Daven A. Armoogum

Multiple conformations of full-length p53 detected with single-molecule fluorescence resonance energy transfer

The tumor suppressor p53 is a member of the emerging class of proteins that have both folded and intrinsically disordered domains, which are a challenge to structural biology. Its N-terminal domain (NTD) is linked to a folded core domain, which has a disordered link to the folded tetramerization domain, which is followed by a disordered C-terminal domain. The quaternary structure of human p53 has been solved by a combination of NMR spectroscopy, electron microscopy, and small-angle X-ray scattering (SAXS), and the NTD ensemble structure has been solved by NMR and SAXS. The murine p53 is reported to have a different quaternary structure, with the N and C termini interacting. Here, we used single-molecule FRET (SM-FRET) and ensemble FRET to investigate the conformational dynamics of the NTD of p53 in isolation and in the context of tetrameric full-length p53 (flp53). Our results showed that the isolated NTD was extended in solution with a strong preference for residues 66–86 forming a polyproline II conformation. The NTD associated weakly with the DNA binding domain of p53, but not the C termini. We detected multiple conformations in flp53 that were likely to result from the interactions of NTD with the DNA binding domain of each monomeric p53. Overall, the SM-FRET results, in addition to corroborating the previous ensemble findings, enabled the identification of the existence of multiple conformations of p53, which are often averaged and neglected in conventional ensemble techniques. Our study exemplifies the usefulness of SM-FRET in exploring the dynamic landscape of multimeric proteins that contain regions of unstructured domains.

Regulation of 3-Phosphoinositide-Dependent Protein Kinase 1 Activity by Homodimerization in Live Cells

Spatial and temporal regulation of the homodimerization of PDK1 modulates its activity. Sticking Together The “master kinase” phosphoinositide-dependent kinase 1 (PDK1) plays a central role in such processes as cellular proliferation and survival and has a wide range of targets, including protein kinase B (PKB). PDK1 is downstream of phosphatidylinositol 3-kinase (PI3K), and the generation of phosphatidylinositol 3,4,5-trisphosphate (PIP3) triggers the translocation of PDK1 and PKB to the plasma membrane, where PDK1 phosphorylates PKB. Although the mechanisms by which PDK1 activates its substrates are well studied, less is known about how the activity of PDK1 is regulated. Masters et al. used a combination of Förster resonance energy transfer (FRET)–based analysis of fluorescently tagged proteins in live cells, as well as computational modeling, to show that a subset of cytosolic PDK1 exists in a homodimeric form. Disruption of the homodimeric interface increased the association between PDK1 and PKB, and this and other evidence suggested that monomeric—rather than dimeric—PDK1 was the active form. Together, these data suggest that homodimerization of PDK1 regulates its activity. 3-Phosphoinositide–dependent kinase 1 (PDK1) plays a central role in regulating the activity of protein kinases that are essential for signaling; however, how PDK1 itself is regulated is largely unknown. We found that homodimerization of PDK1 is a spatially and temporally regulated mechanism for controlling PDK1 activity. We used Förster resonance energy transfer monitored by fluorescence lifetime imaging microscopy to observe PDK1 homodimerization in live cells. A pleckstrin homology (PH) domain–dependent, basal dimeric association of PDK1 was increased upon cell stimulation with growth factors; this association was prevented by a phosphatidylinositol 3-kinase inhibitor and by a mutation in, or a complete deletion of, the PH domain of PDK1. The distinct spatial distribution of PDK1 homodimers relative to that of heterodimers of PDK1 and protein kinase B (PKB), and the ability of monomeric mutants of PDK1 to phosphorylate PKB, suggested that the monomer was the active conformation. Mutation of the autophosphorylation residue threonine-513 to glutamate, which was predicted to destabilize the homodimer interface, enhanced the interaction between PDK1 and PKB and the activity of PKB. Through in vitro, time-resolved fluorescence intensity and anisotropy measurements, combined with existing crystal structures and computational molecular modeling, we determined the geometrical arrangement of the PDK1 homodimer. With this approach, we calculated the size of the population of PDK1 dimers in cells. This description of a previously uncharacterized regulatory mechanism for the activation of PDK1 offers possibilities for controlling PDK1 activity therapeutically.

Stimulated emission depletion of two-photon excited states

Abstract Stimulated emission depletion of fluorescence (STED) from a two-photon excited molecular population is demonstrated for fluorescein in ethylene glycol and methanol. Time resolved fluorescence intensity and anisotropy measurements were made using picosecond time-correlated single photon counting (TCSPC). Pump–dump time delayed total fluorescence intensity measurements were used to characterise the response of the system and to provide additional data on the dump transition dynamics. Cross-sections for the stimulated transition in methanol and ethylene glycol were 1.4 and (3.6±1.0)×10 −16 cm 2 , respectively, the corresponding ground state vibrational lifetimes were 636 and 717±99 fs.

Restricted State Selection in Fluorescent Protein Forster Resonance Energy Transfer

The measurement of donor lifetime modification by Förster resonance energy transfer (FRET) is a widely used tool for detecting protein-protein interactions and protein conformation change. Such measurements can be compromised by the presence of a significant noninteracting fraction of molecules. Combining time-resolved intensity and anisotropy measurements gives access to both molecular distance and orientation. Fluorescent proteins frequently used to detect energy transfer in biological systems often exhibit decay characteristics indicative of more than one excited state. However, little attention has thus far been given to the specific modes of energy transfer, in particular, which states are predominantly coupled. Here, we use a previously characterized dimerization system to study energy transfer between EGFP and mCherry. Optically excited EGFP and mCherry both exhibit biexponential decays, and FRET should therefore involve dipole-dipole transfer between these four states. Analysis of the sensitized fluorescence anisotropy and intensity decays indicates that FRET transfer is predominantly from the shorter lived EGFP emitting state (2.43 ns) to the longer lived (ca. 2.77 ns) minority component (ca. 16%) of the optically excited mCherry emission. This high degree of state selection between these two widely used FRET pairs highlights the fundamental differences that can arise between direct optical excitation of an isotropic molecular population and dipole-dipole coupling in a far from isotropic interaction geometry and has consequences regarding the accurate interpretation of fluorescent protein FRET data.

Stimulated Emission Depletion and Fluorescence Correlation Spectroscopy of a Branched Quadrupolar Chromophore.

Stimulated emission depletion (STED) and single molecule fluorescence correlation spectroscopy (FCS) are used to determine stimulated emission cross-sections and investigate non-radiative relaxation in a branched quadrupolar chromophore (OM77). The results are used as inputs to simulations of single molecule STED by which the feasibility of STED control of the single molecule fluorescence cycle can be assessed. Single molecule STED in OM77 is shown to be readily achievable; however its effectiveness in reducing triplet trapping is apparently mediated by fast non-radiative relaxation processes other than intersystem crossing and rapid quenching of the triplet state in a non-deoxygenated environment.

Stimulated emission depletion dynamics in push-push polyenes

Two-photon fluorescence polarisation and stimulated emission depletion dynamics are investigated in three high two-photon cross-section push-push polyenes: OM62, LP79 and OM77 and compared to the behaviour of a standard fluorophore (rhodamine 6G). Two-photon fluorescence anisotropy measurements (R(0) and Omega) were undertaken using picosecond time-correlated single photon counting (TCSPC). For OM62 and LP79 these are consistent with a diagonal two-dimensional transition tensor with SXX>SYY. For OM77 the contribution of off-diagonal elements (SXY & SYX) appears significant. Two-photon fluorescence anisotropy decay data is combined with streak camera measurements of excited state population depletion to determine stimulated emission cross-sections and ground state vibrational relaxation times. Cross-sections for STED in all three polyenes were found to be significantly higher than those for rhodamine 6G. The efficiency of STED is however dependent on the degree to which the S1→S0 transition is saturated by the DUMP pulse; this is mediated by fast ground state vibrational relaxation. Of the three polyenes, LP79 is seen to combine a large stimulated emission cross-section (c.a. 13σ(r6G)) with rapid ground state relaxation (τR=240fs).

Stimulated emission depletion studies of molecular probe dynamics

Stimulated emission depletion (STED) population and polarisation dynamics are used to determine the degree of hexadecapole alignment created in ensembles of rhodamine 6G molecules in solution following two-photon excitation. Hexadecapole molecular alignment is an unavoidable consequence of two-photon excitation but is not observed in spontaneous emission. For a single element diagonal transition tensor measurements of the fluorescence anisotropy R(t) in systems undergoing small step isotropic rotational diffusion can in principle be used to determine . STED measurements of rhodamine 6G yield a value for that is larger than that predicted for a single element transition tensor (SXX). Recent work in our laboratory indicates that whilst SXX is dominant SYY, SXY and SYX are finite, measurements of appear to be a sensitive probe of the structure of the two-photon transition tensor. STED and fluorescence anisotropy measurements are extended to Rhodamine 6G in the isotropic phase of 5CB a system where small step isotropic rotational relaxation does not take place. Here the values of are considerably larger. These results are discussed in terms of the initial hexadecapole alignment and relaxation dynamics in a restricted geometry.

Time-resolved stimulated emission depletion and energy transfer dynamics in two-photon excited EGFP

Time and polarization-resolved stimulated emission depletion (STED) measurements are used to investigate excited state evolution following the two-photon excitation of enhanced green fluorescent protein (EGFP). We employ a new approach for the accurate STED measurement of the hitherto unmeasured degree of hexadecapolar transition dipole moment alignment α40 present at a given excitation-depletion (pump-dump) pulse separation. Time-resolved polarized fluorescence measurements as a function of pump-dump delay reveal the time evolution of α40 to be considerably more rapid than predicted for isotropic rotational diffusion in EGFP. Additional depolarization by homo-Förster resonance energy transfer is investigated for both α20 (quadrupolar) and α40 transition dipole alignments. These results point to the utility of higher order dipole correlation measurements in the investigation of resonance energy transfer processes.

Stimulated emission depletion following two photon excitation

The technique of stimulated emission depletion of fluorescence (STED) from a two photon excited molecular population is demonstrated in the S1 excited state of fluorescein in ethylene glycol and methanol. Two photon excitation (pump) is achieved using the partial output of a regeneratively amplified Ti:Sapphire laser in conjunction with an optical parametric amplifier whose tuneable output provides a synchronous depletion (dump) pulse. Time resolved fluorescence intensity and anisotropy measurements of the fluorescein emission are made using picosecond time-correlated single photon counting. Pump-dump time delayed fluorescence intensity measurements are used to characterise the response of the system and to provide additional data on saturation dynamics of the dump transition. Two photon STED is modelled using both approximate analytical techniques in the weak dump limit and by numerical solutions to the appropriate rate equations. The latter are used to fit experimental data from which it is possible to determine the cross-section for the stimulated transition and lifetime of the upper vibrational levels of the ground state.

Quadrupole and hexadecapole transition dipole moment alignment in fluorescent protein Homo-FRET

Polarized time resolved fluorescence measurements are used to characterise the structure of the two-photon tensor in the enhanced green fluorescent protein (EGFP) and predict the “hidden” degree of hexadecapole transition dipole alignment 〈α40〉 created by two-photon absorption (TPA). We employ a new method for the accurate STED measurement of the evolution of 〈α40〉 by analysing the saturation dynamics of the orthogonally polarized components of two-photon excited EGFP fluorescence as a function of the time delay between the 800 nm pump and 570 nm dump pulses. The relaxation of 〈α40〉 by homo-FRET is found to be considerably greater than that for the fluorescence anisotropy which directly measures the quadrupolar transition dipole moment alignment 〈α20〉. Our results indicate that higher order dipole moment correlation measurements promise to be a sensitive probe of resonance energy transfer dynamics.