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Table 3 Sequences and phage ELISA profiles of selected clones

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

  

Amino acid sequenceA

Phage ELISA signal ratioB

 

Library

Clone

HCDR3

LCDR1

LCDR2

LCDR3

5-Helix/BSA (ratio)

5-Helix/LF (ratio)

5-Helix/KLH (ratio)

F competitive C

 

D5 WT D

95 DNPTLL

28 GIYHW

49 YKASSL

91 YSNYPL

    

D5-Lib-I

6G10

DAPPSP

SPDYY

DASYYH

DDHSPY

0.4/0.1 (5)

0.4/0.2 (3)

0.4/0.1 (3)

1.0

 

6G12

DNPTLL

GIYHW

SDYYSY

HAA YPH

0.6/0.1 (6)

0.6/0.3 (2)

0.6/0.2 (3)

0.8

 

6D9

DYPHHY

GIYHW

YHDYYP

SYP DPH

0.4/0.1 (5)

0.4/0.2 (3)

0.4/0.1 (3)

0.7

 

6B11

SHPDDD

DDADD

PYYASD

YDDHPP

0.4/0.1 (5)

0.4/0.2 (2)

0.4/0.2 (2)

1.0

D5-Lib-II

25B8

DNPTLL

N I NRN

SR A SR L

RYNY P Y

2.9/0.1 (22)

2.9/0.1 (21)

2.9/0.2 (12)

0.2

 

25C10

DNPTLL

N I YGN

SR A SR L

RYTY P L

3.2/0.1 (34)

3.2/0.1 (33)

3.2/0.2 (18)

0.1

 

25D8

DNPTLL

G I SSN

SR A YR L

RATY P L

3.2/0.1 (30)

3.2/0.1 (22)

3.2/0.2 (18)

0.2

 

25A10

DNPTLL

S I SHN

SN A SR L

YSNYPL

3.2/0.1 (23)

3.2/0.1 (22)

3.2/0.2 (14)

0.1

 

25D9

DNPTLL

D I LGR

YR A SR L

RANY P L

3.0/0.1 (23)

3.0/0.1 (24)

3.0/0.2 (17)

0.2

 

25G8

DNPTLL

S I GRS

YR A SR L

SSTT P L

2.1/0.1 (24)

2.1/0.1 (25)

2.1/0.1 (16)

0.1

 

25C6

DNPTLL

N I SSR

SN A YH L

RSNY P H

1.8/0.1 (25)

1.8/0.1 (20)

1.8/0.1 (15)

0.2

 

25C12

DNPTLL

D I SSV

YN A SR L

RANN P H

2.2/0.1 (23)

2.2/0.1 (18)

2.2/0.2 (10)

0.3

 

25D6

DNPTLL

N I YSN

SS A SR L

NSNN P H

1.6/0.1 (21)

1.6/0.1 (19)

1.6/0.1 (14)

0.1

 

25D3

DNPTLL

N I HRR

YS A YS L

NSDY P H

1.6/0.1 (20)

1.6/0.1 (17)

1.6/0.2 (10)

0.1

 

25F1

DNPTLL

G I NNS

SR A SR L

YSST P H

2.3/0.1 (24)

2.3/0.1 (20)

2.3/0.1 (15)

0.1

 

25B6

DNPTLL

N I RSG

YR A SR L

YDDY P H

1.4/0.1 (16)

1.4/0.1 (15)

1.4/0.1 (11)

0.1

 

25F10

DNPTLL

G I HNR

SH A SN L

YSNY P L

1.7/0.1 (22)

1.7/0.1 (22)

1.7/0.1 (13)

0.1

 

25A12

DNPTLL

G I HRY

YH A SR L

RANY P Y

3.2/0.1 (27)

3.2/0.2 (20)

3.2/0.3 (12)

0.1

 

25A5

DNPTLL

S I RSH

SR A SR L

SSDY P H

3.5/0.1 (24)

3.5/0.1 (24)

3.5/0.2 (15)

0.1

 

16F6

DNPTLL

S I SSI

SN A SR L

RSNY P F

3.0/0.2 (13)

3.0/0.3 (11)

3.0/0.7 (4)

0.8

 

25C5

DNPTLL

D I HDY

SR A SR L

NDSY P Y

0.7/0.1 (10)

0.7/0.1 (8)

0.7/0.1 (6)

0.5

 

16D10

DNPTLL

N I RGS

YR A SR L

HSDY P H

3.0/0.1 (20)

3.0/0.2 (20)

3.0/0.5 (7)

0.7

 

16G6

DNPTLL

G I RRS

SN A SH L

YYNY P R

2.3/0.2 (14)

2.3/0.2 (12)

2.3/0.3 (7)

0.3

 

16B7

DNPTLL

N I LRL

YY A SS L

RADY P Y

3.0/0.1 (33)

3.0/0.1 (22)

3.0/0.5 (6)

0.6

 

16E12

DNPTLL

G I RRS

SN A SH L

YYNY P R

3.1/0.4 (9)

3.1/0.3 (12)

3.1/0.7 (5)

0.1

 

25F12

DNPTLL

G I IGH

YN A SR L

RDDY P L

2.7/0.1 (27)

2.7/0.1 (23)

2.7/0.2 (12)

0.2

 

25B4

DNPTLL

G I RNG

SR A SH L

YYAY P H

2.9/0.1 (29)

2.9/0.1 (31)

2.9/0.1 (22)

0.1

 

16E8

DNPTLL

S I YGS

SH A SH L

NDTY P H

3.0/0.1 (21)

3.0/0.2 (12)

3.0/0.3 (9)

0.4

 

25E1

DNPTLL

D I GGS

SH A YS L

HATY P H

3.0/0.1 (32)

3.0/0.1 (28)

3.0/0.2 (20)

0.1

 

25A6

DNPTLL

G I YDG

SR A YY L

RANY P H

3.1/0.2 (20)

3.1/0.1 (25)

3.1/0.2 (16)

0.1

 

16E3

DNPTLL

G I RYG

SR A SR L

HYAY P H

3.0/0.3 (11)

3.0/0.4 (8)

3.0/0.6 (5)

0.7

 

2H10

DNPTLL

D I YRS

SR A SR L

YSNYPL

1.9/0.1 (15)

1.9/0.1 (19)

1.9/0.2 (10)

0.1

 

25C4

DNPTLL

S I LGS

YR A SH L

YSNYPL

2.5/0.1 (32)

2.5/0.1 (26)

2.5/0.1 (19)

0.1

 

16F5

DNPTLL

N I NDH

SR A YR L

YADT P F

3.0/0.2 (19)

3.0/0.2 (12)

3.0/0.3 (11)

0.2

  1. A In cases where selection of the entire CDR was observed (for HCDR3 and LCDR3), the sequence is italicized. Positions that were not randomized are underlined.
  2. B For each clone, the raw ELISA signal (OD450) is shown against both 5-Helix and control proteins BSA, lactoferrin (LF), or keyhole limpet hemocyanin (KLH). The ratio of ELISA signals for 5-Helix over each of the three control proteins is shown in parentheses.
  3. C The reduction in ELISA signal observed upon preincubation with free 5-Helix (500 nM, D5-Lib-I; 40 nM, D5-Lib-II) as a fraction of the signal observed in the absence of the competitor.
  4. D Kabat numbering for the first residue of each CDR is shown for D5 WT.
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BMC Biochemistry

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