Genetically encoded sensors of protein hydrodynamics and molecular proximity

• Published in: Proceedings of the National Academy of Sciences - PNAS 2015-05, Vol.112 (20), p.E2569-E2574
• Main Authors: Hoepker, Alexander C., Wang, Ariel, Le Marois, Alix, Suhling, Klaus, Yan, Yuling, Marriott, Gerard
• Format: Article
• Language: English
• Subjects: Bacterial proteins; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biochemistry; Biological Sciences; Bioluminescence; cdc42 GTP-Binding Protein - metabolism; DNA Primers - genetics; Escherichia coli; Fish; Fluid mechanics; Fluorescence Polarization - methods; Fluorescence Resonance Energy Transfer; Genetic Engineering - methods; Gram-negative bacteria; Hydrodynamics; Image Processing, Computer-Assisted; Luminescent Proteins - genetics; Luminescent Proteins - metabolism; Microscopy, Confocal; Molecular Probes - metabolism; Multiprotein Complexes - genetics; Multiprotein Complexes - metabolism; Photobacterium leiognathi; Plasmids - genetics; PNAS Plus; Protein synthesis; Proteins - analysis; Thrombin - analysis
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1424021112

Significance The lumazine binding protein (LUMP) emits a cyan-colored fluorescence and has the longest average fluorescence lifetime of any genetically encoded fluorescent protein complex. Coupled with a small mass of 20 kDa, LUMP and its fusion with capture sequences are exploited as unique sensors of protein hydrodynamics and are shown to enable quantitative fluorescence anisotropy imaging of specific target proteins in vitro and in vivo. Moreover, the surface location of the lumazine probe is shown to improve the efficiency of Förster resonance energy transfer (FRET) with the Venus acceptor protein compared with CFP, which is used in the development of a new class of FRET-based sensor. The specialized light organ of the ponyfish supports the growth of the bioluminescent symbiont Photobacterium leiognathi . The bioluminescence of P . leiognathi is generated within a heteromeric protein complex composed of the bacterial luciferase and a 20-kDa lumazine binding protein (LUMP), which serves as a Föörster resonance energy transfer (FRET) acceptor protein, emitting a cyan-colored fluorescence with an unusually long excited state lifetime of 13.6 ns. The long fluorescence lifetime and small mass of LUMP are exploited for the design of highly optimized encoded sensors for quantitative fluorescence anisotropy (FA) measurements of protein hydrodynamics. In particular, large differences in the FA values of the free and target-bound states of LUMP fusions appended with capture sequences of up to 20 kDa are used in quantitative FA imaging and analysis of target proteins. For example, a fusion protein composed of LUMP and a 5-kDa G protein binding domain is used as an FA sensor to quantify the binding of the GTP-bound cell division control protein 42 homolog (Cdc42) (21 kDa) in solution and within Escherichia coli . Additionally, the long fluorescence lifetime and the surface-bound fluorescent cofactor 6,7-dimethyl-8- (1′-dimethyl-ribityl) lumazine in LUMP are utilized in the design of highly optimized FRET probes that use Venus as an acceptor probe. The efficiency of FRET in a zero-length LUMP-Venus fusion is 62% compared to ∼31% in a related CFP-Venus fusion. The improved FRET efficiency obtained by using LUMP as a donor probe is used in the design of a FRET-optimized genetically encoded LUMP-Venus substrate for thrombin.