Journal: bioRxiv

Article Title: Distinct allosteric remodeling of HIV-1 Env dynamics on virions by gp41-directed antibodies reveals two modes of neutralization

doi: 10.64898/2026.01.27.702099

Figure Lengend Snippet: ( A ) Genetic code expansion via amber suppression. Amber suppressor tRNA and tRNA synthetase (tRNA Pyl /NESPylRS AF ) incorporate the ncAA trans-cyclooct-2-en-L-lysine (TCO*A) at TAG codons engineered into Env (S401 TAG in gp120 and R542 TAG in gp41) on intact virions produced in mammalian cells. The supply of TCO*A to transfected cells enables its incorporation at the designated positions, providing reactive handles for subsequent fluorophore conjugation. ( B ) Bioorthogonal click labeling via SPIEDAC. Tetrazine-conjugated Cy3 and Cy5 derivatives (LD555-TTZ and LD655-TTZ) react with the strained alkene of TCO*A through strain-promoted inverse electron-demand Diels–Alder cycloaddition (SPIEDAC). The conjugated fluorophores (dyes) are depicted as red spheres. TCO*A Functional groups are shown in the modeled membrane-present Env trimers (right panel).

Article Snippet: The ncAA trans-cyclooct-2-en-L-lysine (TCO*A; SiChem #SC8008) was added to the culture medium at a final concentration of 250 μM.

Techniques: Produced, Transfection, Conjugation Assay, Labeling, Functional Assay, Membrane

Journal: The Journal of Biological Chemistry

Article Title: Evidence that non-cognate proteinogenic amino acids generate immunogenic neoepitopes

doi: 10.1016/j.jbc.2026.111349

Figure Lengend Snippet: Schematic representation of tRNA mischarging with a non-canonical amino acid (NCAA) . A proteinogenic NCAA can compete with a cognate amino acid for tRNA charging (aminoacylation) by the aminoacyl tRNA synthetase, and if not removed by a proofreading mechanism, can compete with the correctly charged tRNA for insertion into a protein.

Article Snippet: A potential link between the proteinogenic NCAA canavanine (2-amino-4-guanidinoxybutanoic acid) and a lupus-like syndrome was reported following the use of alfalfa ( Medicago sativa ) seeds to reduce plasma cholesterol levels ( , ).

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Evidence that non-cognate proteinogenic amino acids generate immunogenic neoepitopes

doi: 10.1016/j.jbc.2026.111349

Figure Lengend Snippet: Mechanisms increasing the antigenicity of a neoepitope due to the presence of an NCAA . Neoepitopes can be generated from endogenous and exogenous proteins by the action of proteases. The presence of an NCAA residue in the neoepitope can create an anchor that increases the binding affinity of the peptide towards the MHC molecule. An NCAA residue facing the T-cell receptor (TCR) binding site can increase the TCR-binding properties of the neoepitope, thereby enabling recognition by T-cells.

Article Snippet: A potential link between the proteinogenic NCAA canavanine (2-amino-4-guanidinoxybutanoic acid) and a lupus-like syndrome was reported following the use of alfalfa ( Medicago sativa ) seeds to reduce plasma cholesterol levels ( , ).

Techniques: Generated, Residue, Binding Assay