Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites

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Item Type:	Article
Title:	Structural and energetic origins of sequence-specific DNA bending: Monte Carlo simulations of papillomavirus E2-DNA binding sites
Creators Name:	Rohs, R., Sklenar, H. and Shakked, Z.
Abstract:	DNA bending is an important structural feature for indirect readout in protein-DNA recognition. The binding of papillomavirus E2 transcription factors to their DNA binding sites is associated with DNA bending, providing an attractive model system to study the origins of sequence-specific DNA bending. The consensus E2 target is of the general form ACCGN4CGGT with a variable four base pair region. We applied a new all-atom Monte Carlo (MC) algorithm that combines effective sampling with fast conformational equilibration. The resulting MC ensembles resemble the corresponding high-resolution crystal structures very well. Distinct bending is observed for the E2-DNA binding site with a central AATT linker in contrast to an essentially straight DNA with a central ACGT linker. Contributions of specific base pair steps to the overall bending are shown in terms of local structural parameters. The analysis of conformational substates provides new insights into the energetic origins of intrinsic DNA bending.
Keywords:	Algorithms, Base Pairing, Binding Sites, Computer Simulation, Monte Carlo Method, Nucleic Acid Conformation, Protein Conformation, Transcription Factors, Viral DNA, Viral Oncogene Proteins, X-Ray Crystallography
Source:	Structure with Folding & Design
ISSN:	0969-2126
Publisher:	Cell Press
Volume:	13
Number:	10
Page Range:	1499-1509
Date:	1 October 2005
Official Publication:	https://doi.org/10.1016/j.str.2005.07.005
PubMed:	View item in PubMed

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