Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis

Oleg V Kovalenko, Andrea Olland, Nicole Piché-Nicholas, Adarsh Godbole, Daniel King, Kristine Svenson, Valerie Calabro, Mischa R Müller, Caroline Barelle, William Somers, Davinder S Gill, Lidia Mosyak, Lioudmila Tchistiakova

Research output: Contribution to journalArticle

32 Citations (Scopus)

Abstract

The immunoglobulin new antigen receptors (IgNARs) are a class of Ig-like molecules of the shark immune system that exist as heavy chain-only homodimers and bind antigens by their single domain variable regions (V-NARs). Following shark immunization and/or in vitro selection, V-NARs can be generated as soluble, stable, and specific high affinity monomeric binding proteins of ∼12 kDa. We have previously isolated a V-NAR from an immunized spiny dogfish shark, named E06, that binds specifically and with high affinity to human, mouse, and rat serum albumins. Humanization of E06 was carried out by converting over 60% of non-complementarity-determining region residues to those of a human germ line Vκ1 sequence, DPK9. The resulting huE06 molecules have largely retained the specificity and affinity of antigen binding of the parental V-NAR. Crystal structures of the shark E06 and its humanized variant (huE06 v1.1) in complex with human serum albumin (HSA) were determined at 3- and 2.3-Å resolution, respectively. The huE06 v1.1 molecule retained all but one amino acid residues involved in the binding site for HSA. Structural analysis of these V-NARs has revealed an unusual variable domain-antigen interaction. E06 interacts with HSA in an atypical mode that utilizes extensive framework contacts in addition to complementarity-determining regions that has not been seen previously in V-NARs. On the basis of the structure, the roles of various elements of the molecule are described with respect to antigen binding and V-NAR stability. This information broadens the general understanding of antigen recognition and provides a framework for further design and humanization of shark IgNARs.
Original languageEnglish
Pages (from-to)17408-17419
Number of pages12
JournalThe Journal of Biological Chemistry
Volume288
Issue number24
Early online date30 Apr 2013
DOIs
Publication statusPublished - 14 Jun 2013

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Sharks
Antigen Receptors
Structural analysis
Immunoglobulins
Serum Albumin
Antigens
Molecules
Squalus acanthias
Complementarity Determining Regions
Immunization
Immune system
Germ Cells
Rats
Immune System
Carrier Proteins
Crystal structure
Binding Sites
Amino Acids

Keywords

  • amino acid sequence
  • animals
  • antibodies, monoclonal, humanized
  • COS cells
  • cercopithecus aethiops
  • crystallography, x-ray
  • fish proteins
  • humans
  • hydrogen bonding
  • hydrophobic and hydrophilic interactions
  • mice
  • models, molecular
  • molecular sequence data
  • protein binding
  • protein engineering
  • protein structure, quaternary
  • protein structure, secondary
  • rats
  • sequence homology, amino acid
  • serum albumin
  • sharks
  • single-chain antibodies
  • albumin
  • antibodies
  • antibody engineering
  • antigen
  • crystal structure
  • humanization
  • IgNAR
  • V-NAR

Cite this

Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis. / Kovalenko, Oleg V; Olland, Andrea; Piché-Nicholas, Nicole; Godbole, Adarsh; King, Daniel; Svenson, Kristine; Calabro, Valerie; Müller, Mischa R; Barelle, Caroline; Somers, William; Gill, Davinder S; Mosyak, Lidia; Tchistiakova, Lioudmila.

In: The Journal of Biological Chemistry, Vol. 288, No. 24, 14.06.2013, p. 17408-17419.

Research output: Contribution to journalArticle

Kovalenko, OV, Olland, A, Piché-Nicholas, N, Godbole, A, King, D, Svenson, K, Calabro, V, Müller, MR, Barelle, C, Somers, W, Gill, DS, Mosyak, L & Tchistiakova, L 2013, 'Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis' The Journal of Biological Chemistry, vol. 288, no. 24, pp. 17408-17419. https://doi.org/10.1074/jbc.M112.435289
Kovalenko, Oleg V ; Olland, Andrea ; Piché-Nicholas, Nicole ; Godbole, Adarsh ; King, Daniel ; Svenson, Kristine ; Calabro, Valerie ; Müller, Mischa R ; Barelle, Caroline ; Somers, William ; Gill, Davinder S ; Mosyak, Lidia ; Tchistiakova, Lioudmila. / Atypical antigen recognition mode of a shark immunoglobulin new antigen receptor (IgNAR) variable domain characterized by humanization and structural analysis. In: The Journal of Biological Chemistry. 2013 ; Vol. 288, No. 24. pp. 17408-17419.
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AU - King, Daniel

AU - Svenson, Kristine

AU - Calabro, Valerie

AU - Müller, Mischa R

AU - Barelle, Caroline

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N2 - The immunoglobulin new antigen receptors (IgNARs) are a class of Ig-like molecules of the shark immune system that exist as heavy chain-only homodimers and bind antigens by their single domain variable regions (V-NARs). Following shark immunization and/or in vitro selection, V-NARs can be generated as soluble, stable, and specific high affinity monomeric binding proteins of ∼12 kDa. We have previously isolated a V-NAR from an immunized spiny dogfish shark, named E06, that binds specifically and with high affinity to human, mouse, and rat serum albumins. Humanization of E06 was carried out by converting over 60% of non-complementarity-determining region residues to those of a human germ line Vκ1 sequence, DPK9. The resulting huE06 molecules have largely retained the specificity and affinity of antigen binding of the parental V-NAR. Crystal structures of the shark E06 and its humanized variant (huE06 v1.1) in complex with human serum albumin (HSA) were determined at 3- and 2.3-Å resolution, respectively. The huE06 v1.1 molecule retained all but one amino acid residues involved in the binding site for HSA. Structural analysis of these V-NARs has revealed an unusual variable domain-antigen interaction. E06 interacts with HSA in an atypical mode that utilizes extensive framework contacts in addition to complementarity-determining regions that has not been seen previously in V-NARs. On the basis of the structure, the roles of various elements of the molecule are described with respect to antigen binding and V-NAR stability. This information broadens the general understanding of antigen recognition and provides a framework for further design and humanization of shark IgNARs.

AB - The immunoglobulin new antigen receptors (IgNARs) are a class of Ig-like molecules of the shark immune system that exist as heavy chain-only homodimers and bind antigens by their single domain variable regions (V-NARs). Following shark immunization and/or in vitro selection, V-NARs can be generated as soluble, stable, and specific high affinity monomeric binding proteins of ∼12 kDa. We have previously isolated a V-NAR from an immunized spiny dogfish shark, named E06, that binds specifically and with high affinity to human, mouse, and rat serum albumins. Humanization of E06 was carried out by converting over 60% of non-complementarity-determining region residues to those of a human germ line Vκ1 sequence, DPK9. The resulting huE06 molecules have largely retained the specificity and affinity of antigen binding of the parental V-NAR. Crystal structures of the shark E06 and its humanized variant (huE06 v1.1) in complex with human serum albumin (HSA) were determined at 3- and 2.3-Å resolution, respectively. The huE06 v1.1 molecule retained all but one amino acid residues involved in the binding site for HSA. Structural analysis of these V-NARs has revealed an unusual variable domain-antigen interaction. E06 interacts with HSA in an atypical mode that utilizes extensive framework contacts in addition to complementarity-determining regions that has not been seen previously in V-NARs. On the basis of the structure, the roles of various elements of the molecule are described with respect to antigen binding and V-NAR stability. This information broadens the general understanding of antigen recognition and provides a framework for further design and humanization of shark IgNARs.

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KW - models, molecular

KW - molecular sequence data

KW - protein binding

KW - protein engineering

KW - protein structure, quaternary

KW - protein structure, secondary

KW - rats

KW - sequence homology, amino acid

KW - serum albumin

KW - sharks

KW - single-chain antibodies

KW - albumin

KW - antibodies

KW - antibody engineering

KW - antigen

KW - crystal structure

KW - humanization

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JO - The Journal of Biological Chemistry

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