Origin of Tryptophan Fluorescence Lifetimes. Part 2: Fluorescence Lifetimes Origin of Tryptophan in Proteins

Characterization and classification of pathogenic bacteria using native fluorescence and spectral deconvolution

Identification and classification of pathogenic bacterial strains is of current interest for the early treatment of diseases. In this work, protein fluorescence from eight different pathogenic bacterial strains were characterized using steady state and time resolved fluorescence spectroscopy. The spectral deconvolution method was also employed to decompose the emission contribution from different intrinsic fluorophores and extracted various key parameters, such as intensity, emission maxima, emission line width of the fluorophores, and optical redox ratio. The change in average lifetime values across different bacterial strains exhibits good statistical significance (p ≤ 0.01). The variations in the photophysical characteristics of bacterial strains are due to the different conformational states of the proteins. The stepwise multiple linear discriminate analysis of fluorescence emission spectra at 280 nm excitation across eight different bacterial strains classifies the original groups and cross validated group with 100% and 99.5% accuracy, respectively.

Modeling the temperature dependence of the fluorescence properties of Indole in aqueous solution

In a recent paper, we proposed a scheme to describe the relaxation mechanism of the excited Indole in aqueous solution, involving the fluctuations among the diabatic electronic states 1Lb, 1La and 1πσ∗. Such a theoretical and computational model reproduced accurately the available experimental data at room temperature. Following these results, in the present work, we model the complex temperature dependence of the fluorescence properties of Indole in aqueous solution, with results further validating the proposed relaxation scheme. This scheme is able to explain the temperature effects on the fluorescence behavior indicating the water fluctuations as the main cause of (i) the stabilization of the dark state (1πσ∗) and (ii) the increase in temperature of the kinetics of the irreversible transition towards such a state.

One-pot synthesis of alginate-antimicrobial peptide nanogel

Nanosized alginate-based particles (NAPs) were obtained in a one-pot solvent-free synthesis procedure, achieving the design of a biocompatible nanocarrier for the encapsulation of IbM6 antimicrobial peptide (IbM6). IbM6 is integrated in the nascent nanosized hydrogel self-assembly guided by electrostatic interactions and by weak interactions, typical of soft matter. The formation of the nanogel is a dynamic and complex process, which presents an interesting temporal evolution. In this work, we optimized the synthesis conditions of IbM6-NAPs based on small-angle X-ray scattering (SAXS) measurements and evaluated its time evolution over several weeks by sensing the IbM6 environment in IbM6-NAPs from photochemical experiments. Fluorescence deactivation experiments revealed that the accessibility of different quenchers to the IbM6 peptide embedded in NAPs is dependent on the aging time of the alginate network. Lifetimes measurements indicate that the deactivation paths of the excited state of the IbM6 in the nanoaggregates are reduced when compared with those exhibited by the peptide in aqueous solution, and are also dependent on the aging time of the nanosized alginate network. Finally, the entrapment of IbM6 in NAPs hinders the degradation of the peptide by trypsin, increasing its antimicrobial activity against Escherichia coli K-12 in simulated operation conditions.

Probing cell metabolism using the two-photon excitation autofluorescence lifetime of tryptophan

Compared to intensity detection, fluorescence lifetime has the advantage of being unaffected by variations in excitation intensity, fluorophore concentration, or attenuation due to biological absorption and scattering. In this Letter, to the best of our knowledge, we present the use of the two-photon excitation autofluorescence lifetime imaging of tryptophan (TRP) to probe cell metabolism for the first time. Tests of pure chemical samples showed that the fluorescence lifetime of TRP was highly sensitive to changes in molecular conformation and the environment. In in vitro cell experiments, we successfully utilized the fluorescence lifetime of TRP to distinguish tumor cells from healthy cells, track the therapeutic effect of the tumor immunotherapy drug 1-MT for HeLa cells, and monitor cells in response to carbonyl cyanide 3-chlorophenylhydrazone (CCCP)-induced cell apoptosis. These results reveal that the two-photon excitation autofluorescence lifetime of TRP could be a sensitive natural probe of cell metabolism in living cells.

Detection and identification of amino acids and proteins using their intrinsic fluorescence in the visible light spectrum

The detection and identification of biomolecules are essential in the modern era of medical diagnostics. Several approaches have been established, but they have significant limitations such as laborious and time-consuming sample preparation, analysis, and the need to use external probes which provide adequate but not desired levels of accuracy and sensitivity. Herein, we have explored successfully a non-invasive technique to detect and identifybiomolecules such as amino acids and proteins by utilizing their intrinsic fluorescence. The developed confocal microscopy method revealed high and photostable emission counts of these biomolecules including amino acids (tryptophan, phenylalanine, tyrosine, proline, histidine, cysteine, aspartic acid, asparagine, isoleucine, lysine, glutamic acid, arginine) and proteins (HSA, BSA) when they are excited with a green laser. The fluorescence lifetime of the samples enabled the identification and distinction of known and blind samples of biomolecules from each other. The developed optical technique is straightforward, non-destructive and does not require laborious labeling to identify specific proteins, and may serve as the basis for the development of a device that would quickly and accurately identify proteins at an amino acid level. Therefore, this approach would open an avenue for precise detection in imaging and at the same time increases our understanding of chemical dynamics at the molecular level.

Steady-State and Time-Resolved Fluorescence Study of Selected Tryptophan-Containing Peptides in an AOT Reverse Micelle Environment

The aim of this study was to demonstrate the utility of time-resolved fluorescence spectroscopy in the detection of subtle changes in the local microenvironment of a tryptophan chromophore in a confined and crowded medium of AOT reverse micelles, which mimic biological membranes and cell compartmentalization. For this purpose, fluorescence properties of L-tryptophan and several newly synthesized tryptophan-containing peptides in buffer and in an AOT reverse micelle medium were determined. It was shown that insertion of tryptophan and its short di- and tripeptides inside micelles led to evident changes in both the steady-state emission spectra and in fluorescence decay kinetics. The observed differences in spectral characteristics, such as a blue shift in the emission maxima, changes in the average fluorescence lifetime, and the appearance of environmental-dependent fluorescent species, showed the utility of time-resolved fluorescence spectroscopy as a sensitive tool for detecting subtle conformational modifications in tryptophan and its peptides induced by changes in polarity, viscosity, and specific interactions between chromophores and water molecules/polar groups/ions that occur inside reverse micelles.

Time-Resolved Fluorescence Spectroscopy of Blood, Plasma and Albumin as a Potential Diagnostic Tool for Acute Inflammation in COVID-19 Pneumonia Patients

Fluorescence lifetime measurements of blood or plasma offer valuable insights into the microenvironment and molecular interactions of fluorophores, particularly concerning albumin. Neutrophil- and hypoxia-induced oxidative stress in COVID-19 pneumonia patients leads to hyperinflammation, various oxidative modifications of blood proteins, and potential alterations in the fluorescence lifetime of tryptophan-containing proteins, especially albumin. The objective of this study was to investigate the efficacy of time-resolved fluorescence spectroscopy of blood and plasma as a prompt diagnostic tool for the early diagnosis and severity assessment of COVID-19-associated pneumonia. This study examined a cohort of sixty COVID-19 patients with respiratory symptoms. To investigate whether oxidative stress is the underlying cause of the change in fluorescence lifetime, human serum albumin was treated with chloramine T. The time-resolved spectrometer Life Spec II (Edinburgh Instruments Ltd., Livingston, UK), equipped with a sub-nanosecond pulsed 280 nm diode, was used to measure the fluorescence lifetime of blood and plasma. The findings revealed a significant reduction in the fluorescence lifetime of blood (diluted 200 times) and plasma (diluted 20 times) at 360 nm in COVID-19 pneumonia patients compared with their respective values recorded six months post-infection and those of healthy individuals. Significant negative correlations were observed between the mean fluorescence lifetime of blood and plasma at 360 nm and several severity biomarkers and advanced oxidation protein products, while a positive correlation was found with albumin and the albumin-globulin ratio. The time-resolved fluorescence spectroscopy method demonstrates the potential to be used as a preliminary screening technique for identifying patients who are at risk of developing severe complications. Furthermore, the small amount of blood required for the measurements has the potential to enable a rapid fingerstick blood test.

Short-wavelength excitation two-photon intravital microscopy of endogenous fluorophores

The noninvasive two-photon excitation autofluorescence imaging of cellular and subcellular structure and dynamics in live tissue could provide critical in vivo information for biomedical studies. However, the two-photon microscopy of short-wavelength endogenous fluorophores, such as tryptophan and hemoglobin, is extremely limited due to the lack of suitable imaging techniques. In this study, we developed a short-wavelength excitation time- and spectrum-resolved two-photon microscopy system. A 520-nm femtosecond fiber laser was used as the excitation source, and a time-correlated single-photon counting module connected with a spectrograph was used to provide time- and spectrum-resolved detection capability. The system was specially designed for measuring ultraviolet and violet-blue fluorescence signals and thus was very suitable for imaging short-wavelength endogenous fluorophores. Using the system, we systematically compared the fluorescence spectra and fluorescence lifetimes of short-wavelength endogenous fluorophores, including the fluorescent molecules tyrosine, tryptophan, serotonin (5-HT), niacin (vitamin B3), pyridoxine (vitamin B6), and NADH and the protein group (keratin, elastin, and hemoglobin). Then, high-resolution three-dimensional (3D) label-free imaging of different biological tissues, including rat esophageal tissue, rat oral cheek tissue, and mouse ear skin, was performed in vivo or ex vivo. Finally, we conducted time-lapse imaging of leukocyte migration in the lipopolysaccharide injection immunization model and a mechanical trauma immunization model. The results indicate that the system can specifically characterize short-wavelength endogenous fluorophores and provide noninvasive label-free 3D visualization of fine structures and dynamics in biological systems. The microscopy system developed here can empower more flexible imaging of endogenous fluorophores and provide a novel method for the 3D monitoring of biological events in their native environment.

Unveiling the Excited State Dynamics of Indole in Solution

In this paper, we reconstruct in detail the dynamics of the emitting electronic excited state of aqueous indole, investigating its relaxation mechanism and kinetics to be related to the time-dependent fluorescence signal. Taking advantage of the results shown in a very recent paper, we were able to model the relaxation process in solution in terms of the transitions between two gas-phase singlet electronic states (¹L_a and ¹L_b), subsequently irreversibly relaxing to the gas-phase singlet dark state (¹πσ*). A comparison of the results with the available experimental data shows that the relaxation mechanism we obtain by our theoretical-computational model is reliable, reproducing rather accurately all the experimental observables.

On the Nature of Stationary and Time-Resolved Fluorescence Spectroscopy of Collagen Powder from Bovine Achilles Tendon

This paper presents a more systematic study of steady-state and time-resolved autofluorescence spectroscopy of collagen isolated from bovine Achilles tendon. In steady-state fluorescence measurements, the excitation and emission spectra of collagen powder, recorded at different fluorescence excitation and detection wavelengths, were compared with the fluorescence excitation and emission spectra of the amino acids phenylalanine, tyrosine, and tryptophan, as well as with similar spectra for 13 autofluorescent collagen cross-links, which have been identified and described in the literature so far. In time-resolved studies, fluorescence was excited by the pulsed light of different wavelengths, and for each excitation wavelength, fluorescence decay was recorded for several detection wavelengths. Data analysis allowed recovery of the fluorescence decay times for each experimental excitation detection event. The obtained information on the decay times of the measured fluorescent signals was discussed, taking into account the available literature data from similar studies of isolated collagen and collagen-rich tissues. Based on the obtained results, it was found that the shape and position of the measured fluorescence excitation and emission spectra of collagen strongly depend on the emission and excitation wavelengths selected in the measurements. From the recorded excitation and emission bands of collagen, it can be concluded with high probability that there are additional, so far unidentified, collagen cross-links, which can be excited at longer excitation wavelengths. In addition, the collagen excitation spectra were measured at longer emission wavelengths at which the collagen cross-links emit fluorescent light. In addition to the emission spectra obtained for excitation in the deep-UV region, the results of time-resolved fluorescence studies with excitation in the deep-UV region and detection at longer wavelengths suggest that fluorescence excitation energy transfer processes occur from the amino acids to the collagen cross-links, and also between the cross-links themselves.

Label-free autofluorescence lifetime reveals the structural dynamics of ataxin-3 inside droplets formed via liquid-liquid phase separation

Liquid-liquid phase separation is a phenomenon that features the formation of liquid droplets containing concentrated solutes. The droplets of neurodegeneration-associated proteins are prone to generate aggregates and cause diseases. To uncover the aggregation process from the droplets, it is necessary to analyze the protein structure with keeping the droplet state in a label-free manner, but there was no suitable method. In this study, we observed the structural changes of ataxin-3, a protein associated with Machado-Joseph disease, inside the droplets, using autofluorescence lifetime microscopy. Each droplet showed autofluorescence due to tryptophan (Trp) residues, and its lifetime increased with time, reflecting structural changes toward aggregation. We used Trp mutants to reveal the structural changes around each Trp and showed that the structural change consists of several steps on different timescales. We demonstrated that the present method visualizes the protein dynamics inside a droplet in a label-free manner. Further investigations revealed that the aggregate structure formed in the droplets differs from that formed in dispersed solutions and that a polyglutamine repeat extension in ataxin-3 hardly modulates the aggregation dynamics in the droplets. These findings highlight that the droplet environment facilitates unique protein dynamics different from those in solutions.

Electronic Energy Migration in Microtubules

The repeating arrangement of tubulin dimers confers great mechanical strength to microtubules, which are used as scaffolds for intracellular macromolecular transport in cells and exploited in biohybrid devices. The crystalline order in a microtubule, with lattice constants short enough to allow energy transfer between amino acid chromophores, is similar to synthetic structures designed for light harvesting. After photoexcitation, can these amino acid chromophores transfer excitation energy along the microtubule like a natural or artificial light-harvesting system? Here, we use tryptophan autofluorescence lifetimes to probe energy hopping between aromatic residues in tubulin and microtubules. By studying how the quencher concentration alters tryptophan autofluorescence lifetimes, we demonstrate that electronic energy can diffuse over 6.6 nm in microtubules. We discover that while diffusion lengths are influenced by tubulin polymerization state (free tubulin versus tubulin in the microtubule lattice), they are not significantly altered by the average number of protofilaments (13 versus 14). We also demonstrate that the presence of the anesthetics etomidate and isoflurane reduce exciton diffusion. Energy transport as explained by conventional Förster theory (accommodating for interactions between tryptophan and tyrosine residues) does not sufficiently explain our observations. Our studies indicate that microtubules are, unexpectedly, effective light harvesters.

A flaw in applying the FRET technique to evaluate the distance between ligands and tryptophan residues in human serum albumin: Proposal of correction

Due to its primordial function as a drug carrier, human serum albumin (HSA) is extensively studied regarding its binding affinity with developing drugs. Förster resonance energy transfer (FRET) is frequently applied as a spectroscopic molecular ruler to measure the distance between the binding site and the ligand. In this work, we have shown that most of the published results that use the FRET technique to estimate the distance from ligands to the binding sites do not corroborate the crystallography data. By comparing the binding affinity of dansyl-proline with HSA and ovotransferrin, we demonstrated that FRET explains the quenching provoked by the interaction of ligands in albumin. So, why does the distance calculation via FRET not corroborate the crystallography data? We have shown that this inconsistency is related to the fact that a one-to-one relationship between donor and acceptor is not present in most experiments. Hence, the quenching efficiency used for calculating energy transfer depends on distance and binding constant, which is inconsistent with the correct application of FRET as a molecular ruler. We have also shown that the indiscriminate attribution of 2/3 to the relative orientation of transition dipoles of the acceptor and donor (κ²) generates inconsistencies. We proposed corrections based on the experimental equilibrium constant and theoretical orientation of transition dipoles to correct the FRET results.

Understanding Conformational Changes in Human Serum Albumin and Its Interactions with Gold Nanorods: Do Flexible Regions Play a Role in Corona Formation?

The importance of protein-nanoparticle (NP) conjugates for biomedical applications has seen an exponential growth in the past few years. The protein corona formation on NPs with human serum albumin (HSA), being the most abundant protein in blood serum, has become one of the most studied protein analyses under NP-protein interactions as HSA is readily adsorbed on the surface of the NPs. Understanding the fate of the NPs in physiological media along with the change in biological responses due to the formation of the protein corona thus becomes important. We analyzed the HSA protein corona formation on gold nanorods (AuNRs) through different spectroscopic studies in addition to the effects of change in the protein concentration on the protein-NP interactions. Different imaging techniques such as high-resolution transmission electron microscopy, field emission scanning electron microscopy, and atomic force microscopy were used to determine the morphology and the dimensions of the nanorods and the protein-nanorod conjugates. Fourier-transform infrared data showed a reduction in the α-helix content and an increase in β-sheet content for the HSA-AuNR conjugate compared to the native protein. A decrease in steady-state fluorescence intensity occurred with instant addition of AuNR to HSA showing better and efficient quenching of Trp fluorescence for the lower concentration of protein. Time-correlated single photon counting results showed greater energy transfer efficiency and faster decay rate for higher concentrations of proteins. The circular dichroism study gives insight into the secondary structural changes due to unfolding, and a greater change was observed for lower concentrations of protein due to a thermodynamically stable protein corona formation. Surface-enhanced Raman spectroscopy (SERS) indicated the presence of aromatic residues such as Phe, Tyr, and Cys that appear to be close to the surface of the AuNRs in addition to hydrophobic interactions between AuNR and the protein. The disordered and flexible regions mapped onto HSA (PDB: 1AO6), predicted by the intrinsically disordered region predictors, point toward the interactions of similar residues with the nanorods observed from SERS and fluorescence studies. These studies could provide a clearer understanding of the interactions between HSA and AuNRs for possible biological applications.

A study of the oxidative processes in human plasma by time-resolved fluorescence spectroscopy

The aim of this study was to examine the usefulness of time-resolved fluorescence spectroscopy in the evaluation of the oxidative processes in human plasma. To investigate the impact of oxidative stress on the fluorescence of plasma, five studied markers (thiobarbituric acid-reactive substances, ischemia modified albumin, carbonyl groups, hydrogen peroxide, advanced oxidation protein products) were chosen as oxidative damage approved markers. Our method presents several advantages over traditional methods as it is a direct, non-time-consuming, repeatable, and non-invasive technique that requires only simple pre-treatment of samples without additional reagents and the sample size needed for analysis is small. In principle, each modification of the protein in plasma can be expected to modify its fluorescence properties and hence its lifetime or intensity. The study involved 59 blood donors with no evidence of disease. The research was conducted at excitation wavelengths of 280 nm and 360 nm, and emission was measured at wavelengths of 350 nm and 440 nm, respectively. Our results, although preliminary, suggest that the application of fluorescence measurements can be considered as an effective marker of oxidative stress. Regression analyses showed that a notable growth in fluorescence intensity at 440 nm and a simultaneous decrease in fluorescence intensity and mean fluorescence lifetime at 350 nm are associated with higher levels of oxidative stress.

Vibronic spectra of jet-cooled 1-methyl-2(1H)-quinolinone studied by Fluorescence spectroscopy and Quantum chemical calculation

1-methyl-2(1H)-quinolinone (MeQone) forms the framework of several hundred quinolone alkaloid molecules, both natural and synthetic, which are being used in various biological applications. In this work, we present experimental and theoretical spectroscopic investigation on the MeQone in its ground and first electronic excited states. The vibronically resolved fluorescence excitation (FE) spectrum of MeQone is recorded within 700 cm^-1 to the electronic origin under the supersonic jet-cooled condition. The dispersed fluorescence (DF) spectra for bands observed in the FE spectrum were also recorded. Bands observed in DF spectra were identified and assigned with the help of Density Functional Theory (DFT) calculated harmonic vibrational frequencies. Based on the assignments of bands in the ground electronic state and TD-DFT calculated frequencies for the first excited state, we have identified and successfully assigned the bands observed in FE spectrum. This study could be helpful to understand the photophysical properties of MeQone derivatives, the quinolone alkaloids.

Fluorescence Characterization of Standard, Mutant and Sweet Corn

This work resulted in the development of a method based on fluorescence spectroscopy to differentiate between three corn varieties, standard, mutant and sweet, and to characterize the corn variety present in finished products. This was achieved by recording fluorescence emission spectra as a function of excitation wavelength. For a standard, non-transgenic and non-sweet corn, the maximum of the first peak is around 412-414 nm at the excitation wavelength equal to 280 nm and shifts to the longer emission wavelengths as the excitation wavelength increases. Also, the second peak is located at 535 nm or is slightly higher (537 to 540 nm) and does not vary for excitation wavelengths from 280 to 360 nm. For mutant corn, the position of the first peak is located at 420 nm and above for λ_ex = 280 nm, while the second peak starts at 525-530 nm (depending on the mutant) and never reaches 535 nm. Finally, for a sweet corn, the position of the first fluorescence emission peak is around 430 nm. If the sweet corn is non-hybrid, the position of the second emission peak is at 535 nm. A hybrid sweet corn has its second peak around 530 nm. Thus, fluorescence emission at 530 is characteristic of corn that has undergone natural or artificial genetic transformation. Finally, we found simple mathematical equations to calculate the percentage of amylopectin and amylose in a given corn.

Probing of carotenoid-tryptophan hydrogen bonding dynamics in the single-tryptophan photoactive Orange Carotenoid Protein

The photoactive Orange Carotenoid Protein (OCP) plays a key role in cyanobacterial photoprotection. In OCP, a single non-covalently bound keto-carotenoid molecule acts as a light intensity sensor, while the protein is responsible for forming molecular contacts with the light-harvesting antenna, the fluorescence of which is quenched by OCP. Activation of this physiological interaction requires signal transduction from the photoexcited carotenoid to the protein matrix. Recent works revealed an asynchrony between conformational transitions of the carotenoid and the protein. Intrinsic tryptophan (Trp) fluorescence has provided valuable information about the protein part of OCP during its photocycle. However, wild-type OCP contains five Trp residues, which makes extraction of site-specific information impossible. In this work, we overcame this problem by characterizing the photocycle of a fully photoactive OCP variant (OCP-3FH) with only the most critical tryptophan residue (Trp-288) in place. Trp-288 is of special interest because it forms a hydrogen bond to the carotenoid's keto-oxygen to keep OCP in its dark-adapted state. Using femtosecond pump-probe fluorescence spectroscopy we analyzed the photocycle of OCP-3FH and determined the formation rate of the very first intermediate suggesting that generation of the recently discovered S* state of the carotenoid in OCP precedes the breakage of the hydrogen bonds. Therefore, following Trp fluorescence of the unique photoactive OCP-3FH variant, we identified the rate of the H-bond breakage and provided novel insights into early events accompanying photoactivation of wild-type OCP.

Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy

Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.

Using Synchronous Fluorescence to Investigate Chemical Interactions Influencing Foam Characteristics in Sparkling Wines

The appearance of bubbles and foam can influence the likeability of a wine even before its consumption. Since foams are essential to visual and taste attributes of sparkling wines, it is of great importance to understand which compounds affect bubbles and foam characteristics. The aim of this work was to investigate the effect of interactions among proteins, amino acids, and phenols on the characteristics of foam in sparkling wines by using synchronous fluorescence spectroscopy techniques. Results have shown that several compounds present in sparkling wines influence foam quality differently, and importantly, highlighted how the interaction of those compounds might result in different effects on foam parameters. Amongst the results, mannoproteins were found to be most likely to promote foam and collar stability, while phenols were likely to increase the small bubbles and collar height in the foam matrix. In summary, this work contributes to a better understanding of the effect of wine compounds on foam quality as well as the effect of the interactions between those compounds.

Experimental approach to study the effect of mutations on the protein folding pathway

Is it possible to compare the physicochemical properties of a wild-type protein and its mutant form under the same conditions? Provided the mutation has destabilized the protein, it may be more correct to compare the mutant protein under native conditions to the wild-type protein destabilized with a small amount of the denaturant. In general, is it appropriate to compare the properties of proteins destabilized by different treatments: mutations, pH, temperature, and denaturants like urea? These issues have compelled us to search for methods and ways of presentation of experimental results that would allow a comparison of mutant forms of proteins under different conditions and lead to conclusions on the effect of mutations on the protein folding/unfolding pathway. We have studied equilibrium unfolding of wild-type bovine carbonic anhydrase II (BCA II) and its six mutant forms using different urea concentrations. BCA II has been already studied in detail and is a good model object for validating new techniques. In this case, time-resolved fluorescence spectroscopy was chosen as the basic research method. The main features of this experimental method allowed us to compare different stages of unfolding of studied proteins and prove experimentally that a single substitution of the amino acid in three mutant forms of BCA II affected the native state of the protein but did not change its unfolding pathway. On the contrary, the inserted disulfide bridge in three other mutant forms of BCA II affected the protein unfolding pathway. An important result of this research is that we have validated the new approach allowing investigation of the effect of mutations on the folding of globular proteins, because in this way it is possible to compare proteins in the same structural states rather than under identical conditions.

Single-cell redox states analyzed by fluorescence lifetime metrics and tryptophan FRET interaction with NAD(P)H

Redox changes in live HeLa cervical cancer cells after doxorubicin treatment can either be analyzed by a novel fluorescence lifetime microscopy (FLIM)-based redox ratio NAD(P)H-a2%/FAD-a1%, called fluorescence lifetime redox ratio or one of its components (NAD(P)H-a2%), which is actually driving that ratio and offering a simpler and alternative metric and are both compared. Auto-fluorescent NAD(P)H, FAD lifetime is acquired by 2- photon excitation and Tryptophan by 3-photon, at 4 time points after treatment up to 60 min demonstrating early drug response to doxorubicin. Identical Fields-of-view (FoV) at each interval allows single-cell analysis, showing heterogeneous responses to treatment, largely based on their initial control redox state. Based on a discrete ROI selection method, mitochondrial OXPHOS and cytosolic glycolysis are discriminated. Furthermore, putative FRET interaction and energy transfer between tryptophan residue carrying enzymes and NAD(P)H correlate with NAD(P)H-a2%, as does the NADPH/NADH ratio, highlighting a multi-parametric assay to track metabolic changes in live specimens. © 2019 International Society for Advancement of Cytometry.

Studies on the Interaction between Angiotensin-Converting Enzyme (ACE) and ACE Inhibitory Peptide from Saurida elongata

Angiotensin-converting enzyme (ACE) inhibitory peptides derived from food protein exhibited antihypertensive effects by inhibiting ACE activity. In this work, the interaction between ACE inhibitory peptide GMKCAF (GF-6) and ACE was studied by isothermal titration calorimetry (ITC), molecular docking, ultraviolet absorption spectroscopy, fluorescence spectroscopy, and circular dichroism spectroscopy. Experimental results revealed that the binding of GF-6 to ACE was a spontaneous exothermic process driven by both enthalpy and entropy. The interaction occurred via a static quenching mechanism and involved the alteration of the conformation of ACE. In addition, ITC and molecular docking results indicated binding of GF-6 to ACE via multiple binding sites on the protein surface. This study could be deemed helpful for the better understanding of the inhibitory mechanism of ACE inhibitory peptides.

Quenching of tryptophan fluorescence in a highly scattering solution: Insights on protein localization in a lung surfactant formulation

CHF5633 (Chiesi Farmaceutici, Italy) is a synthetic surfactant developed for respiratory distress syndrome replacement therapy in pre-term newborn infants. CHF5633 contains two phospholipids (dipalmitoylphosphatidylcholine and 1-palmitoyl-2oleoyl-sn-glycero-3-phosphoglycerol sodium salt), and peptide analogues of surfactant protein C (SP-C analogue) and surfactant protein B (SP-B analogue). Both proteins are fundamental for an optimal surfactant activity in vivo and SP-B genetic deficiency causes lethal respiratory failure after birth. Fluorescence emission of the only tryptophan residue present in SP-B analogue (SP-C analogue has none) could in principle be exploited to probe SP-B analogue conformation, localization and interaction with other components of the pharmaceutical formulation. However, the high light scattering activity of the multi-lamellar vesicles suspension characterizing the pharmaceutical surfactant formulation represents a challenge for such studies. We show here that quenching of tryptophan fluorescence and Singular Value Decomposition analysis can be used to accurately calculate and subtract background scattering. The results indicate, with respect to Trp microenvironment, a conformationally homogeneous population of SP-B. Trp is highly accessible to the water phase, suggesting a surficial localization on the membrane of phospholipid vesicles, similarly to what observed for full length SP-B in natural lung surfactant, and supporting an analogous role in protein anchoring to the lipid phase.

Cyano-tryptophans as dual infrared and fluorescence spectroscopic labels to assess structural dynamics in proteins

By moving the cyano group position on the indole ring, both artificial amino acids report differently to their microscopic environment.

Fluorescence lifetime components reveal kinetic intermediate states upon equilibrium denaturation of carbonic anhydrase II

In most cases, intermediate states of multistage folding proteins are not 'visible' under equilibrium conditions but are revealed in kinetic experiments. Time-resolved fluorescence spectroscopy was used in equilibrium denaturation studies. The technique allows for detecting changes in the conformation and environment of tryptophan residues in different structural elements of carbonic anhydrase II which in its turn has made it possible to study the intermediate states of carbonic anhydrase II under equilibrium conditions. The results of equilibrium and kinetic experiments using wild-type bovine carbonic anhydrase II and its mutant form with the substitution of leucine for alanine at position 139 (L139A) were compared. The obtained lifetime components of intrinsic tryptophan fluorescence allowed for revealing that, the same as in kinetic experiments, under equilibrium conditions the unfolding of carbonic anhydrase II ensues through formation of intermediate states.

Photophysics of N,N-dimethyl-3-(1-indolyl)propan-1-ammonium chloride and related derivatives

The photophysical properties of two new indole derivatives have been examined by steady-state and dynamic spectroscopic methods. The ground-state structures and conformations of 3-(1-indolyl)-N,N-dimethylpropan-1-ammonium chloride (InCl) and 3-(1-indolyl)-N,N,N-trimethylpropan-1-ammonium chloride (MeInCl) have been examined through density functional theory calculations. These calculations reveal a preference for a 'closed' conformation which places the cationic ammonium group in proximity to the π-electron cloud in low polarity environments. This interaction is best described as an intramolecular hydrogen-π bond in the case of InCl and a cation-π interaction for MeInCl. The ground-state conformational equilibria are influenced by changes in the dielectric constant of the solvent, resulting in a variety of photophysical behaviors. The excitation/emission spectra, fluorescence quantum yields, and excited-state lifetimes, are reported for InCl, MeInCl, and a reference compound, 1-methylindole, in 1,4-dioxane (ε = 2), acetonitrile (ε = 37), and water (ε = 78) where solubility allows. Data from these solvents provide evidence for independent fluorescence quenching pathways for InCl and MeInCl. In addition, they lead to insights into the complexities of indole photophysics by demonstrating the sensitivity of the locally-excited states to changes in charge-density and solvent environment.

Tryptophan Fluorescence Yields and Lifetimes as a Probe of Conformational Changes in Human Glucokinase

Five variants of glucokinase (ATP-D-hexose-6-phosphotransferase, EC 2.7.1.1) including wild type and single Trp mutants with the Trp residue at positions 65, 99, 167 and 257 were prepared. The fluorescence of Trp in all locations studied showed intensity changes when glucose bound, indicating that conformational change occurs globally over the entire protein. While the fluorescence quantum yield changes upon glucose binding, the enzyme's absorption spectra, emission spectra and fluorescence lifetimes change very little. These results are consistent with the existence of a dark complex for excited state Trp. Addition of glycerol, L-glucose, sucrose, or trehalose increases the binding affinity of glucose to the enzyme and increases fluorescence intensity. The effect of these osmolytes is thought to shift the protein conformation to a condensed, high affinity form. Based upon these results, we consider the nature of quenching of the Trp excited state. Amide groups are known to quench indole fluorescence and amides of the polypeptide chain make interact with excited state Trp in the relatively unstructured, glucose-free enzyme. Also, removal of water around the aromatic ring by addition of glucose substrate or osmolyte may reduce the quenching.

Time resolved fluorescence of cow and goat milk powder

Milk powder is an international dairy commodity. Goat and cow milk powders are significant sources of nutrients and the investigation of the authenticity and classification of milk powder is particularly important. The use of time-resolved fluorescence techniques to distinguish chemical composition and structure modifications could assist develop a portable and non-destructive methodology to perform milk powder classification and determine composition. This study goal is to differentiate milk powder samples from cows and goats using fluorescence lifetimes. The samples were excited at 315nm and the fluorescence intensity decay registered at 468nm. We observed fluorescence lifetimes of 1.5±0.3, 6.4±0.4 and 18.7±2.5ns for goat milk powder; and 1.7±0.3, 6.9±0.2 and 29.9±1.6ns for cow's milk powder. We discriminate goat and cow powder milk by analysis of variance using Fisher's method. In addition, we employed quadratic discriminant analysis to differentiate the milk samples with accuracy of 100%. Our results suggest that time-resolved fluorescence can provide a new method to the analysis of powder milk and its composition.

Stability improvement of natural food colors: Impact of amino acid and peptide addition on anthocyanin stability in model beverages

Anthocyanins are prone to chemical degradation and color fading in the presence of vitamin C. The potential of three amino acids (l-phenylalanine, l-tyrosine, l-tryptophan) and a polypeptide (ε-poly-l-lysine) in prolonging the color stability of purple carrot anthocyanins (0.025%) in model beverages (0.05% l-ascorbic acid, citric acid, pH 3.0) stored at elevated temperature (40°C/7 days) was examined. In the absence of amino acids or peptides, anthocyanin degraded at first-order reaction rate. Addition of amino acids or peptide (0.1%) increased the color stability of anthocyanins, with the most significant improvement observed for l-tryptophan. The average half-life of anthocyanin color increased from 2 days to 6 days with l-tryptophan addition. Fluorescence quenching measurements revealed that the l-tryptophan interacted with anthocyanins mainly through hydrogen bonding, although some hydrophobic interaction may also have been involved. Overall, this study suggests that amino acid or peptide addition may prolong the color stability of anthocyanin in beverage products.

Effect of Short Chain Poly(ethylene glycol)s on the Hydration Structure and Dynamics around Human Serum Albumin

We report the changes in the hydration dynamics around a globular protein, human serum albumin (HSA), in the presence of two short chain crowding agents, namely poly(ethylene glycol)s (PEG 200 and 400). The change in the network water structure is investigated using FTIR spectroscopy in the far-infrared (FIR) frequency range. Site specific changes are obtained by time-resolved fluorescence spectroscopic technique using the intrinsic fluorophore tryptophan (Trp214) of HSA. The collective hydration dynamics of HSA in the presence of PEG molecules are obtained using terahertz (THz) time domain spectroscopy (TTDS) and high intensity p-Ge THz measurements. Our study affirms a considerable perturbation of HSA hydration beyond a critical concentration of PEG.

Effect of Quencher, Denaturants, Temperature and pH on the Fluorescent Properties of BSA Protected Gold Nanoclusters

In this paper, we have synthesized BSA protected gold nanoclusters (BSA Au nanocluster) and studied the effect of quencher, protein denaturant, pH and temperature on the fluorescence properties of the tryptophan molecule of the BSA Au nanocluster and native BSA. We have also studied their effect on the peak emission of BSA Au nanoclusters (650 nm). The phtophysical characterization of a newly developed fluorophore in different environments is absolutely necessary to futher develop their biomedical and analytical applications. It was observed from our experiments that the tryptophan in BSA Au nanoclusters is better shielded from the polar environment. Tryptophan in native BSA showed a red shift in its peak emission wavelength position. Tryptophan is a highly polarity sensitive dye and a minimal change in its microenvironment can be easily observed in its photophysical properties.

Exploring protein solution structure: Second moments of fluorescent spectra report heterogeneity of tryptophan rotamers

Trp fluorescent spectra appear as a log-normal function but are usually analyzed with λmax, full width at half maximum, and the first moment of incomplete spectra. Log-normal analyses have successfully separated fluorescence contributions from some multi-Trp proteins but deviations were observed in single Trp proteins. The possibility that disparate rotamer environments might account for these deviations was explored by moment spectral analysis of single Trp mutants spanning the sequence of tear lipocalin as a model. The analysis required full width Trp spectra. Composite spectra were constructed using log-normal analysis to derive the inaccessible blue edge, and the experimentally obtained spectra for the remainder. First moments of the composite spectra reflected the site-resolved secondary structure. Second moments were most sensitive for spectral deviations. A novel parameter, derived from the difference of the second moments of composite and simulated log-normal spectra correlated with known multiple heterogeneous rotamer conformations. Buried and restricted side chains showed the most heterogeneity. Analyses applied to other proteins further validated the method. The rotamer heterogeneity values could be rationalized by known conformational properties of Trp residues and the distribution of nearby charged groups according to the internal Stark effect. Spectral heterogeneity fits the rotamer model but does not preclude other contributing factors. Spectral moment analysis of full width Trp emission spectra is accessible to most laboratories. The calculations are informative of protein structure and can be adapted to study dynamic processes.

Fluorescence quenching study of resveratrol binding to zein and gliadin: Towards a more rational approach to resveratrol encapsulation using water-insoluble proteins

Several health benefits have been ascribed to consumption of resveratrol, a polyphenol that can be extracted from grape skins. However, its use as a nutraceutical ingredient is compromised by its low water solubility, chemical stability, and bioavailability. Encapsulation of resveratrol in protein nanoparticles can be used to overcome these issues. Fluorescence quenching experiments were used to study the interaction of resveratrol with gliadin and zein. Resveratrol interacted with both proteins, but the binding constant was higher for zein than for gliadin at 35 °C. Furthermore, binding between resveratrol and gliadin increased at higher temperatures, which was not observed for zein. Analysis of the thermodynamic parameters suggested that resveratrol-gliadin binding mainly occurs through hydrophobic interactions while the binding with zein is predominantly mediated through hydrogen bonds. These results help rationalise ingredient selection and production of protein nanoparticles and microparticles for encapsulation, protection and release of resveratrol and potentially other bioactive compounds.

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.