Topological measurement of protein-induced DNA bend angles - PubMed (original) (raw)
. 1996 Sep 6;261(5):620-33.
doi: 10.1006/jmbi.1996.0488.
Affiliations
- PMID: 8800211
- DOI: 10.1006/jmbi.1996.0488
Topological measurement of protein-induced DNA bend angles
L C Lutter et al. J Mol Biol. 1996.
Abstract
A new method measures independently the changes in the DNA bend and winding angles that occur when a protein binds to its specific site in DNA. The procedure requires an investigation of the change in DNA topology induced when the protein binds to tandemly repeated sites of varying repeat length in circular DNA. This new method is superior to currently used methods because topology permits the measurements to be derived absolutely from first principles, and no comparison standards are required. The method is used to determine the bend and winding angles induced when catabolite gene activator protein binds to its site. The bend value obtained (69 +/- 4 degrees) is intermediate to those reported for two crystal forms of the complex.
Similar articles
- Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.
Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH. Kapanidis AN, et al. J Mol Biol. 2001 Sep 21;312(3):453-68. doi: 10.1006/jmbi.2001.4976. J Mol Biol. 2001. PMID: 11563909 - Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics.
Kahn JD, Crothers DM. Kahn JD, et al. J Mol Biol. 1998 Feb 13;276(1):287-309. doi: 10.1006/jmbi.1997.1515. J Mol Biol. 1998. PMID: 9514724 - Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation.
Murphy EC, Zhurkin VB, Louis JM, Cornilescu G, Clore GM. Murphy EC, et al. J Mol Biol. 2001 Sep 21;312(3):481-99. doi: 10.1006/jmbi.2001.4977. J Mol Biol. 2001. PMID: 11563911 - Protein-nucleic acid interactions and DNA conformation in a complex of human immunodeficiency virus type 1 reverse transcriptase with a double-stranded DNA template-primer.
Ding J, Hughes SH, Arnold E. Ding J, et al. Biopolymers. 1997;44(2):125-38. doi: 10.1002/(SICI)1097-0282(1997)44:2<125::AID-BIP2>3.0.CO;2-X. Biopolymers. 1997. PMID: 9354757 Review.
Cited by
- Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.
Leng F. Leng F. Biophys Rev. 2016 Sep;8(3):197-207. doi: 10.1007/s12551-016-0204-z. Epub 2016 Jun 10. Biophys Rev. 2016. PMID: 28510223 Free PMC article. Review. - Protein-induced DNA linking number change by sequence-specific DNA binding proteins and its biological effects.
Leng F. Leng F. Biophys Rev. 2016 Nov;8(Suppl 1):123-133. doi: 10.1007/s12551-016-0239-1. Epub 2016 Nov 14. Biophys Rev. 2016. PMID: 28510217 Free PMC article. Review. - Induced fit and the entropy of structural adaptation in the complexation of CAP and lambda-repressor with cognate DNA sequences.
Dixit SB, Andrews DQ, Beveridge DL. Dixit SB, et al. Biophys J. 2005 May;88(5):3147-57. doi: 10.1529/biophysj.104.053843. Epub 2005 Feb 24. Biophys J. 2005. PMID: 15731390 Free PMC article. - Axis curvature and ligand induced bending in the CAP-DNA oligomers.
Dixit SB, Beveridge DL. Dixit SB, et al. Biophys J. 2005 Jan;88(1):L04-6. doi: 10.1529/biophysj.104.053058. Epub 2004 Nov 19. Biophys J. 2005. PMID: 15556974 Free PMC article. - Role of histone N-terminal tails and their acetylation in nucleosome dynamics.
Morales V, Richard-Foy H. Morales V, et al. Mol Cell Biol. 2000 Oct;20(19):7230-7. doi: 10.1128/MCB.20.19.7230-7237.2000. Mol Cell Biol. 2000. PMID: 10982840 Free PMC article.