Oligomerization of the tetramerization domain of p53 probed by two- and three-color single-molecule FRET

Abstract

We describe a method that combines two-and three-color singlemolecule FRET spectroscopy with 2D FRET efficiency-lifetime analysis to probe the oligomerization process of intrinsically disordered proteins. This method is applied to the oligomerization of the tetramerization domain (TD) of the tumor suppressor protein p53. TD exists as a monomer at subnanomolar concentrations and forms a dimer and a tetramer at higher concentrations. Because the dissociation constants of the dimer and tetramer are very close, as we determine in this paper, it is not possible to characterize different oligomeric species by ensemble methods, especially the dimer that cannot be readily separated. However, by using single-molecule FRET spectroscopy that includes measurements of fluorescence lifetime and two-and three-color FRET efficiencies with corrections for submillisecond acceptor blinking, we show that it is possible to obtain structural information for individual oligomers at equilibrium and to determine the dimerization kinetics. From these analyses, we show that the monomer is intrinsically disordered and that the dimer conformation is very similar to that of the tetramer but the C terminus of the dimer is more flexible.single-molecule spectroscopy | three-color FRET | intrinsically disordered protein | p53 oligomerization | fluorescence lifetime I t is well known that intrinsically disordered proteins (IDPs) can fold into different structures when attaching to their binding targets. This structural flexibility and binding promiscuity are required for the formation of protein-protein interaction networks in various biological processes such as signal transduction and gene transcription (1-3). On the other hand, some IDPs selfassemble and form oligomers, many of which are implicated in the development of diseases such as Alzheimer's disease (amyloid-β protein) (4, 5) and Parkinson's disease (α-synuclein) (6). An ensemble of these oligomers with different sizes and conformations is not easy to separate, and therefore, their characterization is very difficult. However, single-molecule spectroscopy can be a very powerful tool because it can probe subpopulations in a mixture without the need for separation. Single-molecule spectroscopy has been successfully used for characterizing individual molecular states such as the folded and unfolded states of proteins (7-9), intermediate states (10, 11), and transition paths (12-17) and for identifying specific molecular species and complexes (18)(19)(20)(21)(22). In this paper, we describe the development of a singlemolecule fluorescence method that probes individual oligomers in a mixture, characterizes their conformations, and determines oligomerization kinetics.We have used two-and three-color Förster resonance energy transfer (FRET) spectroscopy. Compared with two-color FRET that monitors a single distance, three-color FRET can determine three distances and therefore has great potential to obtain 3D structural information for a molecule or a molecular complex. Multicolor FRET has been d...

Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation

“…2D FRET efficiency-lifetime analysis (51,56,61,(72)(73)(74)(75), which visualizes the correlation between the FRET efficiency and the donor fluorescence lifetime, provides further evidence that Ab is disordered. For this analysis, we collected trajectories of immobilized molecules illuminated by a picosecond-pulsed laser.…”

“…Details of free-diffusion, immobilization, and nsFCS experiments are described in the Supporting Material. For the accurate determination of the FRET efficiency and donor lifetime, we performed various corrections for background, donor leak into the acceptor channel, ratios of the detection efficiencies, and quantum yields of the donor and acceptor (g-factor) and acceptor blinking (55,56). See the Supporting Material for the details.…”

“…The single peak at E $ 0.6 can be explained by the protein having a single state on the millisecond timescale (the bin time is 2 ms). This state could be a disordered (unfolded) state as the FRET efficiency is similar to that of a 42-residue IDP, the tetramerization domain of p53 (56). It is also possible, however, that this state could be well structured.…”

Pitching Single-Focus Confocal Data Analysis One Photon at a Time with Bayesian Nonparametrics

“…Indeed, existing methods make assumptions that render them inapplicable to diffusion through inhomogeneously illuminated volumes. For example, they assume uniform illumination [24,29], apply downsampling or binning and thereby reduce temporal resolution to exploit existing mathematical frameworks such as the hidden Markov model [22,25,28,81,82], or focus on immobile molecules [25,[32][33][34]. More recently, fluorescence-based nanosecond FCS approaches, in which the data are still correlated under the assumption that the time trace reports on processes at equilibrium, have been used to obtain information on rapid fluctuations in proteins [35].…”

“…Previously proposed methods to analyze single-photon measurements [22][23][24][25][26][27][28][29][30] make assumptions that render them inappropriate for imaging molecules moving through inhomogeneously illuminated volumes [24]. For example, for the analysis of single molecule fluorescence resonance energy transfer (FRET), existing methods assume that the photon interarrival times reflect only biomolecular conformational transitions [24,25,31] but not diffusive motion of the entire biomolecule [25,[32][33][34], and so are appropriate only for experiments on immobilized molecules. Along the same lines, existing methods combine FRET with FCS [35] to quantify nanosecond dynamics; however, they do not directly exploit single-photon measurements.…”