DNA contacts and water release†

Daniel Barr‡a  and  Arjan van der Vaart*b  

* Corresponding authors

a Department of Chemistry and Biochemistry, Center for Biological Physics, Arizona State University, PO Box 871604, Tempe, USA

b Department of Chemistry, University of South Florida, 4202 East Fowler Avenue CHE 205, Tampa, USA
E-mail: avandervaart@usf.edu
Tel: +1 813-974-8762

Abstract

We performed molecular dynamics simulations of the lac repressor headpiece—O1 operator complex for natural, over and underbent DNA to assess the factors that determine the natural DNA bending angle. At the natural angle, the specific and nonspecific contacts between the protein and DNA are optimized. Protein–DNA contacts show different angle dependences in the right and left sites, with the left site generally getting weaker and the right site getting stronger as the bending angle increases. Two entropic factors were identified as well: at the natural bending angle, water release and the quasiharmonic protein configurational entropy are maximized. The gain in protein configurational entropy might stem from an entropy–entropy compensation mechanism, in which a reduction in protein fluctuations is offset by a loss in correlations between the right and left sites.

Graphical abstract: The natural DNA bending angle in the lac repressor headpiece–O1 operator complex is determined by protein–DNA contacts and water release

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Article information

DOI
https://doi.org/10.1039/C2CP23780F
Article type
Paper
Submitted
28 Nov 2011
Accepted
05 Dec 2011
First published
09 Dec 2011

Phys. Chem. Chem. Phys., 2012,14, 2070-2077

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The natural DNA bending angle in the lac repressor headpiece–O1 operator complex is determined by protein–DNA contacts and water release

D. Barr and A. V. D. Vaart, Phys. Chem. Chem. Phys., 2012, 14, 2070 DOI: 10.1039/C2CP23780F

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