Learning about antibodies

Last updated: 2023-06-26

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File	Version	Author	Date	Message
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.

UniProt Accession Number of Target Protein: P03420
Alternative Name(s) of Target: F2; Fusion glycoprotein F0; Protein F; F gycoprotein; Human respiratory syncytial virus; humanized mAb 129
Immunogen: The original antibody was generated by immunizing female BALB/c mice by primary intranasal infection with A2 strain of RSV.
Specificity: This antibody recognizes the site A of the RSV F glycoprotein. This antibody binds the NSELLSLINDMPITNDQKKLMSNN epitope (PMID: 20098425).

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.

An antibody (a.k.a. immunoglobulin) is a large Y-shaped protein produced by B cells. They are used by the immune system to neutralise foreign objects.
Fab region determines its antigen specificity (Fv region and CDR).
Fc region determines the effects.

Each antibody (Ab) only binds to a specific antigen (Ag).
Ab and Ag interact by spatial complementarity.
Ab-Ag interaction are based on weak and non-covalent binding between Ab and Ag:
- Electrostatic interactions
- Hydrogen bonds
- Van der Waals forces
- Hydrophobic interactions
The hinge region allows better binding.
Ab-Ag binding is reversible.

Ab binding residues are mainly located in Complementarity Determining Regions (CDRs)
6 CDRs form the combining site: L1, L2, L3, H1, H2, and H3
CDR-H3 and L3 have a distinctive role in antigen recognition.

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):
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 [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