The effect of the trp repressor from Escherichia coli on the structure and dynamics of dA20dT20

Andrew N. Lane; Jean Francois Lefévre; Oleg Jardetzky

doi:10.1016/0167-4781(86)90028-X

The effect of the trp repressor from Escherichia coli on the structure and dynamics of dA₂₀dT₂₀

Andrew N. Lane
, Jean Francois Lefévre
, Oleg Jardetzky

Research output: Contribution to journal › Article › peer-review

12 Scopus citations

Abstract

We have determined the effect of the tryptophan (trp) repressor from Escherichia coli on the structure and dynamics of dA₂₀dT₂₀. The structure was determined using time-dependent nuclear Overhauser effects and spin-lattice relaxation times. The deoxyribose conformation is near C3′ endo for the thymine residues, and a mixture of about 30% C3′ endo and 70% C2′ endo for the adenine residues. The glycosidic torsion angles are -50° for T and -60° for A. The roll is 20° and the propellor twist is about 29°. The conformation is consistent with recent calculations (Rao, K. and Kollman, P.A. (1985) J. Am. Chem. Soc. 107, 1507-1511). The rate constant for exchange of the imino protons is similar to that usually found for AT base-pairs, with an activation energy of 20 ± 2 kcal/mol, and an activation entropy of 17 ± 7 cal/mol per K. The repressor greatly retards the exchange of imino protons, and the activation energy increases to 38 kcal/mol. There are small changes in the structure of the DNA on forming the complex, with the adenine and thymidine residues becoming more similar in conformation.

Original language	English
Pages (from-to)	45-56
Number of pages	12
Journal	Biochimica et Biophysica Acta - Gene Structure and Expression
Volume	867
Issue number	1-2
DOIs	https://doi.org/10.1016/0167-4781(86)90028-X
State	Published - May 27 1986

Bibliographical note

Funding Information:
This work was supported by NIH Grant No. RR00711 and NIGMS Grant No. GM33385. A.N.L. is grateful to EMBO for a Long Term Fellowship, and J.F.L. to La Fondation pour la Recherche Medicale for similar support. We thank, too, Drs. R.W. Behling and D.R. Kearns for sending us a preprint of their article on the structure of poly(dA) • poly(dT).

Funding

This work was supported by NIH Grant No. RR00711 and NIGMS Grant No. GM33385. A.N.L. is grateful to EMBO for a Long Term Fellowship, and J.F.L. to La Fondation pour la Recherche Medicale for similar support. We thank, too, Drs. R.W. Behling and D.R. Kearns for sending us a preprint of their article on the structure of poly(dA) • poly(dT).

Funders	Funder number
National Institutes of Health (NIH)	RR00711
National Institute of General Medical Sciences	R01GM033385
European Molecular Biology Organization

Keywords

Imino proton exchange
NMR
Nucleic acid structure
trp repressor

ASJC Scopus subject areas

Structural Biology
Biophysics
Biochemistry
Genetics

Access to Document

10.1016/0167-4781(86)90028-X

Cite this

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title = "The effect of the trp repressor from Escherichia coli on the structure and dynamics of dA20dT20",

abstract = "We have determined the effect of the tryptophan (trp) repressor from Escherichia coli on the structure and dynamics of dA20dT20. The structure was determined using time-dependent nuclear Overhauser effects and spin-lattice relaxation times. The deoxyribose conformation is near C3′ endo for the thymine residues, and a mixture of about 30\% C3′ endo and 70\% C2′ endo for the adenine residues. The glycosidic torsion angles are -50° for T and -60° for A. The roll is 20° and the propellor twist is about 29°. The conformation is consistent with recent calculations (Rao, K. and Kollman, P.A. (1985) J. Am. Chem. Soc. 107, 1507-1511). The rate constant for exchange of the imino protons is similar to that usually found for AT base-pairs, with an activation energy of 20 ± 2 kcal/mol, and an activation entropy of 17 ± 7 cal/mol per K. The repressor greatly retards the exchange of imino protons, and the activation energy increases to 38 kcal/mol. There are small changes in the structure of the DNA on forming the complex, with the adenine and thymidine residues becoming more similar in conformation.",

keywords = "Imino proton exchange, NMR, Nucleic acid structure, trp repressor",

author = "Lane, \{Andrew N.\} and Lef{\'e}vre, \{Jean Francois\} and Oleg Jardetzky",

note = "Funding Information: This work was supported by NIH Grant No. RR00711 and NIGMS Grant No. GM33385. A.N.L. is grateful to EMBO for a Long Term Fellowship, and J.F.L. to La Fondation pour la Recherche Medicale for similar support. We thank, too, Drs. R.W. Behling and D.R. Kearns for sending us a preprint of their article on the structure of poly(dA) • poly(dT).",

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AU - Lefévre, Jean Francois

AU - Jardetzky, Oleg

N1 - Funding Information: This work was supported by NIH Grant No. RR00711 and NIGMS Grant No. GM33385. A.N.L. is grateful to EMBO for a Long Term Fellowship, and J.F.L. to La Fondation pour la Recherche Medicale for similar support. We thank, too, Drs. R.W. Behling and D.R. Kearns for sending us a preprint of their article on the structure of poly(dA) • poly(dT).

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N2 - We have determined the effect of the tryptophan (trp) repressor from Escherichia coli on the structure and dynamics of dA20dT20. The structure was determined using time-dependent nuclear Overhauser effects and spin-lattice relaxation times. The deoxyribose conformation is near C3′ endo for the thymine residues, and a mixture of about 30% C3′ endo and 70% C2′ endo for the adenine residues. The glycosidic torsion angles are -50° for T and -60° for A. The roll is 20° and the propellor twist is about 29°. The conformation is consistent with recent calculations (Rao, K. and Kollman, P.A. (1985) J. Am. Chem. Soc. 107, 1507-1511). The rate constant for exchange of the imino protons is similar to that usually found for AT base-pairs, with an activation energy of 20 ± 2 kcal/mol, and an activation entropy of 17 ± 7 cal/mol per K. The repressor greatly retards the exchange of imino protons, and the activation energy increases to 38 kcal/mol. There are small changes in the structure of the DNA on forming the complex, with the adenine and thymidine residues becoming more similar in conformation.

AB - We have determined the effect of the tryptophan (trp) repressor from Escherichia coli on the structure and dynamics of dA20dT20. The structure was determined using time-dependent nuclear Overhauser effects and spin-lattice relaxation times. The deoxyribose conformation is near C3′ endo for the thymine residues, and a mixture of about 30% C3′ endo and 70% C2′ endo for the adenine residues. The glycosidic torsion angles are -50° for T and -60° for A. The roll is 20° and the propellor twist is about 29°. The conformation is consistent with recent calculations (Rao, K. and Kollman, P.A. (1985) J. Am. Chem. Soc. 107, 1507-1511). The rate constant for exchange of the imino protons is similar to that usually found for AT base-pairs, with an activation energy of 20 ± 2 kcal/mol, and an activation entropy of 17 ± 7 cal/mol per K. The repressor greatly retards the exchange of imino protons, and the activation energy increases to 38 kcal/mol. There are small changes in the structure of the DNA on forming the complex, with the adenine and thymidine residues becoming more similar in conformation.

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