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Contemporary HIV-1 consensus Env with AI-assisted redesigned hypervariable loops promote antibody binding

Nat Commun. 2024-05; 
Hongjun Bai, Eric Lewitus, Yifan Li, Paul V. Thomas, Michelle Zemil, Mélanie Merbah, Caroline E. Peterson, Thujitha Thuraisamy, Phyllis A. Rees, Agnes Hajduczki, Vincent Dussupt, Bonnie Slike, Letzibeth Mendez-Rivera, Annika Schmid, Erin Kavusak, Mekhala Rao, Gabriel Smith, Jessica Frey, Alicea Sims, Lindsay Wieczorek, Victoria Polonis, Shelly J. Krebs, Julie A. Ake, Sandhya Vasan, Diane L. Bolton, M. Gordon Joyce, Samantha Townsley & Morgane Rolland
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Gene Synthesis Sequences, codon-optimized for expression in human cells, were synthesized (Genscript) and cloned into a custom pcDNA3.4 (ThermoFisher) expression vector (plasmids are available with a Material Transfer Agreement). Get A Quote

摘要

An effective HIV-1 vaccine must elicit broadly neutralizing antibodies (bnAbs) against highly diverse Envelope glycoproteins (Env). Since Env with the longest hypervariable (HV) loops is more resistant to the cognate bnAbs than Env with shorter HV loops, we redesigned hypervariable loops for updated Env consensus sequences of subtypes B and C and CRF01_AE. Using modeling with AlphaFold2, we reduced the length of V1, V2, and V5 HV loops while maintaining the integrity of the Env structure and glycan shield, and modified the V4 HV loop. Spacers are designed to limit strain-specific targeting. All updated Env are infectious as pseudoviruses. Preliminary structural characterization suggests that the modified HV loo... More

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