Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate

Levani Zandarashvili, Dan Nguyen, Kurtis M. Anderson, Mark White, David G. Gorenstein, Junji Iwahara

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH<inf>3</inf><sup>+</sup> groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.

Original languageEnglish (US)
Pages (from-to)1026-1037
Number of pages12
JournalBiophysical Journal
Volume109
Issue number5
DOIs
StatePublished - Sep 2 2015

Fingerprint

Sulfur
Phosphates
Oxygen
DNA
Calorimetry
Crystallography
Proteins
X-Rays
Lysine
Fluorescence
Ions
Entropy
Thermodynamics
Hydrogen
Magnetic Resonance Spectroscopy

ASJC Scopus subject areas

  • Biophysics

Cite this

Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. / Zandarashvili, Levani; Nguyen, Dan; Anderson, Kurtis M.; White, Mark; Gorenstein, David G.; Iwahara, Junji.

In: Biophysical Journal, Vol. 109, No. 5, 02.09.2015, p. 1026-1037.

Research output: Contribution to journalArticle

Zandarashvili, Levani ; Nguyen, Dan ; Anderson, Kurtis M. ; White, Mark ; Gorenstein, David G. ; Iwahara, Junji. / Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate. In: Biophysical Journal. 2015 ; Vol. 109, No. 5. pp. 1026-1037.
@article{4b841cbdd8f04445affb963c7e3b553a,
title = "Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate",
abstract = "Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3+ groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.",
author = "Levani Zandarashvili and Dan Nguyen and Anderson, {Kurtis M.} and Mark White and Gorenstein, {David G.} and Junji Iwahara",
year = "2015",
month = "9",
day = "2",
doi = "10.1016/j.bpj.2015.07.032",
language = "English (US)",
volume = "109",
pages = "1026--1037",
journal = "Biophysical Journal",
issn = "0006-3495",
publisher = "Biophysical Society",
number = "5",

}

TY - JOUR

T1 - Entropic Enhancement of Protein-DNA Affinity by Oxygen-to-Sulfur Substitution in DNA Phosphate

AU - Zandarashvili, Levani

AU - Nguyen, Dan

AU - Anderson, Kurtis M.

AU - White, Mark

AU - Gorenstein, David G.

AU - Iwahara, Junji

PY - 2015/9/2

Y1 - 2015/9/2

N2 - Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3+ groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.

AB - Dithioation of DNA phosphate is known to enhance binding affinities, at least for some proteins. We mechanistically characterized this phenomenon for the Antennapedia homeodomain-DNA complex by integrated use of fluorescence, isothermal titration calorimetry, NMR spectroscopy, and x-ray crystallography. By fluorescence and isothermal titration calorimetry, we found that this affinity enhancement is entropy driven. By NMR, we investigated the ionic hydrogen bonds and internal motions of lysine side-chain NH3+ groups involved in ion pairs with DNA. By x-ray crystallography, we compared the structures of the complexes with and without dithioation of the phosphate. Our NMR and x-ray data show that the lysine side chain in contact with the DNA phosphate becomes more dynamic upon dithioation. Our thermodynamic, structural, and dynamic investigations collectively suggest that the affinity enhancement by the oxygen-to-sulfur substitution in DNA phosphate is largely due to an entropic gain arising from mobilization of the intermolecular ion pair at the protein-DNA interface.

UR - http://www.scopus.com/inward/record.url?scp=84940646108&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84940646108&partnerID=8YFLogxK

U2 - 10.1016/j.bpj.2015.07.032

DO - 10.1016/j.bpj.2015.07.032

M3 - Article

VL - 109

SP - 1026

EP - 1037

JO - Biophysical Journal

JF - Biophysical Journal

SN - 0006-3495

IS - 5

ER -