Structural modeling of sequence specificity by an autoantibody against single-stranded DNA

Area of Science:

• Immunology
• Structural Biology
• Computational Biology

Background:

• 11F8 is a pathogenic autoantibody targeting single-stranded DNA (ssDNA), implicated in lupus.
• Understanding autoantibody-DNA interactions is crucial for autoimmune disease research.

Purpose of the Study:

• To elucidate the molecular basis of sequence specificity and high affinity binding of the 11F8 autoantibody to ssDNA.
• To model the complex formed between 11F8 and ssDNA using mutagenesis and biophysical data.

Main Methods:

• Site-directed mutagenesis of the 11F8 autoantibody.
• Fluorescence resonance energy transfer (FRET) to determine intermolecular distances.
• Computational docking to model the 11F8-ssDNA complex.
• Analysis of somatic mutations' effects on binding.

Main Results:

• Six binding site residues contribute significantly to the binding free energy of 11F8 and ssDNA.
• A structural model reveals aromatic stacking and bidentate hydrogen bonds mediating high-affinity, sequence-specific binding.
• 11F8 shares a DNA binding motif with other anti-ssDNA antibodies, recognizing thymine-rich sequences.
• A somatic mutation (R31S) alters binding interface contacts, suggesting a role in modulating ssDNA recognition.

Conclusions:

• The study provides data-driven models of 11F8-ssDNA interactions, offering testable hypotheses for sequence specificity.
• These models highlight the role of specific amino acid residues and hydrogen bonding in autoantibody recognition of ssDNA.
• The findings shed light on how somatic mutations can influence autoantibody binding and potentially disease pathogenesis.