Bioorthogonal click labeling of an amber-free HIV-1 provirus for in-virus single molecule imaging

Structural dynamics of human immunodeficiency virus 1 (HIV -1) envelope (Env) glycoprotein mediate cell entry and facilitate immune evasion. Single -molecule FRET using peptides for Env labeling revealed structural dynamics of Env, but peptide use risks potential effects on structural integrity/dynamics. While incorporating noncanonical amino acids (ncAAs) into Env by amber stop-codon suppression, followed by click chemistry, offers a minimally invasive approach, this has proved to be technically challenging for HIV -1. Here, we develope an intact amber -free HIV -1 system that overcomes hurdles of preexisting viral amber codons. We achieved dual-ncAA incorporation into Env on amber -free virions, enabling single -molecule F & ouml;rster resonance energy transfer (smFRET) studies of click -labeled Env that validated the previous peptide -based labeling approaches by confirming the intrinsic propensity of Env to dynamically sample multiple conformational states. Amber -free click -labeled Env also enabled real-time tracking of single virion internalization and trafficking in cells. Our system thus permits in -virus bioorthogonal labeling of proteins, compatible with studies of virus entry, trafficking, and egress from cells.