title: Side chain requirements for affinity and specificity in D5, an HIV-1 antibody derived from the VH1-69 germline segment.
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.
authors.affiliation: Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Stewart
authors.forename: Joseph S
authors.initials: JS
authors.lastname: Harrison
authors.forename: Lauren K
authors.initials: LK
authors.lastname: Regula
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Lai
mesh_terms: D000595:Amino Acid Sequence; D000915:Antibody Affinity; D022801:Complementarity Determining Regions / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015483:HIV Antibodies / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015700:HIV Envelope Protein gp41 / Q000276:immunology; D015497:HIV-1 / Q000378:metabolism; D006801:Humans; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry; D007147:Immunoglobulin Light Chains / Q000737:chemistry; D019151:Peptide Library; D017433:Protein Structure, Secondary
chemical_list: D022801:Complementarity Determining Regions; D015483:HIV Antibodies; D015700:HIV Envelope Protein gp41; D007143:Immunoglobulin Heavy Chains; D007147:Immunoglobulin Light Chains; D019151:Peptide Library; C514787:gp41 protein, Human immunodeficiency virus 1