Relaxation dynamics of tryptophan in water: A UV fluorescence up-conversion and molecular dynamics study

Unraveling the Photoionization Dynamics of Indole in Aqueous and Ethanol Solutions

The photoionization dynamics of indole, the ultraviolet-B chromophore of tryptophan, were explored in water and ethanol using ultrafast transient absorption spectroscopy with 292, 268, and 200 nm excitation. By studying the femtosecond-to-nanosecond dynamics of indole in two different solvents, a new photophysical model has been generated that explains many previously unsolved facets of indole's complex solution phase photochemistry. Photoionization is only an active pathway for indole in aqueous solution, leading to a reduction in the fluorescence quantum yield in water-rich environments, which is frequently used in biophysical experiments as a key signature of the protein-folded state. Photoionization of indole in aqueous solution was observed for all three pump wavelengths but via two different mechanisms. For 200 nm excitation, electrons are ballistically ejected directly into the bulk solvent. Conversely, 292 and 268 nm excitation populates an admixture of two 1ππ* states, which form a dynamic equilibrium with a tightly bound indole cation and electron-ion pair. The ion pair dissociates on a nanosecond time scale, generating separated solvated electrons and indole cations. The charged species serve as important precursors to triplet indole production and greatly enhance the overall intersystem crossing rate. Our proposed photophysical model for indole in aqueous solution is the most appropriate for describing photoinduced dynamics of tryptophan in polypeptide sequences; tryptophan in aqueous pH 7 solution is zwitterionic, unlike in peptides, and resultantly has a competitive excited state proton transfer pathway that quenches the tryptophan fluorescence.

Ultraviolet Superradiance from Mega-Networks of Tryptophan in Biological Architectures

Networks of tryptophan (Trp)─an aromatic amino acid with strong fluorescence response─are ubiquitous in biological systems, forming diverse architectures in transmembrane proteins, cytoskeletal filaments, subneuronal elements, photoreceptor complexes, virion capsids, and other cellular structures. We analyze the cooperative effects induced by ultraviolet (UV) excitation of several biologically relevant Trp mega-networks, thus giving insights into novel mechanisms for cellular signaling and control. Our theoretical analysis in the single-excitation manifold predicts the formation of strongly superradiant states due to collective interactions among organized arrangements of up to >105 Trp UV-excited transition dipoles in microtubule architectures, which leads to an enhancement of the fluorescence quantum yield (QY) that is confirmed by our experiments. We demonstrate the observed consequences of this superradiant behavior in the fluorescence QY for hierarchically organized tubulin structures, which increases in different geometric regimes at thermal equilibrium before saturation, highlighting the effect's persistence in the presence of disorder. Our work thus showcases the many orders of magnitude across which the brightest (hundreds of femtoseconds) and darkest (tens of seconds) states can coexist in these Trp lattices.

Examining the origins of observed terahertz modes from an optically pumped atomistic model protein in aqueous solution

The microscopic origins of terahertz (THz) vibrational modes in biological systems are an active and open area of current research. Recent experiments [Phys Rev X. 8, 031061 (2018)] have revealed the presence of a pronounced mode at ∼0.3 THz in fluorophore-decorated bovine serum albumin (BSA) protein in aqueous solution under nonequilibrium conditions induced by optical pumping. This result was heuristically interpreted as a collective elastic fluctuation originating from the activation of a low-frequency phonon mode. In this work, we show that the sub-THz spectroscopic response emerges in a statistically significant manner (> 2 σ ) from such collective behavior, illustrating how photoexcitation can alter specific THz vibrational modes. We revisit the theoretical analysis with proof-of-concept molecular dynamics that introduce optical excitations into the simulations. Using information theory techniques, we show that these excitations can give rise to a multiscale response involving two optically excited chromophores (tryptophans), other amino acids in the protein, ions, and water. Our results motivate new experiments and fully nonequilibrium simulations to probe these phenomena, as well as the refinement of atomistic models of Fröhlich condensates that are fundamentally determined by nonlinear interactions in biology.

Ultrafast Energy Transfer from Photoexcited Tryptophan to the Haem in Cytochrome c

We report femtosecond Fe K-edge absorption (XAS) and nonresonant X-ray emission (XES) spectra of ferric cytochrome C (Cyt c) upon excitation of the haem (>300 nm) or mixed excitation of the haem and tryptophan (<300 nm). The XAS and XES transients obtained in both excitation energy ranges show no evidence for electron transfer processes between photoexcited tryptophan (Trp) and the haem, but rather an ultrafast energy transfer, in agreement with previous ultrafast optical fluorescence and transient absorption studies. The reported (J. Phys. Chem. B 2011, 115 (46), 13723-13730) decay times of Trp fluorescence in ferrous (∼350 fs) and ferric (∼700 fs) Cyt c are among the shortest ever reported for Trp in a protein. The observed time scales cannot be rationalized in terms of Förster or Dexter energy transfer mechanisms and call for a more thorough theoretical investigation.

Environment-Driven Coherent Population Transfer Governs the Ultrafast Photophysics of Tryptophan

By combining UV transient absorption spectroscopy with sub-30-fs temporal resolution and CASPT2/MM calculations, we present a complete description of the primary photoinduced processes in solvated tryptophan. Our results shed new light on the role of the solvent in the relaxation dynamics of tryptophan. We unveil two consecutive coherent population transfer events involving the lowest two singlet excited states: a sub-50-fs nonadiabatic L_a → L_b transfer through a conical intersection and a subsequent 220 fs reverse L_b → L_a transfer due to solvent-assisted adiabatic stabilization of the L_a state. Vibrational fingerprints in the transient absorption spectra provide compelling evidence of a vibronic coherence established between the two excited states from the earliest times after photoexcitation and lasting until the back-transfer to L_a is complete. The demonstration of response to the environment as a driver of coherent population dynamics among the excited states of tryptophan closes the long debate on its solvent-assisted relaxation mechanisms and extends its application as a local probe of protein dynamics to the ultrafast time scales.

Initial Excited State Dynamics of Lumichrome upon Ultraviolet Excitation

Lumichrome (LC) is the major photodegradation product of biologically important flavin cofactors. Since LC serves as a structural comparison to the flavins; understanding excited states of LC is fundamentally important to establish a connection with photophysics of different flavins, such as lumiflavin (LF), riboflavin (RF), flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). Herein, we deduce the initial excited state structural dynamics of LC using UV resonance Raman (UVRR) intensity analysis. The UVRR spectra at wavelengths across the 260 nm absorption band of LC were measured and resulting Raman excitation profiles and absorption spectrum were self consistently simulated using a time-dependent wave packet formalism to extract the initial excited state structural and solvent broadening parameters. These results are compared with those obtained for other flavins following UV excitations. We find that LC undergoes a very distinct instantaneous charge redistribution than flavins, which is attributed to the extended π-conjugation present in flavins but missing in LC. The homogeneous broadening linewidth of LC appears to be lower than that of LF, while the inhomogeneous broadening values are comparable, indicating greater solvent interaction with excited flavin on ultrafast timescale compared to LC, whereas on longer timescale these interactions are almost similar.

Fluorescence of KCl Aqueous Solution: A Possible Spectroscopic Signature of Nucleation

Ion pairing in water solutions alters both the water hydrogen-bond network and ion solvation, modifying the dynamics and properties of electrolyte water solutions. Here, we report an anomalous intrinsic fluorescence of KCl aqueous solution at room temperature and show that its intensity increases with the salt concentration. From the ab initio density functional theory (DFT) and time-dependent DFT modeling, we propose that the fluorescence emission could originate from the stiffening of the hydrogen bond network in the hydration shell of solvated ion-pairs that suppresses the fast nonradiative decay and allows the slower radiative channel to become a possible decay pathway. Because computations suggest that the fluorophores are the local ion-water structures present in the prenucleation phase, this band could be the signature of the incoming salt precipitation.

The influence of aqueous solvent on the electronic structure and non-adiabatic dynamics of indole explored by liquid-jet photoelectron spectroscopy

Time-resolved photoelectron spectroscopy (TRPES) in a liquid micro-jet is implemented here to investigate the influence of water on the electronic structure and dynamics of indole, the chromophore of the amino acid tryptophan.

The interaction of photoexcited carbon nanodots with metal ions disclosed down to the femtosecond scale

Fluorescent carbon nanodots are a novel family of carbon-based nanoscale materials endowed with an outstanding combination of properties that make them very appealing for applications in nanosensing, photonics, solar energy harvesting and photocatalysis. One of the remarkable properties of carbon dots is their strong sensitivity to the local environment, especially to metal ions in solution. These interactions provide a testing ground for their marked photochemical properties, highlighted by many studies, and frequently driven by charge transfer events. Here we combine several optical techniques, down to femtosecond time resolution, to understand the interplay between carbon nanodots and aqueous metal ions such as Cu²⁺ and Zn²⁺. We find that copper inhibits the fluorescence of carbon dots through static and diffusional quenching mechanisms, and our measurements allow discriminating between the two. Ultrafast optical methods are then used to address the dynamics of copper-dot complexes, wherein static quenching takes place, and unveil the underlying complexity of their photocycle. We propose an initial increase of electronic charge on the surface of the dot, upon photo-excitation, followed by a partial electron transfer to the nearby ion, with 0.2 ps and 1.9 ps time constants, and finally a very fast (≪1 ps) non-radiative electron-hole recombination which brings the system back to the ground state. Notably, we find that the electron transfer stage is governed by an ultrafast water rearrangement around photo-excited dots, pointing out the key role of solvent interactions in the photo-physics of these systems.

Observation of the Global Dynamic Collectivity of a Hydration Shell around Apomyoglobin

Protein surface hydration is critical to the protein's structural properties and biological activities. However, it is still unknown whether the hydration shell is intrinsically connected and how its fluctuations dynamically interact with protein motion. Here, by selecting five site-specific locations with distinctly different environments around the surface of apomyoglobin, we used a tryptophan scan with femtosecond fluorescence spectroscopy and simultaneously detected hydration water dynamics and tryptophan side-chain relaxations with temperature dependence. We observed two types of relaxations for both interfacial hydration water and the tryptophan side chain. The former is always faster than the latter, and both motions show direct linear correlations with temperature changes, indicating one origin of their motions and hydration water driving of side-chain fluctuations. Significantly, we found the relaxation energy barriers are uniform across the entire protein surface, all less than 20 kJ/mol, strongly suggesting highly extended cooperative water networks and the nature of global dynamic collectivity of the entire hydration shell.

Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism

A major question remaining in glycobiology is how a glycosyltransferase (GT) that retains the anomeric linkage of a sugar catalyzes the reaction. Xyloside α-1,3-xylosyltransferase (XXYLT1) is a retaining GT that regulates Notch receptor activation by adding xylose to the Notch extracellular domain. Here, using natural acceptor and donor substrates and active Mus musculus XXYLT1, we report a series of crystallographic snapshots along the reaction, including an unprecedented natural and competent Michaelis reaction complex for retaining enzymes. These structures strongly support the SNi-like reaction as the retaining mechanism for XXYLT1. Unexpectedly, the epidermal growth factor-like repeat acceptor substrate undergoes a large conformational change upon binding to the active site, providing a structural basis for substrate specificity. Our improved understanding of this retaining enzyme will accelerate the design of retaining GT inhibitors that can modulate Notch activity in pathological situations in which Notch dysregulation is known to cause cancer or developmental disorders.

Mode-specific reorganization energies and ultrafast solvation dynamics of Tryptophan from Raman line-shape analysis

Tryptophan is widely used as an intrinsic fluorophore for studies of protein structure and dynamics. Its fluorescence is known to have two decay components with lifetimes of 0.5 and 3.1 ns. In this work we measure the ultrafast dynamics of Tryptophan at <100 fs through measurements and modeling of the Raman excitation profiles with time-dependent wave packet propagation theory. We use a Brownian oscillator model to simulate the water-tryptophan interaction. Upon photoexcitation to the higher singlet electronic state (Bb) the structure of tryptophan is distorted to an overall expansion of the pyrrole and benzene rings. The total reorganization energy for Trp in water is estimated to be 2169 cm(-1) with a 1230 cm(-1) contribution from the inertial response of water. The value of reorganization energy of water corresponding to the fast response is found to be higher than that obtained upon excitation to the La state by previous studies that used computational simulations. The long-time dynamics of Trp manifests as a conformational heterogeneity at shorter times and contributes to inhomogeneous broadening of the Raman profiles (315 cm(-1)).

Ultrafast Nonradiative Relaxation Channels of Tryptophan

The nonradiative relaxation channels of gas-phase tryptophan excited along the S1-S4 excited states (287-217 nm) have been tracked by femtosecond time-resolved ionization. In the low-energy region, λ ≥ 240 nm, the measured transient signals reflect nonadiabatic interactions between the two bright La and Lb states of ππ* character and the dark dissociative πσ* state of the indole NH. The observed dynamical behavior is interpreted in terms of the ultrafast conversion of the prepared La state, which simultaneously populates the fluorescent Lb> and the dissociative πσ* states. At higher energies, after excitation of the S4 state, the tryptophan dynamics diverges from that observed in indole, pointing to the opening of a relaxation channel that could involve states of the amino acid part. The work provides a detailed picture of the processes and electronic states involved in the relaxation of the molecule, after photoexcitation in the near part of its UV absorption spectrum.

Validation of response function construction and probing heterogeneous protein hydration by intrinsic tryptophan

Protein solvation dynamics usually occur on multiple time scales with site specificity, and the characterization of such heterogeneous dynamics requires a convenient optical probe. We proposed a tryptophan methodology, and with site-directed mutagenesis we can use a tryptophan scan to probe any desirable position around protein surfaces. Here, we report our extended solvation model for construction of response functions for probes such as tryptophan with multiple emission peaks and lifetimes. We show our systematic construction procedure and careful analyses of the possible missing percentage of an initial ultrafast component with the established zero-time emission spectrum and limited temporal resolution through two methods of the direct mapping of femtosecond-resolved fluorescence spectra (3D FRES) and the constructed FRES (2D) from the fluorescence transients. We unambiguously validate our extended model with reexamination of solvation dynamics (methanol, water, and proteins) using conventional dye coumarin, intrinsic tryptophan, and cofactor flavin. Using mutant proteins of GB1, we show again the generality of the powerful probe tryptophan for protein hydration (solvation) and the slowdown of the hydration layer dynamics especially at the water-protein interface. These results justify the necessity of our extended solvation model, clarify the confusion of protein hydration in the recent literature, and establish the universal optical probe of tryptophan for heterogeneous protein dynamics.

Femtosecond conical intersection dynamics of tryptophan in proteins and validation of slowdown of hydration layer dynamics

Water motion probed by intrinsic tryptophan shows the significant slowdown around protein surfaces, but it is unknown how the ultrafast internal conversion of two nearly degenerate states of Trp ((1)L(a) and (1)L(b)) affects the initial hydration in proteins. Here, we used a mini-protein with 10 different tryptophan locations one at a time through site-directed mutagenesis and extensively characterized the conversion dynamics of the two states. We observed all the conversion time scales in 40-80 fs by measurement of their anisotropy dynamics. This result is significant and shows no noticeable effect on the initial observed hydration dynamics and unambiguously validates the slowdown of hydration layer dynamics as shown here again in two mutant proteins.

Coherent manipulation of free amino acids fluorescence

Coherent manipulation of molecular wavepackets in biomolecules might contribute to the quest towards label-free cellular imaging and protein identification. We report the use of optimally tailored UV laser pulses in pump-probe depletion experiments that selectively enhance or decrease fluorescence between two aromatic amino acids: tryptophan (Trp) and tyrosine (Tyr). Selective fluorescence modulation is achieved with a contrast of ~35%. A neat modification of the time-dependent fluorescence depletion signal of Trp is observed, while the Tyr transient trace remains unchanged. The mechanism invoked for explaining the change of the depletion of Trp is a less efficient coupling between the fluorescing state and the higher non-radiative excited states by the optimally shaped pulse, than by the reference pulse.

Ultrafast photophysics of the isolated indole molecule

The relaxation dynamics of the isolated indole molecule has been tracked by femtosecond time-resolved ionization. The excitation region explored (283-243 nm) covers three excited states: the two ππ* L(b) and L(a) states, and the dark πσ* state with dissociative character. In the low energy region (λ > 273 nm) the transients collected reflect the absorption of the long living L(b) state. The L(a) state is met 1000-1500 cm(-1) above the L(b) origin, giving rise to an ultrafast lifetime of 40 fs caused by the internal conversion to the lower L(b) minimum through a conical intersection. An additional ~400 fs component, found at excitation wavelengths shorter than 263 nm, is ascribed to dynamics along the πσ* state, which is likely populated through coupling to the photoexcited L(a) state. The study provides a general view of the indole photophysics, which is driven by the interplay between these three excited surfaces and the ground state.