Conformational Changes Spanning Angstroms to Nanometers via a Combined Protein-Induced Fluorescence Enhancement-Förster Resonance Energy Transfer Method.
Förster resonance energy transfer (FRET)-based single-molecule techniques have revolutionized our understanding of conformational dynamics in biomolecular systems. Recently, a new single-molecule technique based on protein-induced fluorescence enhancement (PIFE) has aided studies in which minimal (<3 nm) displacements occur. Concerns have been raised regarding whether donor fluorophore intensity (and correspondingly fluorescence quantum yield Φf) fluctuations, intrinsic to PIFE methods, may adversely affect FRET studies when retrieving the donor-acceptor dye distance. Here, we initially show through revisions of Förster's original equation that distances may be calculated in FRET experiments regardless of protein-induced intensity (and Φf) fluctuations occurring in the donor fluorophore. We additionally demonstrate by an analysis of the recorded emission intensity and competing decay pathways that PIFE and FRET methods may be conveniently combined, providing parallel complementary information in a single experiment. Single-molecule studies conducted with Cy3- and ATTO647N-labeled RNA structures and the HCV-NS5B polymerase protein undergoing binding dynamics along the RNA backbone provide a case study to validate the results. The analysis behind the proposed method enables for PIFE and FRET changes to be disentangled when both FRET and PIFE fluctuate over time following protein arrival and, for example, sliding. A new method, intensity-FRET, is thus proposed to monitor conformational changes spanning from angstroms to nanometers.
Department of Chemistry and Center for Self-Assembled Chemical Structures (CSACS-CRMAA), McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
Yasser
Y
Gidi
Department of Biochemistry and Department of Medical Microbiology and Immunology, University of Alberta , 6020K Katz Group Centre, Edmonton, Alberta, Canada T6G 2E1.
Matthias
0000-0001-6213-5806
M
Götte
Department of Chemistry and Center for Self-Assembled Chemical Structures (CSACS-CRMAA), McGill University , 801 Sherbrooke Street West, Montreal, Quebec, Canada H3A 0B8.
Gonzalo
0000-0003-0064-1345
G
Cosa
D031541:Fluorescence Resonance Energy Transfer; D008968:Molecular Conformation; D053758:Nanoparticles / Q000737:chemistry*; D017361:Viral Nonstructural Proteins / Q000737:chemistry* / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase
D017361:Viral Nonstructural Proteins; C087036:NS-5 protein, hepatitis C virus; D012324:RNA-Dependent RNA Polymerase