Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment

Public Deposited
Analytics

Downloadable Content

Download PDF
Request Version for Screen Reader
Creator
  • Stewart, Alex
    • Other Affiliation: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
  • Harrison, Joseph S
    • Other Affiliation: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
  • Lai, Jonathan R
    • Other Affiliation: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
  • Regula, Lauren K
    • Other Affiliation: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
Abstract
  • 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.
Date of publication
DOI
Identifier
Resource type
  • Article
Rights statement
  • In Copyright
Rights holder
  • Alex Stewart et al.; licensee BioMed Central Ltd.
License
Journal title
  • BMC Biochemistry
Journal volume
  • 14
Journal issue
  • 1
Page start
  • 9
Language
  • English
Is the article or chapter peer-reviewed?
  • Yes
ISSN
  • 1471-2091
Bibliographic citation
  • BMC Biochemistry. 2013 Apr 08;14(1):9
Publisher
  • BioMed Central Ltd
Access right
  • Open Access
Date uploaded
  • April 12, 2013

Relations

Parents:

This work has no parents.

Items

Thumbnail Title Date Uploaded Visibility Actions
file details 1471-2091-14-9.pdf 2019-05-07 Public Download
file details 1471-2091-14-9.xml 2019-05-07 Public Download
file details Amino acid alignment of D5 and CR6261 variable domains; list of structures used for design of D5-Lib-II; design and CD characterization of 6-Helix-Fd; full competitive ELISA profiles. 2019-05-07 Public Download