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Article
Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment
BMC Biochemistry
  • Alex Stewart
  • Joseph S. Harrison, University of the Pacific
  • Lauren K. Regula
  • Jonathan R. Lai, Albert Einstein College of Medicine
ORCID
Joseph Harrison: 0000-0002-2118-6524
Document Type
Article
Department
Chemistry
DOI
10.1186/1471-2091-14-9
Publication Date
4-8-2013
Abstract

BACKGROUND: Analysis of factors contributing to high affinity antibody-protein interactions provides insight into natural antibody evolution, and guides the design of antibodies with new or enhanced function. We previously studied the interaction between antibody D5 and its target, a designed protein based on HIV-1 gp41 known as 5-Helix, as a model system [Da Silva, G. F.; Harrison, J. S.; Lai, J. R., Biochemistry, 2010, 49, 5464-5472]. Antibody D5 represents an interesting case study because it is derived from the VH1-69 germline segment; this germline segment is characterized by a hydrophobic second heavy chain complementarity determining region (HCDR2) that constitutes the major functional paratope in D5 and several antibodies derived from the same progenitor.

RESULTS: Here we explore side chain requirements for affinity and specificity in D5 using phage display. Two D5-based libraries were prepared that contained diversity in all three light chain complementarity determining regions (LCDRs 1-3), and in the third HCDR (HCDR3). The first library allowed residues to vary among a restricted set of six amino acids (Tyr/Ala/Asp/Ser/His/Pro; D5-Lib-I). The second library was designed based on a survey of existing VH1-69 antibody structures (D5-Lib-II). Both libraries were subjected to multiple rounds of selection against 5-Helix, and individual clones characterized. We found that selectants from D5-Lib-I generally had moderate affinity and specificity, while many clones from D5-Lib-II exhibited D5-like properties. Additional analysis of the D5-Lib-II functional population revealed position-specific biases for particular amino acids, many that differed from the identity of those side chains in D5.

CONCLUSIONS: Together these results suggest that there is some permissiveness for alternative side chains in the LCDRs and HCDR3 of D5, but that replacement with a minimal set of residues is not tolerated in this scaffold for 5-Helix recognition. This work provides novel information about this high-affinity interaction involving an antibody from the VH1-69 germline segment.

Creative Commons License
Creative Commons Attribution 4.0 International
Citation Information
Alex Stewart, Joseph S. Harrison, Lauren K. Regula and Jonathan R. Lai. "Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment" BMC Biochemistry Vol. 14 Iss. 9 (2013) p. 1 - 15 ISSN: 1471-2091
Available at: http://works.bepress.com/joseph-harrison/29/