Ultrafast dynamics of nonequilibrium resonance energy transfer and probing globular protein flexibility of myoglobin

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.

Dynamics and mechanism of light harvesting in UV photoreceptor UVR8

Photosynthetic pigments form light-harvesting networks to enable nearly perfect quantum efficiency in photosynthesis via excitation energy transfer. However, similar light-harvesting mechanisms have not been reported in light sensing processes in other classes of photoreceptors during light-mediated signaling. Here, based on our earlier report, we mapped out a striking energy-transfer network composed of 26 structural tryptophan residues in the plant UV-B photoreceptor UVR8. The spectra of the tryptophan chromophores are tuned by the protein environments, funneling all excitation energy to a cluster of four tryptophan residues, a pyramid center, where the excitation-induced monomerization is initiated for cell signaling. With extensive site-directed mutagenesis, various time-resolved fluorescence techniques, and combined QM/MM simulations, we determined the energy-transfer rates for all donor–acceptor pairs, revealing the time scales from tens of picoseconds to nanoseconds. The overall light harvesting quantum efficiency by the pyramid center is significantly increased to 73%, compared to a direct excitation probability of 35%. UVR8 is the only photoreceptor discovered so far using a natural amino-acid tryptophan without utilizing extrinsic chromophores to form a network to carry out both light harvesting and light perception for biological functions.

The light-harvesting network from distal and peripheral to central tryptophans with transfer efficiencies determined from measured energy-transfer rates.

A leap in quantum efficiency through light harvesting in photoreceptor UVR8

Plants utilize a UV-B (280 to 315 nm) photoreceptor UVR8 (UV RESISTANCE LOCUS 8) to sense environmental UV levels and regulate gene expression to avoid harmful UV effects. Uniquely, UVR8 uses intrinsic tryptophan for UV-B perception with a homodimer structure containing 26 structural tryptophan residues. However, besides 8 tryptophans at the dimer interface to form two critical pyramid perception centers, the other 18 tryptophans’ functional role is unknown. Here, using ultrafast fluorescence spectroscopy, computational methods and extensive mutations, we find that all 18 tryptophans form light-harvesting networks and funnel their excitation energy to the pyramid centers to enhance light-perception efficiency. We determine the timescales of all elementary tryptophan-to-tryptophan energy-transfer steps in picoseconds to nanoseconds, in excellent agreement with quantum computational calculations, and finally reveal a significant leap in light-perception quantum efficiency from 35% to 73%. This photoreceptor is the first system discovered so far, to be best of our knowledge, using natural amino-acid tryptophans to form networks for both light harvesting and light perception.

Photoreceptor UVR8 in plants senses environmental UV levels through 26 structural tryptophan residues, but the role of 18 of them was unknown. The authors show, by experiments and computations, how these form a light-harvesting network that funnels the excitation to the pyramid centers enhancing the light-perception efficiency.

Does Fungicide "Dodine" Unfold Protein like Kosmo-Chaotropic Agent?

The nontargeted action of fungicides affects the structure of protein, which leads to several serious diseases such as nausea, cancer, fetus malformations, movement dysfunction, and behavioral changes in human and animals. Hence, understanding of the structural change in protein induced by fungicides is of utmost importance to decode its mode of nontargeted action. In this study, we have investigated the structural change of myoglobin by an important fungicide, namely, dodine (n-dodecylguanidinium acetate), as well as its analogues n-hexylguanidinium acetate (HGA) and guanidinium chloride (GdmCl) using spectroscopic and thermodynamic methods. The amount of dodine and HGA required for the unfolding of myoglobin is significantly less than GdmCl. GdmCl, dodine, and HGA unfold the myoglobin by decreasing the content of the helical and tertiary structures. However, the decrease in the content of tertiary structure is significantly higher than that of the secondary structure for dodine and HGA, in contrast to GdmCl, where the decrease in secondary and tertiary contents of protein is not biased. Thermodynamic and spectroscopic data depict that the unfolding of the dodine and HGA is driven by the hydrophobic interaction, whereas the hydrogen bonding of GdmCl with the amino acids of protein plays a key role in the unfolding. The long alkyl chain of dodine and HGA get accommodated at the surface of the helices of myoglobin, inducing strong hydrophobic interaction, which causes its unfolding. This study depicts that dodine unfolds protein by the chaotropic effect in which its hydrocarbon chain destabilizes the protein by the hydrophobic effect, unlike in an earlier study, where dodine was claimed to be a kosmo-chaotropic agent as its hydrocarbon group stabilizes the protein.

Can Förster Theory Describe Stereoselective Energy Transfer Dynamics in a Protein-Ligand Complex?

Förster resonance energy transfer (FRET) reactions involving ligands and aromatic amino acids can substantially impact the fluorescence properties of a protein-ligand complex, an impact intimately related to the corresponding binding mode. Structural characterization of such binding events in terms of intermolecular distances can be done through the well-known R^-6 distance-dependent Förster rate expression. However, such an interpretation suffers from uncertainties underlying Förster theory in the description of the electronic coupling that promotes FRET, mostly related to the dipole-dipole orientation factor, dielectric screening effects, and deviations from the ideal dipole approximation. Here, we investigate how Förster approximations impact the prediction of energy transfer dynamics in the complex between flurbiprofen (FBP) and human serum albumin (HSA), as well as a model FBP-Trp dyad, in which recent observation of enantioselective fluorescence quenching has been ascribed to energy transfer from FBP to Trp. To this end, we combine classical molecular dynamics simulations with polarizable quantum mechanics/molecular mechanics calculations that allow overcoming Förster approximations. On the basis of our results, we discuss the potential of structure-based simulations in the characterization of drug-binding events through fluorescence techniques. Overall, we find an excellent agreement between theory and experiment both in terms of enantioselectivity and FRET times, thus strongly supporting the reliability of the binding modes proposed for the (S) and (R) enantiomers of FBP. In particular, we show that the dynamic quenching arises from a small fraction of drug bound to the secondary site of HSA at the interface between subdomains IIA and IIB, whereas the enantioselectivity arises from the larger flexibility of the (S)-FBP enantiomer in the binding pocket.

Electron transfer mechanisms of DNA repair by photolyase

Photolyase is a flavin photoenzyme that repairs two DNA base damage products induced by ultraviolet (UV) light: cyclobutane pyrimidine dimers and 6-4 photoproducts. With femtosecond spectroscopy and site-directed mutagenesis, investigators have recently made significant advances in our understanding of UV-damaged DNA repair, and the entire enzymatic dynamics can now be mapped out in real time. For dimer repair, six elementary steps have been characterized, including three electron transfer reactions and two bond-breaking processes, and their reaction times have been determined. A unique electron-tunneling pathway was identified, and the critical residues in modulating the repair function at the active site were determined. The dynamic synergy between the elementary reactions for maintaining high repair efficiency was elucidated, and the biological nature of the flavin active state was uncovered. For 6-4 photoproduct repair, a proton-coupled electron transfer repair mechanism has been revealed. The elucidation of electron transfer mechanisms and two repair photocycles is significant and provides a molecular basis for future practical applications, such as in rational drug design for curing skin cancer.

Cellular metabolites modulate in vivo signaling of Arabidopsis cryptochrome-1

Cryptochromes are blue-light absorbing flavoproteins with multiple signaling roles. In plants, cryptochrome (cry1, cry2) biological activity has been linked to flavin photoreduction via an electron transport chain to the protein surface comprising 3 evolutionarily conserved tryptophan residues known as the 'Trp triad.' Mutation of any of the Trp triad residues abolishes photoreduction in isolated cryptochrome protein in vitro and therefore had been suggested as essential for electron transfer to the flavin. However, photoreduction of the flavin in Arabidopsis cry2 proteins occurs in vivo even with mutations in the Trp triad, indicating the existence of alternative electron transfer pathways to the flavin. These pathways are potentiated by metabolites in the intracellular environment including ATP, ADP, AMP, and NADH. In the present work we extend these observations to Arabidopsis cryptochrome 1 and demonstrate that Trp triad substitution mutants at W400F and W324F positions which are not photoreduced in vitro can be photoreduced in whole cell extracts, albeit with reduced efficiency. We further show that the flavin signaling state (FADH°) is stabilized in an in vivo context. These data illustrate that in vivo modulation by metabolites in the cellular environment may play an important role in cryptochrome signaling, and are discussed with respect to possible effects on the conformation of the C-terminal domain to generate the biologically active conformational state.

Direct determination of resonance energy transfer in photolyase: structural alignment for the functional state

Photoantenna is essential to energy transduction in photoinduced biological machinery. A photoenzyme, photolyase, has a light-harvesting pigment of methenyltetrahydrofolate (MTHF) that transfers its excitation energy to the catalytic flavin cofactor FADH¯ to enhance DNA-repair efficiency. Here we report our systematic characterization and direct determination of the ultrafast dynamics of resonance energy transfer from excited MTHF to three flavin redox states in E. coli photolyase by capturing the intermediates formed through the energy transfer and thus excluding the electron-transfer quenching pathway. We observed 170 ps for excitation energy transferring to the fully reduced hydroquinone FADH¯, 20 ps to the fully oxidized FAD, and 18 ps to the neutral semiquinone FADH^•, and the corresponding orientation factors (κ²) were determined to be 2.84, 1.53 and 1.26, respectively, perfectly matching with our calculated theoretical values. Thus, under physiological conditions and over the course of evolution, photolyase has adopted the optimized orientation of its photopigment to efficiently convert solar energy for repair of damaged DNA.

Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics

Most proteins are nanomachines that are selected to execute specific functions and therefore should have some degree of flexibility. The driving force that excites specific motions of domains and smaller chain elements is the thermal fluctuations of the solvent bath which are channeled to selected modes of motions by the structural constraints. Consequently characterization of the ensembles of conformers of proteins and their dynamics should be expressed in statistical terms, i.e., determination of probability distributions of the various conformers. This can be achieved by measurements of time-resolved dynamic non-radiative excitation energy transfer (trFRET) within ensembles of site specifically labeled protein molecules. Distributions of intramolecular segmental end-to-end distances and their fast fluctuations can be determined, and fast and slow conformational transitions within selected sections of the molecule can be monitored and analyzed. Both ensemble and single-molecule detection methods can be applied for data collection. In combination with synchronization methods, time-resolved FRET was also used for studies of fast conformational transitions, in particular the folding/unfolding transitions.

Ultrafast tryptophan-to-heme electron transfer in myoglobins revealed by UV 2D spectroscopy

Tryptophan is commonly used to study protein structure and dynamics, such as protein folding, as a donor in fluorescence resonant energy transfer (FRET) studies. By using ultra-broadband ultrafast two-dimensional (2D) spectroscopy in the ultraviolet (UV) and transient absorption in the visible range, we have disentangled the excited state decay pathways of the tryptophan amino acid residues in ferric myoglobins (MbCN and metMb). Whereas the more distant tryptophan (Trp(7)) relaxes by energy transfer to the heme, Trp(14) excitation predominantly decays by electron transfer to the heme. The excited Trp(14)→heme electron transfer occurs in <40 picoseconds with a quantum yield of more than 60%, over an edge-to-edge distance below ~10 angstroms, outcompeting the FRET process. Our results raise the question of whether such electron transfer pathways occur in a larger class of proteins.