An autoantibody to single‐stranded DNA: Comparison of the three‐dimensional structures of the unliganded fab and a deoxynucleotide–fab complex

Abstract

Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was accompanied by small adjustments in the orientations of the variable (VL and VH) domains. In addition, there were local conformational changes in the first hypervariable loop of the light chain and the third hypervariable loop of the heavy chain, which together with the domain shifts led to an improvement in the complementarity of nucleotide and Fab. The sugar-phosphate chain adopted an extended and "open" conformation, with the base, sugar, and phosphate components available for interactions with the protein. Nucleotide 1 (5'-end) was associated exclusively with the heavy chain, nucleotide 2 was shared by both heavy and light chains, and nucleotide 3 was bound by the light chain. The orientation of phosphate 1 was stabilized by hydrogen bonds with serine H52a and asparagine H53. Phosphate 2 formed an ion pair with arginine H52, but no other charge-charge interactions were observed. Insertion of the side chain of histidine L27d between nucleotides 2 and 3 resulted in a bend in the sugar-phosphate chain. The most dominant contacts with the protein involved the central thymine base, which was immobilized by cooperative stacking and hydrogen bonding interactions. This base was intercalated between a tryptophan ring (no. H100a) from the heavy chain and a tyrosine ring (no. L32) from the light chain. The resulting orientation of thymine was favorable for the simultaneous formation of two hydrogen bonds with the backbone carbonyl oxygen and the side chain hydroxyl group of serine L91 (the thymine atoms were the hydrogen on nitrogen 3 and keto oxygen 4).

Evolving concepts of specificity in immune reactions

“…The idea emerging from kinetic studies that interconvertible Ab conformations differ in ligand-binding activity was in accord with X-ray crystal structures that showed conformation differences, which were pronounced in some cases, between ligand-bound and free Abs (41)(42)(43). A comprehensive kinetic and X-ray crystallographic analysis of the Fv fragment of the anti-DNP Ab referred to above (SPE7) is especially illuminating (28).…”

Bactericidal Antibody Recognition of Meningococcal PorA by Induced Fit

“…It illustrates the intrinsic flexibility of antibodies in adapting to the shape of an antigen. The largest V L -V H rotations have been observed for anti-DNA Fab BV0 -401 (7.5°) (26) and for anti-HIV Fab 50.1 upon complexation with a V3 loop peptide (16°) (25). Unlike MN12H2, these Fab structures show a large decrease in the number of V L -V H interface contacts upon complexation with their antigen.…”

Crystallization and preliminary structure determination of an intact human immunoglobulin, b12: an antibody that broadly neutralizes primary isolates of HIV-1

“…The successful search model used for the two Fab domains displays a mere 52% sequence identity to b12 (PDB entry 1cbv; Herron et al, 1991). Upon correction of the model sequence to the b12 sequence, R cryst and R free were reduced to 0.37 and 0.44, respectively.…”