Conformational engineering of HIV-1 Env based on mutational tolerance in the CD4 and PG16 bound states

Jeremiah D. Heredia, Jihye Park, Hannah Choi, Kevin S. Gill, Erik Procko

Research output: Contribution to journalArticle

Abstract

HIV-1 infection is initiated by viral Env engaging the host receptor CD4, triggering Env to transition from a “closed” to “open” conformation during the early events of virus-cell membrane fusion. To understand how Env sequence accommodates this conformational change, mutational landscapes decoupled from virus replication were determined for Env from BaL (clade B) and DU422 (clade C) isolates interacting with CD4 or antibody PG16 that preferentially recognizes closed trimers. Sequence features uniquely important to each bound state were identified, including glycosylation and binding sites. Notably, the Env apical domain and trimerization interface are under selective pressure for PG16 binding. Based on this key observation, mutations were found that increase presentation of quaternary epitopes associated with properly conformed trimers when Env is expressed at the plasma membrane. Many mutations reduce electrostatic repulsion at the Env apex and increase PG16 recognition of Env sequences from clades A and B. Other mutations increase hydrophobic packing at the gp120 inner-outer domain interface and were broadly applicable for engineering Env from diverse strains spanning tiers 1, 2, and 3 across clades A, B, C, and BC recombinants. Core mutations predicted to introduce steric strain in the open state show markedly reduced CD4 interactions. Finally, we demonstrate how our methodology can be adapted to interrogate interactions between membrane-associated Env and the matrix domain of Gag. These findings and methods may assist vaccine design. IMPORTANCE HIV-1 Env is dynamic and undergoes large conformational changes that drive fusion of virus and host cell membranes. Three Env proteins in a trimer contact each other at their apical tips to form a closed conformation that presents epitopes recognized by broadly neutralizing antibodies. The apical tips separate, among other changes, to form an open conformation that binds tightly to host receptors. Understanding how Env sequence facilitates these structural changes can inform the biophysical mechanism and aid immunogen design. Using deep mutational scans decoupled from virus replication, we report mutational landscapes for Env from two strains interacting with conformation-dependent binding proteins. Residues in the Env trimer interface and apical domains are preferentially conserved in the closed conformation, and conformational diversity is facilitated by electrostatic repulsion and an underpacked core between domains. Specific mutations are described that enhance presentation of the trimeric closed conformation across diverse HIV-1 strains.

Original languageEnglish (US)
Article numbere0021919
JournalJournal of virology
Volume93
Issue number11
DOIs
StatePublished - Jan 1 2019

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Human immunodeficiency virus 1
HIV-1
engineering
mutation
Mutation
electrostatic interactions
Cell Membrane
Virus Replication
virus replication
Static Electricity
epitopes
cell membranes
Epitopes
env Gene Products
Virus Internalization
viruses
CD4 Antigens
receptors
Cell Fusion
glycosylation

Keywords

  • Broadly neutralizing antibody
  • CD4
  • Conformational change
  • Deep mutational scan
  • Directed evolution
  • Env
  • Gp160
  • Human immunodeficiency virus
  • Protein engineering
  • Quaternary epitope

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology

Cite this

Conformational engineering of HIV-1 Env based on mutational tolerance in the CD4 and PG16 bound states. / Heredia, Jeremiah D.; Park, Jihye; Choi, Hannah; Gill, Kevin S.; Procko, Erik.

In: Journal of virology, Vol. 93, No. 11, e0021919, 01.01.2019.

Research output: Contribution to journalArticle

Heredia, Jeremiah D. ; Park, Jihye ; Choi, Hannah ; Gill, Kevin S. ; Procko, Erik. / Conformational engineering of HIV-1 Env based on mutational tolerance in the CD4 and PG16 bound states. In: Journal of virology. 2019 ; Vol. 93, No. 11.
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