NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells

TLDR

Protein‑fragment complementation assays are common for probing protein interactions, yet their fragments are structurally compromised and poorly characterized for accurate assessment. The authors engineered NanoBiT, a NanoLuc‑based complementation reporter, to improve accuracy in measuring protein interactions. NanoBiT’s 1.3‑kDa peptide and 18‑kDa polypeptide subunits weakly associate (KD ≈ 190 µM, kon = 500 M⁻¹ s⁻¹, koff = 0.2 s⁻¹), and their luminescent assembly reflects the interaction of appended target proteins, as validated with SME‑1 β‑lactamase and cellular FRB/FKBP fusions showing rapid, reversible, temperature‑robust dynamics. NanoBiT accurately quantified kinase‑inhibitor pharmacology that promotes BRAF–CRAF interaction, demonstrating reliable, dynamic representation of protein interactions in cells.

Abstract

Protein-fragment complementation assays (PCAs) are widely used for investigating protein interactions. However, the fragments used are structurally compromised and have not been optimized nor thoroughly characterized for accurately assessing these interactions. We took advantage of the small size and bright luminescence of NanoLuc to engineer a new complementation reporter (NanoBiT). By design, the NanoBiT subunits (i.e., 1.3 kDa peptide, 18 kDa polypeptide) weakly associate so that their assembly into a luminescent complex is dictated by the interaction characteristics of the target proteins onto which they are appended. To ascertain their general suitability for measuring interaction affinities and kinetics, we determined that their intrinsic affinity (KD = 190 μM) and association constants (kon = 500 M(-1) s(-1), koff = 0.2 s(-1)) are outside of the ranges typical for protein interactions. The accuracy of NanoBiT was verified under defined biochemical conditions using the previously characterized interaction between SME-1 β-lactamase and a set of inhibitor binding proteins. In cells, NanoBiT fusions to FRB/FKBP produced luminescence consistent with the linear characteristics of NanoLuc. Response dynamics, evaluated using both protein kinase A and β-arrestin-2, were rapid, reversible, and robust to temperature (21-37 °C). Finally, NanoBiT provided a means to measure pharmacology of kinase inhibitors known to induce the interaction between BRAF and CRAF. Our results demonstrate that the intrinsic properties of NanoBiT allow accurate representation of protein interactions and that the reporter responds reliably and dynamically in cells.