Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy

Kurtis M. Anderson, Alexandre Esadze, Mariappan Manoharan, Rafael Brüschweiler, David G. Gorenstein, Junji Iwahara

Research output: Contribution to journalArticle

45 Citations (Scopus)

Abstract

Ion pairing is one of the most fundamental chemical interactions and is essential for molecular recognition by biological macromolecules. From an experimental standpoint, very little is known to date about ion-pair dynamics in biological macromolecular systems. Absorption, infrared, and Raman spectroscopic methods were previously used to characterize dynamic properties of ion pairs, but these methods can be applied only to small compounds. Here, using NMR 15N relaxation and hydrogen-bond scalar 15N-31P J-couplings (h3JNP), we have investigated the dynamics of the ion pairs between lysine side-chain NH 3 + amino groups and DNA phosphate groups at the molecular interface of the HoxD9 homeodomain-DNA complex. We have determined the order parameters and the correlation times for C-N bond rotation and reorientation of the lysine NH3 + groups. Our data indicate that the NH 3 + groups in the intermolecular ion pairs are highly dynamic at the protein-DNA interface, which should lower the entropic costs for protein-DNA association. Judging from the C-N bond-rotation correlation times along with experimental and quantum-chemically derived h3J NP hydrogen-bond scalar couplings, it seems that breakage of hydrogen bonds in the ion pairs occurs on a sub-nanosecond time scale. Interestingly, the oxygen-to-sulfur substitution in a DNA phosphate group was found to enhance the mobility of the NH3 + group in the intermolecular ion pair. This can partially account for the affinity enhancement of the protein-DNA association by the oxygen-to-sulfur substitution, which is a previously observed but poorly understood phenomenon.

Original languageEnglish (US)
Pages (from-to)3613-3619
Number of pages7
JournalJournal of the American Chemical Society
Volume135
Issue number9
DOIs
StatePublished - Mar 6 2013

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Nuclear magnetic resonance spectroscopy
DNA
Magnetic Resonance Spectroscopy
Observation
Ions
Proteins
Hydrogen
Hydrogen bonds
Sulfur
Lysine
Phosphates
Substitution reactions
Association reactions
Oxygen
Molecular recognition
Infrared absorption
Biological systems
Macromolecules
Nuclear magnetic resonance
Costs and Cost Analysis

ASJC Scopus subject areas

  • Chemistry(all)
  • Catalysis
  • Biochemistry
  • Colloid and Surface Chemistry

Cite this

Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy. / Anderson, Kurtis M.; Esadze, Alexandre; Manoharan, Mariappan; Brüschweiler, Rafael; Gorenstein, David G.; Iwahara, Junji.

In: Journal of the American Chemical Society, Vol. 135, No. 9, 06.03.2013, p. 3613-3619.

Research output: Contribution to journalArticle

Anderson, Kurtis M. ; Esadze, Alexandre ; Manoharan, Mariappan ; Brüschweiler, Rafael ; Gorenstein, David G. ; Iwahara, Junji. / Direct observation of the ion-pair dynamics at a protein-DNA interface by NMR spectroscopy. In: Journal of the American Chemical Society. 2013 ; Vol. 135, No. 9. pp. 3613-3619.
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