Last updated: 2023-06-27
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File | Version | Author | Date | Message |
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Rmd | c90d5b7 | Dave Tang | 2023-06-27 | CDR sequences |
html | b707032 | Dave Tang | 2023-06-26 | Build site. |
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.
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
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
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.
CDR-L1
CDR-L2
CDR-L3
CDR-H1
CDR-H2
CDR-H3
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