Table II. Ab sequence properties
PropertyscFv JL427scFv GL2IgM 2G9
VHVLVHVLVHVL
V gene familyVH3VL1VH4VK3VH4VK10
Germline genes, VV3-48*01LV1-47*01V4-31*06KV3-11*01V2-2*02KV10-96*01
DD2-02*01D5-05*01D1-1*01
JJ6*02LJ3*02J4*02KJ4*01J4*01KJ1*01
Number of R/S mutations (Kabat), CDRs8/14/12/00/10/00/0
FRs4/15/42/50/00/00/0
Number of R/S mutations (IMGT), CDRs6/02/11/00/10/00/0
FRs6/27/43/50/00/00/0
Junctional deletions/insertions (nucleotides)39/430/2826/83/05/06/5
VH Karray residue conservation, %1004350
  • Family assignments according to Kabat/Wu database (69). Germline assignments according to IgBLAST(blast.ncbi.nlm.nih.gov). V-(D)-J junctional deletions and insertions deduced using IMGT/V-QUEST (70). R/S ratio computation excludes mutations attributable to V-(D)-J junctional diversification and PCR primer-annealing region. The Kabat/Wu and IMGT/V-QUEST databases differ in demarcation of CDRs and FRs. R/S ratios computed from both databases are reported. R/S ratios predicted for a random mutational process are as follows: VL-CDRs, 3.56/1; VH-CDRs, 4.16/1; VL-FRs, 2.88/1; VH-FRs, 2.84/1 (71). GenBank accession numbers (http://www.ncbi.nlm.nih.gov/genbank/) for scFv JL427, scFv GL2, IgM 2G9 VH, and IgM 2G9 VL are, respectively, AF329462, JQ343847, JQ412130, and JQ343846. Replacement mutations in scFv V regions were (germline residues listed first, Kabat numbering): scFv JL427 VH, G16:R, S33:G, N35:H, S52:G, S52a:R, S54:G, T56:H, I57:T, Y58:N, A74:S, S77:T, M82:I; scFv JL427 VL, A11:V, T14:A, I28:F, S30:L, Q38:H, L39:F, S50:R, N52:D, D60:A; scFv GL2 VH GL2L, G10:R, E16:G, G32:S, S35b:G; scFv GL2 VL, none. IgM VL and VH regions contain no somatic mutations. scFv JL427 VH contains all 16 Karray residues, 15 encoded by the germline gene, and 1 acquired by somatic mutation (G10, Q13, R19, A23, T28, Y32, G54, K64, K65, Y79, Q81, N82a, R83, E85). scFv GL2 contains 3 identities (Y59, K64, K75), 4 conservative deviations (T28:S, Y32:S, Y79:S, N82a:S), and 9 nonconservative deviations at the Karray positions. Six of the 7 identities/conservations are germline gene encoded. Conservation of Karray residues was computed as in (23). IgM 2G9 contains 7 identities (G10, Q13, Y32, G54, Y59, K75, N82a), 1 conservative deviation (T28:S), and 8 nonconservative deviations at the Karray positions.