Fluorescence Quenching Induced by Conformational Fluctuations in Unsolvated Polypeptides

Unnatural Amino Acids for Biological Spectroscopy and Microscopy

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Gas-phase Förster resonance energy transfer in mass-selected and trapped ions

Förster Resonance Energy transfer (FRET) is a nonradiative process that may occur from an electronically excited donor to an acceptor when the emission spectrum of the donor overlaps with the absorption spectrum of the acceptor. FRET experiments have been done in the gas phase based on specially designed mass-spectroscopy setups with the goal to obtain structural information on biomolecular ions labeled with a FRET pair (i.e., donor and acceptor dyes) and to shed light on the energy-transfer process itself. Ions are accumulated in a radio-frequency ion trap or a Penning trap where mass selection of those of interest takes place, followed by photoexcitation. Gas-phase FRET is identified from detection of emitted light either from the donor, the acceptor, or both, or from a fragmentation channel that is specific to the acceptor when electronically excited. The challenge associated with the first approach is the collection and detection of photons emitted from a thin ion cloud that is not easily accessible while the second approach relies both on the photophysical and chemical behavior of the acceptor. In this review, we present the different instrumentation used for gas-phase FRET, including a discussion of advantages and disadvantages, and examples on how the technique has provided important structural information that is not easily obtainable otherwise. Furthermore, we describe how the spectroscopic properties of the dyes are affected by nearby electric fields, which is readily discernable from experiments on simple model systems with alkyl or π-conjugated bridges. Such spectral changes can have a significant effect on the FRET efficiency. Ideas for new directions are presented at the end with special focus on cold-ion spectroscopy.

A Linear Ion Trap with an Expanded Inscribed Diameter to Improve Optical Access for Fluorescence Spectroscopy

We report a custom-geometry linear ion trap designed for fluorescence spectroscopy of gas-phase ions at ambient to cryogenic temperatures. Laser-induced fluorescence from trapped ions is collected from between the trapping rods, orthogonal to the excitation laser that runs along the axis of the linear ion trap. To increase optical access to the ion cloud, the diameter of the round trapping rods is 80% of the inscribed diameter, rather than the roughly 110% used to approximate purely quadrupolar electric fields. To encompass as much of the ion cloud as possible, the first collection optic has a 25.4 mm diameter and a numerical aperture of 0.6. The choice of geometry and collection optics yields 10⁷ detected photons/s from trapped rhodamine 6G ions. The trap is coupled to a closed-cycle helium refrigerator, which in combination with two 50 Ohm heaters enables temperature control to below 25 K on the rod electrodes. The purpose of the instrument is to broaden the applicability of fluorescence spectroscopy of gas-phase ions to cases where photon emission is a minority relaxation pathway. Such studies are important to understand how the microenvironment of a chromophore influences excited state charge transfer processes. Graphical Abstract ᅟ.

Laser-induced- and dispersed-fluorescence studies of rhodamine 590 and 640 ions formed by electrospray ionization: observation of fluorescence from highly-excited vibrational levels of S1 states

Fluorescence spectra of vibrationally very “hot” S₁ states were observed for the first time under gas phase conditions.

A cylindrical quadrupole ion trap in combination with an electrospray ion source for gas-phase luminescence and absorption spectroscopy

A relatively simple setup for collection and detection of light emitted from isolated photo-excited molecular ions has been constructed. It benefits from a high collection efficiency of photons, which is accomplished by using a cylindrical ion trap where one end-cap electrode is a mesh grid combined with an aspheric condenser lens. The geometry permits nearly 10% of the emitted light to be collected and, after transmission losses, approximately 5% to be delivered to the entrance of a grating spectrometer equipped with a detector array. The high collection efficiency enables the use of pulsed tunable lasers with low repetition rates (e.g., 20 Hz) instead of continuous wave (cw) lasers or very high repetition rate (e.g., MHz) lasers that are typically used as light sources for gas-phase fluorescence experiments on molecular ions. A hole has been drilled in the cylinder electrode so that a light pulse can interact with the ion cloud in the center of the trap. Simulations indicate that these modifications to the trap do not significantly affect the storage capability and the overall shape of the ion cloud. The overlap between the ion cloud and the laser light is basically 100%, and experimentally >50% of negatively charged chromophore ions are routinely photodepleted. The performance of the setup is illustrated based on fluorescence spectra of several laser dyes, and the quality of these spectra is comparable to those reported by other groups. Finally, by replacing the optical system with a channeltron detector, we demonstrate that the setup can also be used for gas-phase action spectroscopy where either depletion or fragmentation is monitored to provide an indirect measurement on the absorption spectrum of the ion.

Distance mapping in proteins using fluorescence spectroscopy: tyrosine, like tryptophan, quenches bimane fluorescence in a distance-dependent manner

Tryptophan-induced quenching of fluorophores (TrIQ) uses intramolecular fluorescence quenching to assess distances in proteins too small (<15 Å) to be easily probed by traditional Forster resonance energy transfer methods. A powerful aspect of TrIQ is its ability to obtain an ultrafast snapshot of a protein conformation, by identifying “static quenching” (contact between the Trp and probe at the moment of light excitation). Here we report new advances in this site-directed fluorescence labeling (SDFL) approach, gleaned from recent studies of T4 lysozyme (T4L). First, we show that like TrIQ, tyrosine-induced quenching (TyrIQ) occurs for the fluorophore bimane in a distance-dependent fashion, although with some key differences. The Tyr “sphere of quenching” for bimane (≤10 Å) is smaller than for Trp (≤15 Å, Cα–Cα distance), and the size difference between the quenching residue (Tyr) and control (Phe) differs by only a hydroxyl group. Second, we show how TrIQ and TyrIQ can be used together to assess the magnitude and energetics of a protein movement. In these studies, we placed a bimane (probe) and Trp or Tyr (quencher) on opposite ends of a “hinge” in T4L and conducted TrIQ and TyrIQ measurements. Our results are consistent with an ∼5 Å change in Cα–Cα distances between these sites upon substrate binding, in agreement with the crystal structures. Subsequent Arrhenius analysis suggests the activation energy barrier (E_a) to this movement is relatively low (∼1.5–2.5 kcal/mol). Together, these results demonstrate that TyrIQ, used together with TrIQ, significantly expands the power of quenching-based distance mapping SDFL studies.

A constitutively activating mutation alters the dynamics and energetics of a key conformational change in a ligand-free G protein-coupled receptor

G protein-coupled receptors (GPCRs) undergo dynamic transitions between active and inactive conformations. Usually, these conversions are triggered when the receptor detects an external signal, but some so-called constitutively activating mutations, or CAMs, induce a GPCR to bind and activate G proteins in the absence of external stimulation, in ways still not fully understood. Here, we investigated how a CAM alters the structure of a GPCR and the dynamics involved as the receptor transitions between different conformations. Our approach used site-directed fluorescence labeling (SDFL) spectroscopy to compare opsin, the ligand-free form of the GPCR rhodopsin, with opsin containing the CAM M257Y, focusing specifically on key movements that occur in the sixth transmembrane helix (TM6) during GPCR activation. The site-directed fluorescence labeling data indicate opsin is constrained to an inactive conformation both in detergent micelles and lipid membranes, but when it contains the M257Y CAM, opsin is more dynamic and can interact with a G protein mimetic. Further study of these receptors using tryptophan-induced quenching (TrIQ) methods indicates that in detergent, the CAM significantly increases the population of receptors in the active state, but not in lipids. Subsequent Arrhenius analysis of the TrIQ data suggests that, both in detergent and lipids, the CAM lowers the energy barrier for TM6 movement, a key transition required for conversion between the inactive and active conformations. Together, these data suggest that the lowered energy barrier is a primary effect of the CAM on the receptor dynamics and energetics.

Gas-phase fluorescence excitation and emission spectroscopy of three xanthene dyes (rhodamine 575, rhodamine 590 and rhodamine 6G) in a quadrupole ion trap mass spectrometer

The gas-phase fluorescence excitation, emission and photodissociation characteristics of three xanthene dyes (rhodamine 575, rhodamine 590, and rhodamine 6G) have been investigated in a quadrupole ion trap mass spectrometer. Measured gas-phase excitation and dispersed emission spectra are compared with solution-phase spectra and computations. The excitation and emission maxima for all three protonated dyes lie at higher energy in the gas phase than in solution. The measured Stokes shifts are significantly smaller for the isolated gaseous ions than the solvated ions. Laser power-dependence measurements indicate that absorption of multiple photons is required for photodissociation. Redshifts and broadening of the dispersed fluorescence spectra at high excitation laser power provide evidence of gradual heating of the ion population, pointing to a mechanism of sequential multiple-photon activation through absorption/emission cycling. The relative brightness in the gas phase follows the order R575(1.00) < R590(1.15) < R6G(1.29). Fluorescence emission from several mass-selected product ions has been measured.

Fluorescence lifetime probe of biomolecular conformations

Methods have been developed to measure the fluorescence lifetime versus temperature of trapped biomolecular ions derivatized with a fluorescent dye. Previous measurements for different sequences of polyproline peptides demonstrated that quenching rates are related to conformations and their spatial fluctuations. This paper presents the results of extending these methods to study the conformational dynamics of larger biomolecules. Vancomycin-peptide noncovalent complexes in the 1+ charge state were studied as a function of temperature for different W-KAA peptide chiralities (L-LDD, D-LDD, L-DLL). Fluorescence-quenching rates, k(q), were found to be stereoselective for these different chiralities with relative magnitudes k(q)(L-LDD) > k(q)(D-LDD) > k(q)(L-DLL). The variation in fluorescent quenching resulting from switching the chirality of the single Trp residue was readily detectable. Molecular dynamics analysis of complexes formed by W-KAA (L-LDD) and W-KAA(L-DLL) indicates that increased flexibility in the (L-DLL) complex is correlated with reduced quenching rates. Fluorescence measurements were also performed for the Trp-cage protein comparing quenching rates in the 1+, 2+, and 3+ charge states for which k(q)(+) >> k(q)(2+) approximately k(q)(3+). Measurements of a sequence including a single-point mutation infer the presence of a salt-bridge structure in the 1+ charge state and its absence in both the 2+ and 3+ states. Molecular dynamics structures of Trp-cage indicate that a salt bridge in the 1+ charge state produces more compact conformations leading to larger quenching rates based on the quenching mechanism. In both these experimental studies the fluorescence-quenching rates were consistent with changes in structure induced by either intermolecular or intramolecular interactions.