Backbone and methyl side-chain resonance assignments of the single chain Fab fragment of trastuzumab.
Escherichia coli
Fragment antigen binding
Monoclonal antibody
NMR spectroscopy
Trastuzumab
Journal
Biomolecular NMR assignments
ISSN: 1874-270X
Titre abrégé: Biomol NMR Assign
Pays: Netherlands
ID NLM: 101472371
Informations de publication
Date de publication:
08 May 2024
08 May 2024
Historique:
received:
25
03
2024
accepted:
30
04
2024
medline:
8
5
2024
pubmed:
8
5
2024
entrez:
8
5
2024
Statut:
aheadofprint
Résumé
Trastuzumab is a therapeutic monoclonal antibody developed to target human epidermal growth factor receptor 2 (HER2) present at higher levels in early cancers. Here we report the near complete resonance assignment of trastuzumab-scFab fragment backbone and the methyl groups of isoleucine, leucine and valine residues, as well as their stereo-assignments. The antibody fragment was produced using a single chain approach in Escherichia coli.
Identifiants
pubmed: 38717571
doi: 10.1007/s12104-024-10177-3
pii: 10.1007/s12104-024-10177-3
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. Crown.
Références
Alderson TR, Charlier Leejh, C., Ying, J., Bax A (2018) Propensity for cis-proline formation in unfolded proteins. ChemBioChem 19:37–42. https://doi.org/10.1002/cbic.201700548
doi: 10.1002/cbic.201700548
Bartels C, Billeter M, Guntert P, Wuthrich K (1996) Automated sequence-specific NMR assignment of homologous proteins using the program GARANT. J Biomol NMR 7:207–213. https://doi.org/10.1007/BF00202037
doi: 10.1007/BF00202037
Bishop AC, Torres-Montalvo G, Kotaru S, Mimun K, Wand AJ (2023) Robust automated backbone triple resonance NMR assignments of proteins using bayesian-based simulated annealing. Nat Commun 14:1556. https://doi.org/10.1038/s41467-023-37219-z
doi: 10.1038/s41467-023-37219-z
Brinson RG, Marino JP, Delaglio F, Arbogast LW, Evans R M, Kearsley A, Gingras G, Ghasriani H, Aubin Y, Pierens G K, et al. 2019. Enabling adoption of 2D-NMR for the higher order structure assessment of monoclonal antibody therapeutics MAbs 11:94–105. https://doi.org/10.1080/19420862.2018.1544454
doi: 10.1080/19420862.2018.1544454
Carmona FJ, Montemurro F, Kannan S, Rossi V, Baselga Vermac, J., Scaltriti M (2016) AKT signaling in ERBB2-amplified breast cancer. Pharmacol Ther 158:63–70. https://doi.org/10.1016/j.pharmthera.2015.11.013
doi: 10.1016/j.pharmthera.2015.11.013
Chao KL, O’Dell WB, Solomon TL, Brinson RG, Marino JP, Kelman Z (2023) Expression of 2H, 13 C, 15 N-labeled NIST-Fab fragment in the methylotrophic yeast Komagataella phaffii for nuclear magnetic resonance studies. EPJ Web Conf 286. https://doi.org/10.1051/epjconf/202328601003
Clubb RT, Wagner G (1992) A triple-resonance pulse scheme for selectively correlating amide 1HN and 15 N nuclei with the 1H alpha proton of the preceding residue. J Biomol NMR 2:389–394. https://doi.org/10.1007/BF01874816
doi: 10.1007/BF01874816
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J and Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
doi: 10.1007/BF00197809
Eletsky A, Kienhofer A, Pervushin K (2001) TROSY NMR with partially deuterated proteins. J Biomol NMR 20:177–180. https://doi.org/10.1023/a:1011265430149
doi: 10.1023/a:1011265430149
GagnÉ D, Sarker M, Gingras G, Hodgson DJ, Frahm G, Creskey M, Lorbetskie B, Bigelow S, Wang J, Zhang X, et al (2023) Strategies for the production of isotopically labelled Fab fragments of therapeutic antibodies in Komagataella phaffii (Pichia pastoris) and Escherichia coli for NMR studies. PLoS ONE 18:e0294406. https://doi.org/10.1371/journal.pone.0294406
doi: 10.1371/journal.pone.0294406
Goto NK, Gardner KH, Mueller GA, Willis RC and Kay LE (1999) A robust and cost-effective method for the production of Val, Leu, Ile (delta 1) methyl-protonated 15 N-, 13 C-, 2H-labeled proteins. J Biomol NMR 13:369–374. https://doi.org/10.1023/a:1008393201236
doi: 10.1023/a:1008393201236
Grzesiek S, Bax A (1993) Amino acid type determination in the sequential assignment procedure of uniformly 13 C/15 N-enriched proteins. J Biomol NMR 3:185–204. https://doi.org/10.1007/BF00178261
doi: 10.1007/BF00178261
Hafsa NE, Arndt D, Wishart DS (2015) CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts. Nucleic Acids Res 43:W370–W377. https://doi.org/10.1093/nar/gkv494
doi: 10.1093/nar/gkv494
Hodgson DJ, Ghasriani H, Aubin Y (2019) Assessment of the higher order structure of Humira®, Remicade®, Avastin®, Rituxan®, Herceptin®, and Enbrel® by 2D-NMR fingerprinting. J Pharm Biomed Anal 163:144–152. https://doi.org/10.1016/j.jpba.2018.09.056
doi: 10.1016/j.jpba.2018.09.056
Hudis CA (2007) Trastuzumab — mechanism of action and use in clinical practice. N Engl J Med 357:39–51. https://doi.org/10.1056/NEJMra043186
doi: 10.1056/NEJMra043186
Johnson BA, Blevins RA (1994) NMR view: a computer program for the visualization and analysis of NMR data. J Biomol NMR 4:603–614. https://doi.org/10.1007/BF00404272
doi: 10.1007/BF00404272
Kim S, Song J, Park S, Ham S, Paek K, Kang M, Chae Y, Seo H, Kim HC, and Flores M (2017) Drifts in ADCC-related quality attributes of Herceptin®: impact on development of a trastuzumab biosimilar. mAbs 9:704–714. https://doi.org/10.1080/19420862.2017.1305530
doi: 10.1080/19420862.2017.1305530
Lee W, Bahrami A, Dashti HT, Eghbalnia HR, Tonelli M, Westler WM and Markley JL (2019) I-PINE web server: an integrative probabilistic NMR assignment system for proteins. J Biomol NMR 73:213–222. https://doi.org/10.1007/s10858-019-00255-3
doi: 10.1007/s10858-019-00255-3
Maciejewski MW, Schuyler AD, GRYK MR, Moraru II, Romero PR, Ulrich EL, Eghbalnia HR, Livny M, Delaglio F and Hoch JC (2017) NMRbox: a resource for Biomolecular NMR computation. Biophys J 112:1529–1534. https://doi.org/10.1016/j.bpj.2017.03.011
Markley JL, Bax A, Arata Y, Hilbers CW, Kaptein R, Sykes BD, Wright PE , Wuthrich K (1998) Recommendations for the presentation of NMR structures of proteins and nucleic acids–IUPAC-IUBMB-IUPAB Inter-union Task Group on the standardization of data bases of protein and nucleic acid structures determined by NMR spectroscopy. Eur J Biochem 256:1–15. https://doi.org/10.1046/j.1432-1327.1998.2560001.x
doi: 10.1046/j.1432-1327.1998.2560001.x
Neri D, Szyperski T, Otting G, Senn H, Wuthrich K (1989) Stereospecific nuclear magnetic resonance assignments of the methyl groups of valine and leucine in the DNA-binding domain of the 434 repressor by biosynthetically directed fractional 13 C labeling. Biochemistry 28:7510–7516. https://doi.org/10.1021/bi00445a003
doi: 10.1021/bi00445a003
Nicholson KM, Anderson NG (2002) The protein kinase B/Akt signalling pathway in human malignancy. Cell Signal 14:381–395. https://doi.org/10.1016/S0898-6568(01)00271-6
doi: 10.1016/S0898-6568(01)00271-6
Patel A, Unni N, Peng Y (2020a) The changing paradigm for the treatment of HER2-Positive breast Cancer. Cancers [Online], 12
Patel A, Unni N, Peng Y (2020b) The changing paradigm for the treatment of HER2-Positive breast Cancer. Cancers(Basel) 12:2081–2097. https://doi.org/10.3390/cancers12082081
doi: 10.3390/cancers12082081
Salzmann M, Pervushin K, Wider G, Senn H, Wuthrich K (1998) TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. Proc Natl Acad Sci U S A 95:13585–13590. https://doi.org/10.1073/pnas.95.23.13585
doi: 10.1073/pnas.95.23.13585
Schulte L, Mao J, Reitz J, Sreeramulu S, Kudlinzki D, Hodirnau VV, Meier-Credo J, Saxena K, Buhr F, Langer JD, et al (2020) Cysteine oxidation and disulfide formation in the ribosomal exit tunnel. Nat Commun 11:5569. https://doi.org/10.1038/s41467-020-19372-x
doi: 10.1038/s41467-020-19372-x
Solomon TL, Chao K, Gingras G, Aubin Y, O’Dell WB, Marino JP, Brinson RG (2023) Backbone NMR assignment of the yeast expressed Fab fragment of the NISTmAb reference antibody. Biomol NMR Assignments. https://doi.org/10.1007/s12104-023-10123-9
doi: 10.1007/s12104-023-10123-9
Tian X, Wei F, Wang L, Yu W, Zhang N, Zhang X, Han Y, Yu J , Ren X (2017) Herceptin enhances the Antitumor Effect of Natural Killer cells on breast Cancer cells expressing human epidermal growth factor Receptor-2. Front Immunol 8:1426. https://doi.org/10.3389/fimmu.2017.01426
doi: 10.3389/fimmu.2017.01426
Tugarinov V, Kay LE (2003) Ile, Leu, and val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. J Am Chem Soc 125:13868–13878. https://doi.org/10.1021/ja030345s
doi: 10.1021/ja030345s
Tugarinov V, Kay LE (2004) Stereospecific NMR assignments of prochiral methyls, rotameric states and dynamics of valine residues in malate synthase G. J Am Chem Soc 126:9827–9836. https://doi.org/10.1021/ja048738u
doi: 10.1021/ja048738u
Yakes FM, Chinratanalab W, Ritter CA, King W, Seelig S , Arteaga CL (2002) Herceptin-induced inhibition of Phosphatidylinositol-3 kinase and akt is required for antibody-mediated effects on p27, cyclin D1, and Antitumor Action1. Cancer Res 62:4132–4141