Crystal structure of an antigen-binding fragment bound to single-stranded DNA

Area of Science:

• Structural Biology
• Immunology
• Molecular Medicine

Background:

• Antibodies to DNA are hallmarks of systemic lupus erythematosus (SLE) and are crucial for studying protein-DNA interactions.
• Anti-DNA antibodies contribute to SLE pathogenesis, particularly kidney damage, through immune complex formation.
• Understanding the structural basis of antibody-DNA recognition and pathogenicity is limited by a lack of experimental structural data.

Purpose of the Study:

• To elucidate the structural mechanisms of anti-single-stranded DNA (ssDNA) antibody recognition.
• To provide a structural framework for understanding antibody-DNA binding thermodynamics and pathogenicity.

Main Methods:

• Determined the 2.1 Å crystal structure of a recombinant anti-ssDNA Fab fragment (DNA-1) in complex with a dT5 oligonucleotide.
• Analyzed the interactions between the antibody's binding site and the ssDNA.

Main Results:

• The DNA-1 antibody binds dT5 by sandwiching thymine bases between tyrosine residues, forming sequence-specific hydrogen bonds.
• Identified a conserved ssDNA recognition module involving specific tyrosine, histidine, and asparagine residues, along with a complementarity determining region H3 aromatic side-chain.
• Observed a novel role for arginine residues in maintaining the structural integrity of the antibody's combining site, rather than forming direct ion pairs.

Conclusions:

• The determined structure provides critical insights into the molecular basis of anti-ssDNA antibody recognition.
• Hydrophobic desolvation may explain the negative enthalpy observed in antibody-DNA binding.
• The unique role of arginine in DNA-1 suggests a new perspective on antibody pathogenicity in SLE, potentially linked to arginine content in antibody hypervariable loops.