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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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Comparison of ligand recognition by LRR family proteins. (a) Superposition of the VLRB.2D-HEL and GpIbα-VWF (1M10) complexes. VLRB.2D is delineated as an orange α-carbon trace, GpIbα as a blue trace, VWF-A1 domain as a rose trace and HEL as a surface representation in green. (b) Superposition of the VLRB.2D-HEL and VLR RBC36-H-trisaccharide (3E6J) complexes. RBC36 is shown as a gray α-carbon trace; H-trisaccharide is drawn in stick presentation.
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Figure 2: Comparison of ligand recognition by LRR family proteins. (a) Superposition of the VLRB.2D-HEL and GpIbα-VWF (1M10) complexes. VLRB.2D is delineated as an orange α-carbon trace, GpIbα as a blue trace, VWF-A1 domain as a rose trace and HEL as a surface representation in green. (b) Superposition of the VLRB.2D-HEL and VLR RBC36-H-trisaccharide (3E6J) complexes. RBC36 is shown as a gray α-carbon trace; H-trisaccharide is drawn in stick presentation.

Mentions: The VLRB.2D-HEL complex buries a total surface of 1685 Å2, similar to the surface buried in complexes between Ig-based antibodies and protein antigens (1400-2300 Å2)13, including the camel cAb-Lys3 VHH-HEL and shark PBLA8 IgNAR-HEL complexes (1706 and 1604 Å2, respectively)14,16, in which the camel and shark antibodies, which contain only a single VH domain, target nearly the same HEL epitope as VLRB.2D (Fig. 1b-d). The VLRB.2D-HEL complex is also reminiscent of the interaction between platelet receptor glycoprotein Ibα (GpIbα), a close structural relative of VLRB.2D (Z-score = 11.9 in a Dali structure homolog search; http://www2.ebi.ac.uk/dali/fssp/), and its protein ligand, von Willebrand factor (VWF)19 (Fig. 2a). However, HEL is shifted towards LRRCT and does not contact LRRNT, whereas VWF engages both N- and C-terminal capping modules of GpIbα. In this respect, the VLRB.2D-HEL complex resembles the VLR RBC36-H-trisaccharide complex4 (Fig. 2b). Of the total buried surface in VLRB.2D-HEL, the LRR (LRR1, LRRV1 and LRRVe), CP and LRRCT modules contribute 27%, 15% and 58%, respectively (Fig. 3a). The interface is characterized by moderate shape complementarity, based on a shape correlation statistic (Sc)20 of 0.67, compared to 0.77 and 0.71 for the cAb-Lys3 VHH-HEL and PBLA8 IgNAR-HEL complexes14,16, respectively.


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)

Comparison of ligand recognition by LRR family proteins. (a) Superposition of the VLRB.2D-HEL and GpIbα-VWF (1M10) complexes. VLRB.2D is delineated as an orange α-carbon trace, GpIbα as a blue trace, VWF-A1 domain as a rose trace and HEL as a surface representation in green. (b) Superposition of the VLRB.2D-HEL and VLR RBC36-H-trisaccharide (3E6J) complexes. RBC36 is shown as a gray α-carbon trace; H-trisaccharide is drawn in stick presentation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2722044&req=5

Figure 2: Comparison of ligand recognition by LRR family proteins. (a) Superposition of the VLRB.2D-HEL and GpIbα-VWF (1M10) complexes. VLRB.2D is delineated as an orange α-carbon trace, GpIbα as a blue trace, VWF-A1 domain as a rose trace and HEL as a surface representation in green. (b) Superposition of the VLRB.2D-HEL and VLR RBC36-H-trisaccharide (3E6J) complexes. RBC36 is shown as a gray α-carbon trace; H-trisaccharide is drawn in stick presentation.
Mentions: The VLRB.2D-HEL complex buries a total surface of 1685 Å2, similar to the surface buried in complexes between Ig-based antibodies and protein antigens (1400-2300 Å2)13, including the camel cAb-Lys3 VHH-HEL and shark PBLA8 IgNAR-HEL complexes (1706 and 1604 Å2, respectively)14,16, in which the camel and shark antibodies, which contain only a single VH domain, target nearly the same HEL epitope as VLRB.2D (Fig. 1b-d). The VLRB.2D-HEL complex is also reminiscent of the interaction between platelet receptor glycoprotein Ibα (GpIbα), a close structural relative of VLRB.2D (Z-score = 11.9 in a Dali structure homolog search; http://www2.ebi.ac.uk/dali/fssp/), and its protein ligand, von Willebrand factor (VWF)19 (Fig. 2a). However, HEL is shifted towards LRRCT and does not contact LRRNT, whereas VWF engages both N- and C-terminal capping modules of GpIbα. In this respect, the VLRB.2D-HEL complex resembles the VLR RBC36-H-trisaccharide complex4 (Fig. 2b). Of the total buried surface in VLRB.2D-HEL, the LRR (LRR1, LRRV1 and LRRVe), CP and LRRCT modules contribute 27%, 15% and 58%, respectively (Fig. 3a). The interface is characterized by moderate shape complementarity, based on a shape correlation statistic (Sc)20 of 0.67, compared to 0.77 and 0.71 for the cAb-Lys3 VHH-HEL and PBLA8 IgNAR-HEL complexes14,16, respectively.

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.

Show MeSH