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Alpha/gamma Transitions in the B-DNA backbone

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posted on 2023-06-07, 21:35 authored by Peter Varnai, Dragana Djuranovic, Richard Lavery, Brigitte Hartmann
In the crystal structures of protein complexes with B DNA, a and ¿ DNA backbone torsion angles often exhibit non canonical values. It is not known if these alternative backbone conformations are easily accessible in solution and can contribute to the specific recognition of DNA by proteins. We have analysed the coupled transition of the a and ¿ torsion angles within the central GpC step of a B DNA dodecamer by computer simulations. Five stable or metastable non canonical a/¿ sub states are found. The most favourable pathway from the canonical a/¿ structure to any unusual form involves a counter rotation of a and ¿, via the trans conformation. However, the corresponding free energy indicates that spontaneous flipping of the torsions is improbable in free B DNA. This is supported by an analysis of the available high resolution crystallographic structures showing that unusual a/¿ states are only encountered in B DNA complexed to proteins. An analysis of the structural consequences of a/¿ transitions shows that the non canonical backbone geometry influences essentially the roll and twist values and reduces the equilibrium dispersion of structural parameters. Our results support the hypothesis that unusual a/¿ backbones arise during protein¿DNA complexation, assisting the fine structural adjustments between the two partners and playing a role in the overall complexation free energy.

History

Publication status

  • Published

File Version

  • Published version

Journal

Nucleic Acids Research

ISSN

0305-1048

Issue

24

Volume

30

Page range

5398-5406

Pages

9.0

Department affiliated with

  • Chemistry Publications

Notes

PV+ BH designed research, DD performed crystal database analysis, PV performed computer simulations and analyzed data, PV, RL+ BH wrote the paper. First combined survey of conformational transitions in the B-DNA backbone from crystal structures and computer simulations identifying five conformational sub-states, cited 28 times.

Full text available

  • Yes

Peer reviewed?

  • Yes

Legacy Posted Date

2012-02-06

First Open Access (FOA) Date

2016-03-22

First Compliant Deposit (FCD) Date

2016-08-17

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