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J Mol Biol. 2013 Nov 15;425(22):4595-613. doi: 10.1016/j.jmb.2013.08.014. Epub 2013 Aug 23.

Malachite green mediates homodimerization of antibody VL domains to form a fluorescent ternary complex with singular symmetric interfaces.

Author information

1
Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA 15213, USA. Electronic address: css@andrew.cmu.edu.

Abstract

We report that a symmetric small-molecule ligand mediates the assembly of antibody light chain variable domains (VLs) into a correspondent symmetric ternary complex with novel interfaces. The L5* fluorogen activating protein is a VL domain that binds malachite green (MG) dye to activate intense fluorescence. Crystallography of liganded L5* reveals a 2:1 protein:ligand complex with inclusive C2 symmetry, where MG is almost entirely encapsulated between an antiparallel arrangement of the two VL domains. Unliganded L5* VL domains crystallize as a similar antiparallel VL/VL homodimer. The complementarity-determining regions are spatially oriented to form novel VL/VL and VL/ligand interfaces that tightly constrain a propeller conformer of MG. Binding equilibrium analysis suggests highly cooperative assembly to form a very stable VL/MG/VL complex, such that MG behaves as a strong chemical inducer of dimerization. Fusion of two VL domains into a single protein tightens MG binding over 1000-fold to low picomolar affinity without altering the large binding enthalpy, suggesting that bonding interactions with ligand and restriction of domain movements make independent contributions to binding. Fluorescence activation of a symmetrical fluorogen provides a selection mechanism for the isolation and directed evolution of ternary complexes where unnatural symmetric binding interfaces are favored over canonical antibody interfaces. As exemplified by L5*, these self-reporting complexes may be useful as modulators of protein association or as high-affinity protein tags and capture reagents.

KEYWORDS:

CDR; CID; FACS; FAP; HIV; MG; MW; PBS; SAS; chemical inducer of dimerization; complementarity-determining region; cooperative binding; directed evolution; fluorescence activated cell sorting; fluorogen activating protein; human immunodeficiency virus; malachite green; molecular weight; phosphate-buffered saline; quaternary structure; solvent-accessible surface; yeast surface display

PMID:
23978698
PMCID:
PMC3919518
DOI:
10.1016/j.jmb.2013.08.014
[Indexed for MEDLINE]
Free PMC Article
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