Fluorescence quenching of (dimethylamino)naphthalene dyes Badan and Prodan by tryptophan in cytochromes P450 and micelles

Transfer of ANS-Like Drugs from Micellar Drug Delivery Systems to Albumin Is Highly Favorable and Protected from Competition with Surfactant by "Reserved" Binding Sites

Micellar drug delivery systems (MDDS) for the intravenous administration of poorly soluble drugs have great advantages over alternative formulations in terms of the safety of their excipients, storage stability, and straightforward production. A classic example is mixed micelles of glycocholate (GC) and lecithin, both endogenous substances in human blood. What limits the use of MDDS is the complexity of the transitions after injection. In particular, as the MDDS disintegrate partially or completely after injection, the drug has to be transferred safely to endogenous carriers in the blood, such as human serum albumin (HSA). If this transfer is compromised, the drug might precipitate─a process that needs to be excluded under all circumstances. The key question of this paper is whether the high local concentration of GC at the moment and site of MDDS dissolution might transiently saturate HSA binding sites and, hence, endanger quick drug transfer. To address this question, we have used a new approach, which is time-resolved fluorescence spectroscopy of the single tryptophan in HSA, Trp-214, to characterize the competitive binding of GC and the drug substitute anilinonaphthalenesulfonate (ANS) to HSA. Time-resolved fluorescence of Trp-214 showed important advantages over established methods for tackling this problem. ANS has been the standard "model drug" to study albumin binding for decades, given its structural similarity to the class of naphthalene-containing acidic drugs and the fact that it is displaced from HSA by numerous drugs (which presumably bind to the same sites). Our complex global fit uses the critical approximation that the average lifetimes behave similarly to a single lifetime, but the resulting errors are found to be moderate and the results provide a convincing explanation of the, at first glance, counterintuitive behavior. Accordingly, and largely in line with the literature, we observed two types of sites binding ANS at HSA: 3 type A, rather peripheral, and 2 type B, likely more central sites. The latter quench Trp-214 by Förster Resonance Energy Transfer (FRET) with a rate constant of ≈0.4 ns-1 per ANS. Adding millimolar concentrations of GC displaces ANS from the A sites but not from B sites. At incomplete ANS saturation, this causes a GC-induced translocation of ANS from A to the more FRET-active B sites. This leads to the apparent paradox that the partial displacement of ANS from HSA increases its quenching effect on Trp-214. The most important conclusion is that (ANS-like) drugs cannot be displaced from the type-B sites, and consequently, drug transfer to these sites is not impaired by competitive binding of GC in the vicinity of a dissolving micelle. The second conclusion is that for unbound GC above the CMC (9 mM), ANS equilibrates between HSA and GC micelles but with a strong preference for free sites on HSA. That means that even persisting micelles would lose their cargo readily once exposed to HSA. For all MDDS sharing this property, targeted drug delivery approaches involving them as the nanocarrier would be pointless.

Design of Polarity-Dependent Immunosensors Based on the Structural Analysis of Engineered Antibodies

"Reagentless" immunosensors are emerging to address the challenge of practical and sensitive detection of important biomarkers in real biological samples without the need for multistep assays and user intervention, with applications ranging from research tools to point-of-care diagnostics. Selective target binding to an affinity reagent is detected and reported in one step without the need for washing or additional reporters. In this study, we used a structure-guided approach to identify a mutation site in an antibody fragment for the polarity-dependent fluorophore, Anap, such that upon binding of the protein target cardiac troponin I, the Anap-labeled antibody would produce a detectable and dose-dependent shift in emission wavelength. We observed a significant emission wavelength shift of the Anap-labeled anti-cTnI mutant, with a blue shift of up to 37 nm, upon binding to the cTnI protein. Key differences in the resulting emission spectra between target peptides in comparison to whole proteins were also found; however, the affinity and binding characteristics remained unaffected when compared to the wild-type antibody. We also highlighted the potential flexibility of the approach by incorporating a near-infrared dye, IRDye800CW, into the same mutation site, which also resulted in a dose-dependent wavelength shift upon target incubation. These reagents can be used in experiments and devices to create simpler and more efficient biosensors across a range of research, medical laboratory, and point-of-care platforms.

Genetic Incorporation of Dansylalanine in Human Ferroportin to Probe the Alternating Access Mechanism of Iron Transport

Ferroportin (Fpn), a member of the major facilitator superfamily (MFS) of transporters, is the only known iron exporter found in mammals and plays a crucial role in regulating cellular and systemic iron levels. MFSs take on different conformational states during the transport cycle: inward open, occluded, and outward open. However, the precise molecular mechanism of iron translocation by Fpn remains unclear, with conflicting data proposing different models. In this work, amber codon suppression was employed to introduce dansylalanine (DA), an environment-sensitive fluorescent amino acid, into specific positions of human Fpn (V46, Y54, V161, Y331) predicted to undergo major conformational changes during metal translocation. The results obtained indicate that different mutants exhibit distinct fluorescence spectra depending on the position of the fluorophore within the Fpn structure, suggesting that different local environments can be probed. Cobalt titration experiments revealed fluorescence quenching and blue-shifts of λmax in Y54DA, V161DA, and Y331DA, while V46DA exhibited increased fluorescence and blue-shift of λmax. These observations suggest metal-induced conformational transitions, interpreted in terms of shifts from an outward-open to an occluded conformation. Our study highlights the potential of genetically incorporating DA into Fpn, enabling the investigation of conformational changes using fluorescence spectroscopy. This approach holds great promise for the study of the alternating access mechanism of Fpn and advancing our understanding of the molecular basis of iron transport.

Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase

The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen-deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein-solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation (Ea) for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.

Unravelling the mechanism of glucose binding in a protein-based fluorescence probe: molecular dynamics simulation with a tailor-made charge model

Fluorophores linked to the glucose/galactose-binding protein (GGBP) are a promising class of glucose sensors with potential application in medical devices for diabetes patients. Several different fluorophores at different positions in the protein were tested experimentally so far, but a deeper molecular understanding of their function is still missing. In this work, we use molecular dynamics simulations to investigate the mechanism of glucose binding in the GGBP-Badan triple mutant and make a comparison to the GGBP wild-type protein. The aim is to achieve a detailed molecular understanding of changes in the glucose binding site due to the mutations and their effect on glucose binding. Free simulations give an insight into the changes of the hydrogen-bonding network in the active site and into the mechanisms of glucose binding. Additionally, metadynamics simulations for wild type and mutant unravel the energetics of binding/unbinding in these proteins. Computed free energies for the opening of the binding pocket for the wild-type and the mutant agree well with the experimental data. Further, the simulations also give an insight into the changes of the chromophore conformations upon glucose binding, which can help to understand fluorescence changes. Therefore, the molecular details unravelled in this work may support effective optimisation strategies for the construction of more efficient glucose sensors.

Solvent-Dependent Excited-State Evolution of Prodan Dyes

Excited-state character and dynamics of two 6-(dimethylamino)-2-acylnaphthalene dyes (Prodan and Badan-SCH₂CH₂OH) were studied by picosecond time-resolved IR spectroscopy (TRIR) in solvents of different polarity and relaxation times: hexane, CD₃OD, and glycerol-d₈. In all these solvents, near-UV excitation initially produced the same S₁(ππ*) excited state characterized by a broad TRIR signal. A very fast decay (3, ∼100 ps) followed in hexane, whereas conversion to a distinct IR spectrum with a ν(C═O) band downshifted by 76 cm^-1 occurred in polar/H-bonding solvents, slowing down on going from CD₃OD (1, 23 ps) to glycerol-d₈ (5.5, 51, 330 ps). The final relaxed excited state was assigned as planar Me₂N → C═O intramolecular charge transfer S₁(ICT) by comparing experimental and TDDFT-calculated spectra. TRIR conversion kinetics are comparable to those of early stages of multiexponential fluorescence decay and dynamic fluorescence red-shift. This work presents a strong evidence that Prodan-type dyes undergo solvation-driven charge separation in their S₁ state, which is responsible for the dynamic fluorescence Stokes shift observed in polar/H-bonding solvents. The time evolution of the optically prepared S₁(ππ*) state to the S₁(ICT) final state reflects environment relaxation and solvation dynamics. This finding rationalizes the widespread use of Prodan-type dyes as probes of environment dynamics and polarity.

Making Nitronaphthalene Fluoresce

Nitroaromatic compounds are inherently nonfluorescent, and the subpicosecond lifetimes of the singlet excited states of many small nitrated polycyclic aromatic hydrocarbons, such as nitronaphthalenes, render them unfeasible for photosensitizers and photo-oxidants, despite their immensely beneficial reduction potentials. This article reports up to a 7000-fold increase in the singlet-excited-state lifetime of 1-nitronaphthalene upon attaching an amine or an N-amide to the ring lacking the nitro group. Varying the charge-transfer (CT) character of the excited states and the medium polarity balances the decay rates along the radiative and the two nonradiative pathways and can make these nitronaphthalene derivatives fluoresce. The strong electron-donating amine suppresses intersystem crossing (ISC) but accommodates CT pathways of nonradiate deactivation. Conversely, the N-amide does not induce a pronounced CT character but slows down ISC enough to achieve relatively long lifetimes of the singlet excited state. These paradigms are key for the pursuit of electron-deficient (n-type) organic conjugates with promising optical characteristics.

Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions

The fluorescent dye BADAN (6-bromoacetyl-2-dimetylaminonaphtalene) is widely used in various fields of life sciences, however, the photophysical properties of BADAN are not fully understood. The study of the spectral properties of BADAN attached to a number of mutant forms of GGBP, as well as changes in its spectral characteristics during structural changes in proteins, allowed to shed light on the photophysical properties of BADAN. It was shown that spectral properties of BADAN are determined by at least one non-fluorescent and two fluorescent isomers with overlapping absorbing bands. It was found that BADAN fluorescence is determined by the unsolvated "PICT" (planar intramolecular charge transfer state) and solvated "TICT" (twisted intramolecular charge transfer state) excited states. While "TICT" state can be formed both as a result of the "PICT" state solvation and as a result of light absorption by the solvated ground state of the dye. BADAN fluorescence linked to GGBP/H152C apoform is quenched by Trp 183, but this effect is inhibited by glucose intercalation. New details of the changes in the spectral characteristics of BADAN during the unfolding of the protein apo and holoforms have been obtained.

ANAP: A versatile, fluorescent probe of ion channel gating and regulation

Fluorescence spectroscopy and microscopy are non-destructive methods that provide real-time measurements of ion channel structural dynamics. As such, they constitute a direct path linking the high-resolution structural models from X-ray crystallography and cryo-electron microscopy with the high-resolution functional data from ionic current measurements. The utility of fluorescence as a reporter of channel structure is limited by the palette of available fluorophores. Thiol-reactive fluorophores are small and bright, but are restricted in terms of the positions on a protein that can be labeled and present significant issues with background incorporation. Genetically encoded fluorescent protein tags are specific to a protein of interest, but are very large and usually only used to label the free N- and C-termini of proteins. L-3-(6-acetylnaphthalen-2-ylamino)-2-aminopropionic acid (ANAP) is a fluorescent amino acid that can be specifically incorporated into virtually any site on a protein of interest using amber stop-codon suppression. Due to its environmental sensitivity and potential as a donor in fluorescence resonance energy transfer experiments, it has been adopted by numerous investigators to study voltage, ligand, and temperature-dependent activation of a host of ion channels. Simultaneous measurements of ionic currents and ANAP fluorescence yield exceptional mechanistic insights into channel function. In this chapter, I will summarize the current literature regarding ANAP and ion channels and discuss the practical aspects of using ANAP, including potential pitfalls and confounds.

BADAN-conjugated β-lactamases as biosensors for β-lactam antibiotic detection

β-Lactam antibiotic detection has significant implications in food safety control, environmental monitoring and pharmacokinetics study. Here, we report the development of two BADAN-conjugated β-lactamases, E166Cb and E166Cb/N170Q, as sensitive biosensors for β-lactam antibiotic detection. These biosensors were constructed by coupling an environment-sensitive BADAN probe onto location 166 at the active site of the PenP β-lactamase E166C and E166C/N170Q mutants. They gave fluorescence turn-on signals in response to β-lactam antibiotics. Molecular dynamics simulation of E166Cb suggested that the turn-on signal might be attributed to a polarity change of the microenvironment of BADAN and the removal of the fluorescence quenching effect on BADAN exerted by a nearby Tyr-105 upon the antibiotic binding. In the detection of four β-lactams (penicillin G, penicillin V, cefotaxime and moxalactam), both E166Cb and E166Cb/N170Q delivered signal outputs in an antibiotic-concentration dependent manner with a dynamic range spanning from 10 nM to 1 μM. Compared to E166Cb, E166Cb/N170Q generally exhibited more stable signals owing to its higher deficiency in hydrolyzing the antibiotic analyte. The overall biosensor performance of E166Cb and E166Cb/N170Q was comparable to that of their respective fluorescein-modified counterparts, E166Cf and E166Cf/N170Q. But comparatively, the BADAN-conjugated enzymes showed a higher sensitivity, displayed a faster response in detecting moxalactam and a more stable fluorescence signals towards penicillin G. This study illustrates the potential of BADAN-conjugated β-lactamases as biosensing devices for β-lactam antibiotics.

The redox-coupled proton-channel opening in cytochrome c oxidase

The interplay of cytochrome c oxidase's cofactor electrostatics, long-range conformational changes, H-bond rearrangement, and water dynamics enables transient proton-channel activation.

Characterization on the toxic mechanism of two fluoroquinolones to trypsin by spectroscopic and computational methods

Ciprofloxacin (CPFX) and enrofloxacin (ENFX), two of the most widely used fluoroquinolones (FQs), pose a great threat to humans and the ecosystem. In this study, the toxic mechanisms between the two FQs and trypsin were evaluated by means of multiple spectroscopic methods, as well as molecular docking. During the fluorescence investigations, both FQs quenched the intrinsic fluorescence of trypsin effectively, which was due to the formation of moderately strong complexes (mainly through van der Waals forces and hydrogen bonds). The binding of two FQs not only caused the conformational and micro-environmental changes of trypsin, but also changed its molecular activity; shown by the UV-Visible absorption spectroscopy, synchronous fluorescence spectroscopy, and functional tests. The established methods in this work can help to comprehensively understand the transport of FQs in the human body.

Hydrogen bond strengthening induces fluorescence quenching of PRODAN derivative by turning on twisted intramolecular charge transfer

Researchers have proposed different effective mechanisms of hydrogen bonding (HB) on the fluorescence of 6-propionyl-2-dimethylaminonaphthalene (PRODAN) and its derivatives. Herein, excited state transition and dynamics analysis confirm that the fluorescence of PD (a derivative of PRODAN with ethyl replaced by 3-hydroxy-2,2-dimethylpropan) emits from the planar intramolecular charge transfer (PICT) state rather than twist ICT (TICT) state, because the fluorescence emission and surface hopping from the TICT state to the twist ground (T-S₀) state is energy forbidden. Nevertheless, the strengthening of intramolecular-HB (intra-HB) and intermolecular-HB (inter-HB) of PD-(methanol)₂ smooth the pathway of surface hopping from TICT to T-S₀ state and the external conversion going to planar ground state by decreasing the energy difference of the two states. This smoothing changes the fluorescence state of PD-(methanol)₂ to the TICT state in which fluorescence emission does not occur but surface hopping, leading to the partial fluorescence quenching of PD in methanol solvent. This conclusion is different from previous related reports. Moreover, the inter-HB strengthening of PD-methanol in PICT state induces the cleavage of intra-HB and a fluorescence red-shift of 54nm compared to PD. This red-shift increases to 66nm for PD-(methanol)₂ for the strengthening of the one intra-HB and two inter-HBs. The dipole moments of PD-methanol and PD-(methanol)₂ respectively increase about 10.3D and 8.1D in PICT state compared to PD. The synergistic effect of intra-HB and inter-HB induces partial quenching of PD in methanol solvent by turning on the TICT state and fluorescence red-shift. This work gives a reasonable description on the fluorescence red-shift and partial quenching of PD in methanol solvent, which will bring insight into the study of spectroscopic properties of molecules owning better spectral characteristics.

Use of bioconjugation with cytochrome P450 enzymes

Bioconjugation, defined as chemical modification of biomolecules, is widely employed in biological and biophysical studies. It can expand functional diversity and enable applications ranging from biocatalysis, biosensing and even therapy. This review summarizes how chemical modifications of cytochrome P450 enzymes (P450s or CYPs) have contributed to improving our understanding of these enzymes. Genetic modifications of P450s have also proven very useful but are not covered in this review. Bioconjugation has served to gain structural information and investigate the mechanism of P450s via photoaffinity labeling, mechanism-based inhibition (MBI) and fluorescence studies. P450 surface acetylation and protein cross-linking have contributed to the investigation of protein complexes formation involving P450 and its redox partner or other P450 enzymes. Finally, covalent immobilization on polymer surfaces or electrodes has benefited the areas of biocatalysis and biosensor design. This article is part of a Special Issue entitled: Cytochrome P450 biodiversity and biotechnology, edited by Erika Plettner, Gianfranco Gilardi, Luet Wong, Vlada Urlacher, Jared Goldstone.

A model for ultra-fast charge transport in membrane proteins

Isolated proteins have recently been observed to transport charge and reactivity over very long distances with extraordinary rates and near perfect efficiencies in spite of their site. This is not the case if the peptide is in water, where the efficiency of charge hopping to the next site is reduced to approximately 2%. Here, water is not an ideal solvent for charge transport. The issue at hand is how to explain such enormous charge transfer quenching in water compared to another typical medium, namely lipid. We performed molecular dynamics simulations to computationally substantiate the novel long-distance charge transfer yield of the polypeptides in lipids. This is characterized by the charge transfer persistent-distance decay constant and not by the rate, which is seldom, if ever, measured and hence not directly addressed here. This model can encompass an extremely wide range of yields over very long distances in peptides in various media. The calculations here demonstrate the good charge transport efficiency in lipids in contrast to the poor efficiency in water. The protein charge transport also exhibits a very strong anisotropic effect in lipids. The peptide secondary structure effect of charge transfer in membranes is analyzed in contrast to that in water. These results suggest that this model can be useful for the prediction of charge transfer efficiency in various environments of interest and indicate that the charge transfer is highly efficient in membrane proteins.

Intrinsic tryptophan fluorescence in the detection and analysis of proteins: a focus on Förster resonance energy transfer techniques

Förster resonance energy transfer (FRET) occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (λ EX ≈ 280 nm, λ EM ≈ 350 nm), in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the proteinlocal environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic Förster resonance energy transfer (iFRET), a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.