skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
 [1];  [1];  [1];  [1];  [1];  [2];  [1];  [3];  [4];  [1];  [5];  [5];  [2];  [6];  [1]
  1. Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology
  2. Northwestern Univ., Evanston, IL (United States). Dept. of Chemistry. Dept. of Molecular Biosciences. Chemistry of Life Processes Inst.
  3. Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology; Wroclaw Univ. of Technology (Poland). Dept. of Biochemistry
  4. Univ. of Chicago, IL (United States). Dept. of Molecular Genetics and Cell Biology
  5. Univ. of North Carolina, Chapel Hill, NC (United States). School of Medicine. Dept. of Biochemistry and Biophysics
  6. Univ. of Chicago, IL (United States). Dept. of Biochemistry and Molecular Biology. Dept. of Molecular Genetics and Cell Biology
+ Show Author Affiliations

Antibodies have a well-established modular architecture wherein the antigen-binding site residing in the antigen-binding fragment (Fab or Fv) is an autonomous and complete unit for antigen recognition. Here, we describe antibodies departing from this paradigm. We developed recombinant antibodies to trimethylated lysine residues on histone H3, important epigenetic marks and challenging targets for molecular recognition. Quantitative characterization demonstrated their exquisite specificity and high affinity, and they performed well in common epigenetics applications. Surprisingly, crystal structures and biophysical analyses revealed that two antigen-binding sites of these antibodies form a head-to-head dimer and cooperatively recognize the antigen in the dimer interface. This “antigen clasping” produced an expansive interface where trimethylated Lys bound to an unusually extensive aromatic cage in one Fab and the histone N terminus to a pocket in the other, thereby rationalizing the high specificity. A long-neck antibody format with a long linker between the antigen-binding module and the Fc region facilitated antigen clasping and achieved both high specificity and high potency. Antigen clasping substantially expands the paradigm of antibody–antigen recognition and suggests a strategy for developing extremely specific antibodies.

Research Organization:
Univ. of Chicago, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC); National Inst. of Health (NIH) (United States); W. M. Keck Foundation (United States); Chicago Biomedical Consortium (United States); Chicago Community Trust (United States)
Contributing Organization:
Wroclaw Univ. of Technology (Poland); Northwestern Univ., Evanston, IL (United States); Univ. of North Carolina, Chapel Hill, NC (United States)
Grant/Contract Number:
AC02-06CH11357; R21 DA025725; RC1 DA028779; GM067193; P30 CA014599
OSTI ID:
1241064
Journal Information:
Proceedings of the National Academy of Sciences of the United States of America, Vol. 113, Issue 8; ISSN 0027-8424
Publisher:
National Academy of Sciences, Washington, DC (United States)Copyright Statement
Country of Publication:
United States
Language:
ENGLISH
Citation Metrics:
Cited by: 27 works
Citation information provided by
Web of Science

References (29)

Separation and Isolation of Fractions of Rabbit Gamma-Globulin containing the Antibody and Antigenic Combining Sites journal September 1958
Variants of the Antibody Herceptin That Interact with HER2 and VEGF at the Antigen Binding Site journal March 2009
Engineered antibody fragments and the rise of single domains journal September 2005
The language of covalent histone modifications journal January 2000
Chromatin Modifications and Their Function journal February 2007
An assessment of histone-modification antibody quality journal December 2010
Antibody recognition of histone post-translational modifications: emerging issues and future prospects journal June 2011
Broad Ranges of Affinity and Specificity of Anti-Histone Antibodies Revealed by a Quantitative Peptide Immunoprecipitation Assay journal December 2012
Recombinant antibodies to histone post-translational modifications journal August 2013
Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design journal October 2011
Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide journal June 2015
WDR5 Associates with Histone H3 Methylated at K4 and Is Essential for H3 K4 Methylation and Vertebrate Development journal June 2005
A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling journal May 2006
Canonical Structure Repertoire of the Antigen-binding Site of Immunoglobulins Suggests Strong Geometrical Restrictions Associated to the Mechanism of Immune Recognition journal December 1995
Analysis of the Antigen Combining Site: Correlations Between Length and Sequence Composition of the Hypervariable Loops and the Nature of the Antigen journal January 2003
The Structural Basis of Peptide-Protein Binding Strategies journal February 2010
How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers journal November 2007
Recognition of trimethyllysine by a chromodomain is not driven by the hydrophobic effect journal June 2007
Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2 journal October 2015
Structure-Function Studies of Two Synthetic Anti-vascular Endothelial Growth Factor Fabs and Comparison with the Avastin™ Fab journal December 2005
Fab MOR03268 Triggers Absorption Shift of a Diagnostic Dye via Packaging in a Solvent-shielded Fab Dimer Interface journal March 2008
High-affinity Antigen Binding by Chelating Recombinant Antibodies (CRAbs) journal February 1995
The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops journal May 2008
Crystal Structure of a Neutralizing Human IgG Against HIV-1: A Template for Vaccine Design journal August 2001
Crystallographic structure of an intact IgG1 monoclonal antibody 1 1Edited by I. A. Wilson journal February 1998
Design of protein function leaps by directed domain interface evolution journal April 2008
Directed Network Wiring Identifies a Key Protein Interaction in Embryonic Stem Cell Differentiation journal June 2014
Measurement of acetylation turnover at distinct lysines in human histones identifies long-lived acetylation sites journal July 2013
Analysis of epigenetic modifications of chromatin at specific gene loci by native chromatin immunoprecipitation of nucleosomes isolated using hydroxyapatite chromatography journal February 2008

Cited By (7)

Advances in the Production and Batch Reformatting of Phage Antibody Libraries journal August 2019
Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription journal June 2017
Synthetic oligonucleotide antigens modified with locked nucleic acids detect disease specific antibodies journal October 2016
Antihomotypic affinity maturation improves human B cell responses against a repetitive epitope journal June 2018
Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq journal November 2016
IgM Antibodies Can Access Cryptic Antigens Denied to IgG: Hypothesis on Novel Binding Mechanism journal August 2019
Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq posted_content October 2016

Figures / Tables (5)

Fig. 1(p. 2)figure Fig. 1
Fig. 2(p. 3)figure Fig. 2
Fig. 3(p. 4)figure Fig. 3
Fig. 4(p. 5)figure Fig. 4
Fig. 5(p. 6)figure Fig. 5

Similar Records

Related Subjects

60 APPLIED LIFE SCIENCES
59 BASIC BIOLOGICAL SCIENCES
antibody engineering
epigenetics
antibody validation
protein–protein interaction
data reproducibility