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Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.

Velikovsky CA, Deng L, Tasumi S, Iyer LM, Kerzic MC, Aravind L, Pancer Z, Mariuzza RA - Nat. Struct. Mol. Biol. (2009)

Bottom Line: The VLR-HEL structure combined with sequence analysis revealed an almost perfect match between ligand-contacting positions and positions with highest sequence diversity.Thus, it is likely that we have defined the generalized antigen-binding site of VLRs.We further demonstrated that VLRs can be affinity-matured by 13-fold to affinities as high as those of IgG antibodies, making VLRs potential alternatives to antibodies for biotechnology applications.

View Article: PubMed Central - PubMed

Affiliation: Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA.

ABSTRACT
Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs are fundamentally different from the antibodies of jawed vertebrates, which consist of immunoglobulin (Ig) domains. We determined the structure of an anti-hen egg white lysozyme (HEL) VLR, isolated by yeast display, bound to HEL. The VLR, whose affinity resembles that of IgM antibodies, uses nearly all its concave surface to bind the protein, in addition to a loop that penetrates into the enzyme active site. The VLR-HEL structure combined with sequence analysis revealed an almost perfect match between ligand-contacting positions and positions with highest sequence diversity. Thus, it is likely that we have defined the generalized antigen-binding site of VLRs. We further demonstrated that VLRs can be affinity-matured by 13-fold to affinities as high as those of IgG antibodies, making VLRs potential alternatives to antibodies for biotechnology applications.

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Structure of the VRLB.2D-HEL complex and comparison with antibody-HEL complexes. (a) Ribbon diagram of the VLRB.2D-HEL complex showing the concave antigen-binding surface of the VLR solenoid. LRRNT (yellow); LRR1, LRRV1 and LRRVe (blue); CP (red); LRRCT (orange); HEL (green). In parentheses are the residue numbers corresponding to each module. (b) The complex is oriented to highlight the interaction between the LRRCT insert and the active site cleft of HEL. (c) Structure of the complex between the camel single-domain VH antibody cAb-Lys3 (violet) and HEL (green) (Protein Data Bank accession code 1MEL). The orientation of HEL is similar to that in (b). (d) The complex between the shark single-domain VH antibody PBLA8 IgNAR (raspberry) and HEL (green) (1T6V).
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Figure 1: Structure of the VRLB.2D-HEL complex and comparison with antibody-HEL complexes. (a) Ribbon diagram of the VLRB.2D-HEL complex showing the concave antigen-binding surface of the VLR solenoid. LRRNT (yellow); LRR1, LRRV1 and LRRVe (blue); CP (red); LRRCT (orange); HEL (green). In parentheses are the residue numbers corresponding to each module. (b) The complex is oriented to highlight the interaction between the LRRCT insert and the active site cleft of HEL. (c) Structure of the complex between the camel single-domain VH antibody cAb-Lys3 (violet) and HEL (green) (Protein Data Bank accession code 1MEL). The orientation of HEL is similar to that in (b). (d) The complex between the shark single-domain VH antibody PBLA8 IgNAR (raspberry) and HEL (green) (1T6V).

Mentions: We determined the structure of the VLRB.2D-HEL complex to 2.2 Å resolution. VLRB.2D adopts a horseshoe-shaped solenoid fold characteristic of LRR proteins, including TLRs18 (Fig. 1a,b). The structure comprises an LRRNT, a 24-residue LRR1, two 24-residue LRRVs (LRRV1 and LRRVe), a 13-residue CP, and an LRRCT. The concave surface of VLRB.2D, through which the VLR binds HEL, is composed of six parallel β-strands (two from LRRNT, three from LRRVs, and one from CP) (Fig. 1a).


Structure of a lamprey variable lymphocyte receptor in complex with a protein antigen.

Velikovsky CA, Deng L, Tasumi S, Iyer LM, Kerzic MC, Aravind L, Pancer Z, Mariuzza RA - Nat. Struct. Mol. Biol. (2009)

Structure of the VRLB.2D-HEL complex and comparison with antibody-HEL complexes. (a) Ribbon diagram of the VLRB.2D-HEL complex showing the concave antigen-binding surface of the VLR solenoid. LRRNT (yellow); LRR1, LRRV1 and LRRVe (blue); CP (red); LRRCT (orange); HEL (green). In parentheses are the residue numbers corresponding to each module. (b) The complex is oriented to highlight the interaction between the LRRCT insert and the active site cleft of HEL. (c) Structure of the complex between the camel single-domain VH antibody cAb-Lys3 (violet) and HEL (green) (Protein Data Bank accession code 1MEL). The orientation of HEL is similar to that in (b). (d) The complex between the shark single-domain VH antibody PBLA8 IgNAR (raspberry) and HEL (green) (1T6V).
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Related In: Results  -  Collection

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Figure 1: Structure of the VRLB.2D-HEL complex and comparison with antibody-HEL complexes. (a) Ribbon diagram of the VLRB.2D-HEL complex showing the concave antigen-binding surface of the VLR solenoid. LRRNT (yellow); LRR1, LRRV1 and LRRVe (blue); CP (red); LRRCT (orange); HEL (green). In parentheses are the residue numbers corresponding to each module. (b) The complex is oriented to highlight the interaction between the LRRCT insert and the active site cleft of HEL. (c) Structure of the complex between the camel single-domain VH antibody cAb-Lys3 (violet) and HEL (green) (Protein Data Bank accession code 1MEL). The orientation of HEL is similar to that in (b). (d) The complex between the shark single-domain VH antibody PBLA8 IgNAR (raspberry) and HEL (green) (1T6V).
Mentions: We determined the structure of the VLRB.2D-HEL complex to 2.2 Å resolution. VLRB.2D adopts a horseshoe-shaped solenoid fold characteristic of LRR proteins, including TLRs18 (Fig. 1a,b). The structure comprises an LRRNT, a 24-residue LRR1, two 24-residue LRRVs (LRRV1 and LRRVe), a 13-residue CP, and an LRRCT. The concave surface of VLRB.2D, through which the VLR binds HEL, is composed of six parallel β-strands (two from LRRNT, three from LRRVs, and one from CP) (Fig. 1a).

Bottom Line: The VLR-HEL structure combined with sequence analysis revealed an almost perfect match between ligand-contacting positions and positions with highest sequence diversity.Thus, it is likely that we have defined the generalized antigen-binding site of VLRs.We further demonstrated that VLRs can be affinity-matured by 13-fold to affinities as high as those of IgG antibodies, making VLRs potential alternatives to antibodies for biotechnology applications.

View Article: PubMed Central - PubMed

Affiliation: Center for Advanced Research in Biotechnology, WM Keck Laboratory for Structural Biology, University of Maryland Biotechnology Institute, Rockville, Maryland, USA.

ABSTRACT
Variable lymphocyte receptors (VLRs) are leucine-rich repeat proteins that mediate adaptive immunity in jawless vertebrates. VLRs are fundamentally different from the antibodies of jawed vertebrates, which consist of immunoglobulin (Ig) domains. We determined the structure of an anti-hen egg white lysozyme (HEL) VLR, isolated by yeast display, bound to HEL. The VLR, whose affinity resembles that of IgM antibodies, uses nearly all its concave surface to bind the protein, in addition to a loop that penetrates into the enzyme active site. The VLR-HEL structure combined with sequence analysis revealed an almost perfect match between ligand-contacting positions and positions with highest sequence diversity. Thus, it is likely that we have defined the generalized antigen-binding site of VLRs. We further demonstrated that VLRs can be affinity-matured by 13-fold to affinities as high as those of IgG antibodies, making VLRs potential alternatives to antibodies for biotechnology applications.

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