Aromatic interactions modulate the 5′-base selectivity of the DNA-binding autoantibody ED-10

Yi An, Rajesh K. Raju, Tongxiang Lu, Steven E. Wheeler

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

We present detailed computational analyses of the binding of four dinucleotides to a highly sequence-selective single-stranded DNA (ssDNA) binding antibody (ED-10) and selected point mutants. Anti-DNA antibodies are central to the pathogenesis of systemic lupus erythematosus (SLE), and a more complete understanding of the mode of binding of DNA and other ligands will be necessary to elucidate the role of anti-DNA antibodies in the kidney inflammation associated with SLE. Classical molecular mechanics based molecular dynamics simulations and density functional theory (DFT) computations were applied to pinpoint the origin of selectivity for the 5′-nucleotide. In particular, the strength of interactions between each nucleotide and the surrounding residues were computed using MMGBSA as well as DFT applied to a cluster model of the binding site. The results agree qualitatively with experimental binding free energies, and indicate that π-stacking, CH/π, NH/π, and hydrogen-bonding interactions all contribute to 5′-base selectivity in ED-10. Most importantly, the selectivity for dTdC over dAdC arises primarily from differences in the strength of π-stacking and XH/π interactions with the surrounding aromatic residues; hydrogen bonds play little role. These data suggest that a key Tyr residue, which is not present in other anti-DNA antibodies, plays a key role in the 5′-base selectivity, while we predict that the mutation of a single Trp residue can tune the selectivity for dTdC over dAdC.

Original languageEnglish
Pages (from-to)5653-5659
Number of pages7
JournalJournal of Physical Chemistry B
Volume118
Issue number21
DOIs
Publication statusPublished - 29 May 2014
Externally publishedYes

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Antinuclear Antibodies
Autoantibodies
antibodies
DNA
deoxyribonucleic acid
Antibodies
selectivity
Systemic Lupus Erythematosus
Density functional theory
Hydrogen bonds
Nucleotides
nucleotides
Molecular mechanics
Single-Stranded DNA
interactions
Molecular Dynamics Simulation
Hydrogen Bonding
Mechanics
Free energy
Molecular dynamics

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Materials Chemistry
  • Surfaces, Coatings and Films
  • Medicine(all)

Cite this

Aromatic interactions modulate the 5′-base selectivity of the DNA-binding autoantibody ED-10. / An, Yi; Raju, Rajesh K.; Lu, Tongxiang; Wheeler, Steven E.

In: Journal of Physical Chemistry B, Vol. 118, No. 21, 29.05.2014, p. 5653-5659.

Research output: Contribution to journalArticle

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