Solution Measurement of DNA Curvature in Papillomavirus E2 Binding Sites

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Aug 22

PMID 12930964

Citations 7

Authors

Jeff M Zimmerman

L James Maher 3rd

Affiliations

Soon will be listed here.

Abstract

'Indirect readout' refers to the proposal that proteins can recognize the intrinsic three-dimensional shape or flexibility of a DNA binding sequence apart from direct protein contact with DNA base pairs. The differing affinities of human papillomavirus (HPV) E2 proteins for different E2 binding sites have been proposed to reflect indirect readout. DNA bending has been observed in X-ray structures of E2 protein-DNA complexes. X-ray structures of three different E2 DNA binding sites revealed differences in intrinsic curvature. DNA sites with intrinsic curvature in the direction of protein-induced bending were bound more tightly by E2 proteins, supporting the indirect readout model. We now report solution measurements of intrinsic DNA curvature for three E2 binding sites using a sensitive electrophoretic phasing assay. Measured E2 site curvature agrees well the predictions of a dinucleotide model and supports an indirect readout hypothesis for DNA recognition by HPV E2.

Citing Articles

Protein flexibility directs DNA recognition by the papillomavirus E2 proteins.

Brown C, Campos-Leon K, Strickland M, Williams C, Fairweather V, Brady R Nucleic Acids Res. 2010; 39(7):2969-80.

PMID: 21131281 PMC: 3074142. DOI: 10.1093/nar/gkq1217.

Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

Blakaj D, Fernandez-Fuentes N, Chen Z, Hegde R, Fiser A, Burk R Front Biosci (Landmark Ed). 2009; 14(3):900-17.

PMID: 19273107 PMC: 3705561. DOI: 10.2741/3285.

Comprehensive comparison of the interaction of the E2 master regulator with its cognate target DNA sites in 73 human papillomavirus types by sequence statistics.

Sanchez I, Dellarole M, Gaston K, de Prat Gay G Nucleic Acids Res. 2007; 36(3):756-69.

PMID: 18084026 PMC: 2241901. DOI: 10.1093/nar/gkm1104.

Recent advances in the search for antiviral agents against human papillomaviruses.

Fradet-Turcotte A, Archambault J Antivir Ther. 2007; 12(4):431-51.

PMID: 17668552 PMC: 4646640.

The recognition of local DNA conformation by the human papillomavirus type 6 E2 protein.

Hooley E, Fairweather V, Clarke A, Gaston K, Brady R Nucleic Acids Res. 2006; 34(14):3897-908.

PMID: 16914454 PMC: 1557802. DOI: 10.1093/nar/gkl466.

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