Last updated: 2023-06-27

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Rmd c90d5b7 Dave Tang 2023-06-27 CDR sequences
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Rmd 9161c86 Dave Tang 2023-06-26 Learning about antibodies

Notes based on the study: Development of a humanized monoclonal antibody (MEDI-493) with potent in vitro and in vivo activity against respiratory syncytial virus.

This study describes the generation of a humanised monoclonal antibody, MEDI-493, that recognises a conserved neutralising epitope on the F glycoprotein of RSV. Broad neutralisation of a panel of 57 clinical isolates of the RSV A and B subtypes was demonstrated.

Antibody information

Additional info.

Fusion glycoprotein sequence

Fusion glycoprotein F0 of Human respiratory syncytial virus A (strain A2).

>sp|P03420|FUS_HRSVA Fusion glycoprotein F0 OS=Human respiratory syncytial virus A (strain A2) OX=11259 GN=F PE=1 SV=1
MELLILKANAITTILTAVTFCFASGQNITEEFYQSTCSAVSKGYLSALRTGWYTSVITIE
LSNIKENKCNGTDAKVKLIKQELDKYKNAVTELQLLMQSTPPTNNRARRELPRFMNYTLN
NAKKTNVTLSKKRKRRFLGFLLGVGSAIASGVAVSKVLHLEGEVNKIKSALLSTNKAVVS
LSNGVSVLTSKVLDLKNYIDKQLLPIVNKQSCSISNIETVIEFQQKNNRLLEITREFSVN
AGVTTPVSTYMLT NSELLSLINDMPITNDQKKLMSNN VQIVRQQSYSIMSIIKEEVLAYV
VQLPLYGVIDTPCWKLHTSPLCTTNTKEGSNICLTRTDRGWYCDNAGSVSFFPQAETCKV
QSNRVFCDTMNSLTLPSEINLCNVDIFNPKYDCKIMTSKTDVSSSVITSLGAIVSCYGKT
KCTASNKNRGIIKTFSNGCDYVSNKGMDTVSVGNTLYYVNKQEGKSLYVKGEPIINFYDP
LVFPSDEFDASISQVNEKINQSLAFIRKSDELLHNVNAGKSTTNIMITTIIIVIIVILLS
LIAVGLLLYCKARSTPVTLSKDQLSGINNIAFSN

Antibody sequence

Design of humanised VL and VH segments based on murine monoclonal antibody 1129. Human framework regions were derived from K102 for VL. VH framework (FR1) region was derived from Cor; remaining framework regions were derived from CE-1 sequence.

VL.

FR1                     CDR1       FR2             CDR2
DIQMTQSPSTLSASVGDRVTITC KCQLSVGYMH WYQQKPGKAPKLLIY DTSKLAS

FR3                              CDR3      FR4
GVPSRFSGSGSGTEFTLTISSLQPDDFATYYC FQGSGYPFT FGGGTKLEIK

VH.

FR1                            CDR1    FR2            CDR2
QVTLRESGPALVKPTQTLTLTCTFSGFSLS TSGMSVG WIRQPPGKALEWLA DIWWDDKKDYNPSLKS

FR3                              CDR3       FR4
RLTISKDTSKNQVVLKVTNMDPADTATYYCAR SMITNWYFDV WGAGTTVTVSS

Basics

Notes from Analysing antibody sequence for recombinant antibody expression.

The framework region is a subdivision of the variable region (Fab) of the antibody. The variable region is composed of seven amino acid regions, four of which are framework regions (FR1-4) and three of which are hypervariable regions. The framework region makes up about 85% of the variable region. Located on the tips of the Y-shaped molecule, the framework regions are responsible for acting as a scaffold for the complementarity determining regions (CDR), also referred to as hypervariable regions, of the Fab. These CDRs are in direct contact with the antigen and are involved in binding antigen, while the framework regions support the binding of the CDR to the antigen and aid in maintaining the overall structure of the four variable domains on the antibody.

Identifying CDRs by sequence

CDR-L1

  • Start - approximately residue 24
  • Residue before - always a Cys
  • Residue after - always a Trp. Typically Trp-Tyr-Gln, but also Trp-Leu-Gln, Trp-Phe-Gln, Trp-Tyr-Leu
  • Length - 10 to 17 residues

CDR-L2

  • Start - always 16 residues after the end of L1
  • Residue before - generally Ile-Tyr, but also, Val-Tyr, Ile-Lys, Ile-Phe
  • Length - always 7 residues (except NEW [7FAB], which has a deletion in this region.)

CDR-L3

  • Start - always 33 residues after end of L2 (except NEW [7FAB], which has the deletion at the end of CDR-L2)
  • Residue before - always Cys
  • Residue after - always Phe-Gly-XXX-Gly
  • Length - 7 to 11 residues

CDR-H1

  • Start - approximately residue 26 (always 4 after a Cys)
  • Residue before - always Cys-XXX-XXX-XXX
  • Residue after - always a Trp. Typically Trp-Val, but also, Trp-Ile, Trp-Ala
  • Length - 10 to 12 residues

CDR-H2

  • Start - always 15 residues after the end of Kabat / AbM definition of CDR-H1
  • Residue before - typically Leu-Glu-Trp-Ile-Gly, but a number of variations
  • Residue after - Lys/Arg-Leu/Ile/Val/Phe/Thr/Ala-Thr/Ser/Ile/Ala
  • Length - Kabat definition 16 to 19 residues

CDR-H3

  • Start - always 33 residues after end of CHR-H2 (always 2 after a Cys)
  • Residue before - always Cys-XXX-XXX (typically Cys-Ala-Arg)
  • Residue after - always Trp-Gly-XXX-Gly
  • Length - 3 to 25 residues

Leader sequence-FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4-Constant region-Stop codon


sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] lubridate_1.9.2 forcats_1.0.0   stringr_1.5.0   dplyr_1.1.2    
 [5] purrr_1.0.1     readr_2.1.4     tidyr_1.3.0     tibble_3.2.1   
 [9] ggplot2_3.4.2   tidyverse_2.0.0 workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] sass_0.4.5       utf8_1.2.3       generics_0.1.3   stringi_1.7.12  
 [5] hms_1.1.3        digest_0.6.31    magrittr_2.0.3   timechange_0.2.0
 [9] evaluate_0.20    grid_4.3.0       fastmap_1.1.1    rprojroot_2.0.3 
[13] jsonlite_1.8.5   processx_3.8.1   whisker_0.4.1    ps_1.7.5        
[17] promises_1.2.0.1 httr_1.4.5       fansi_1.0.4      scales_1.2.1    
[21] jquerylib_0.1.4  cli_3.6.1        rlang_1.1.0      munsell_0.5.0   
[25] withr_2.5.0      cachem_1.0.7     yaml_2.3.7       tools_4.3.0     
[29] tzdb_0.3.0       colorspace_2.1-0 httpuv_1.6.9     vctrs_0.6.2     
[33] R6_2.5.1         lifecycle_1.0.3  git2r_0.32.0     fs_1.6.2        
[37] pkgconfig_2.0.3  callr_3.7.3      pillar_1.9.0     bslib_0.4.2     
[41] later_1.3.0      gtable_0.3.3     glue_1.6.2       Rcpp_1.0.10     
[45] xfun_0.39        tidyselect_1.2.0 rstudioapi_0.14  knitr_1.42      
[49] htmltools_0.5.5  rmarkdown_2.21   compiler_4.3.0   getPass_0.2-2