Difference between revisions of "Part:BBa K3410001"

Revision as of 02:46, 28 October 2020

Nanobody scaffold suitable for grafting.

cAbBCII-10 is a nanobody, originally isolated as an antibody capturing and neutralizing enzymes of the β-lactamase B class [1].
As CDR acceptor (also called "scaffold") we used the nanobody cAbBCII-10 [1] (or also NbBcII10 [2] or 3DWT [3], from here on called "3DWT"). This Nanobody is also available as part of a composite part in the iGEM parts reg (BBa_K2082001). However, the nanobody is not available as basic part, so we also contributed in submitting the basic part of cAbBCII-10 (BBa_K3410001). We used the sequence deposited in the PDB by Vincke et al. [2, 3].
Originally, 3DWT was isolated as an antibody capturing and neutralizing enzymes of the β-lactamase B class [1].

Figure 1: Map of the used nanobody scaffold 3DWT. Marked in purple are the CDRs 1 to 3 and in grey the framework regions. This map was generated with SnapGene.

References
[1] K. E. Conrath et al., “Beta-lactamase inhibitors derived from single-domain antibody fragments elicited in the camelidae,” Antimicrobial Agents and Chemotherapy, vol. 45, no. 10, pp. 2807–2812, 2001, doi: 10.1128/AAC.45.10.2807-2812.2001.
[2] C. Vincke, R. Loris, D. Saerens, S. Martinez-Rodriguez, S. Muyldermans, and K. Conrath, “General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold,” The Journal of biological chemistry, vol. 284, no. 5, pp. 3273–3284, 2009, doi: 10.1074/jbc.M806889200.
[3] C. e. a. Vincke, 3DWT: Structure of CabBCII-10 nanobody.
[4] S. W. Fanning and J. R. Horn, “An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop,” Protein science : a publication of the Protein Society, vol. 20, no. 7, pp. 1196–1207, 2011, doi: 10.1002/pro.648.
References [1] K. E. Conrath et al., “Beta-lactamase inhibitors derived from single-domain antibody fragments elicited in the camelidae,” Antimicrobial Agents and Chemotherapy, vol. 45, no. 10, pp. 2807–2812, 2001, doi: 10.1128/AAC.45.10.2807-2812.2001. [2] C. Vincke, R. Loris, D. Saerens, S. Martinez-Rodriguez, S. Muyldermans, and K. Conrath, “General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold,” The Journal of biological chemistry, vol. 284, no. 5, pp. 3273–3284, 2009, doi: 10.1074/jbc.M806889200. [3] C. e. a. Vincke, 3DWT: Structure of CabBCII-10 nanobody. [4] S. W. Fanning and J. R. Horn, “An anti-hapten camelid antibody reveals a cryptic binding site with significant energetic contributions from a nonhypervariable loop,” Protein science : a publication of the Protein Society, vol. 20, no. 7, pp. 1196–1207, 2011, doi: 10.1002/pro.648. [5] D. Saerens et al., “Identification of a universal VHH framework to graft non-canonical antigen-binding loops of camel single-domain antibodies,” Journal of molecular biology, vol. 352, no. 3, pp. 597–607, 2005, doi: 10.1016/j.jmb.2005.07.038.

Sequence and Features