Algorithm for the Analysis of Tryptophan Fluorescence Spectra and Their Correlation with Protein Structural Parameters

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.

In Vitro and In Silico Explorations of the Protein Conformational Changes of Corynebacterium glutamicum MshA, a Model Retaining GT-B Glycosyltransferase

MshA is a GT-B glycosyltransferase catalyzing the first step in the biosynthesis of mycothiol. While many GT-B enzymes undergo an open-to-closed transition, MshA is unique because its 97° rotation is beyond the usual range of 10-25°. Molecular dynamics (MD) simulations were carried out for MshA in both ligand bound and unbound states to investigate the effect of ligand binding on localized protein dynamics and its conformational free energy landscape. Simulations showed that both the unliganded "opened" and liganded "closed" forms of the enzyme sample a wide degree of dihedral angles and interdomain distances with relatively low overlapping populations. Calculation of the free energy surface using replica exchange MD for the apo "opened" and an artificial generated apo "closed" structure revealed overlaps in the geometries sampled, allowing calculation of a barrier of 2 kcal/mol for the open-to-closed transition in the absence of ligands. MD simulations of fully liganded MshA revealed a smaller sampling of the dihedral angles. The localized protein fluctuation changes suggest that UDP-GlcNAc binding activates the motions of loops in the 1-l-myo-inositol-1-phosphate (I1P)-binding site despite little change in the interactions with UDP-GlcNAc. Circular dichroism, intrinsic fluorescence spectroscopy, and mutagenesis studies were used to confirm the ligand-induced structural changes in MshA. The results support a proposed mechanism where UDP-GlcNAc binds with rigid interactions to the C-terminal domain of MshA and activates flexible loops in the N-terminal domain for binding and positioning of I1P. This model can be used for future structure-based drug development of inhibitors of the mycothiol biosynthetic pathway.

Discovery of first-in-class nanomolar inhibitors of heptosyltransferase I reveals a new aminoglycoside target and potential alternative mechanism of action

A clinically relevant inhibitor for Heptosyltransferase I (HepI) has been sought after for many years because of its critical role in the biosynthesis of lipopolysaccharides on bacterial cell surfaces. While many labs have discovered or designed novel small molecule inhibitors, these compounds lacked the bioavailability and potency necessary for therapeutic use. Extensive characterization of the HepI protein has provided valuable insight into the dynamic motions necessary for catalysis that could be targeted for inhibition. Structural inspection of Kdo2-lipid A suggested aminoglycoside antibiotics as potential inhibitors for HepI. Multiple aminoglycosides have been experimentally validated to be first-in-class nanomolar inhibitors of HepI, with the best inhibitor demonstrating a Ki of 600 ± 90 nM. Detailed kinetic analyses were performed to determine the mechanism of inhibition while circular dichroism spectroscopy, intrinsic tryptophan fluorescence, docking, and molecular dynamics simulations were used to corroborate kinetic experimental findings. While aminoglycosides have long been described as potent antibiotics targeting bacterial ribosomes' protein synthesis leading to disruption of the stability of bacterial cell membranes, more recently researchers have shown that they only modestly impact protein production. Our research suggests an alternative and novel mechanism of action of aminoglycosides in the inhibition of HepI, which directly leads to modification of LPS production in vivo. This finding could change our understanding of how aminoglycoside antibiotics function, with interruption of LPS biosynthesis being an additional and important mechanism of aminoglycoside action. Further research to discern the microbiological impact of aminoglycosides on cells is warranted, as inhibition of the ribosome may not be the sole and primary mechanism of action. The inhibition of HepI by aminoglycosides may dramatically alter strategies to modify the structure of aminoglycosides to improve the efficacy in fighting bacterial infections.

Physicochemical and Biological Characterization of rhC1INH Expressed in CHO Cells

The disfunction or deficiency of the C1 esterase inhibitor (C1INH) is associated with hereditary or acquired angioedema (HAE/AAE), a rare life-threatening condition characterized by swelling in the skin, respiratory and gastrointestinal tracts. The current treatment options may carry the risks of either viral infection (plasma-derived Berinert^®) or immune reaction (human recombinant C1INH from rabbit milk, Ruconest^®). This study describes the physicochemical and biological characterization of a novel recombinant human C1 esterase inhibitor (rhC1INH) from Chinese hamster ovary (CHO) cells for the treatment of hereditary angioedema compared to the marketed products Berinert^® and Ruconest^®. The mass spectrometry results of total deglycosylated rhC1INH revealed a protein with a molecular mass of 52,846 Da. Almost full sequence coverage (98.6%) by nanoLC-MS/MS peptide mapping was achieved. The purity and C1s inhibitory activity of rhC1INH from CHO cells are comparable with Ruconest^®, although we found differences in charge isoforms distribution, intact mass values, and N-glycans profile. Comparison of the specific activity (IC₅₀ value) of the rhC1INH with human C1 esterase inhibitor from blood serum showed similar inhibitory properties. These data allow us to conclude that the novel rhC1INH molecule could become a potential therapeutic option for patients with HAE/AAE.

Synthesis and Properties of Targeted Radioisotope Carriers Based on Poly(Acrylic Acid) Nanogels

Radiation crosslinking was employed to obtain nanocarriers based on poly(acrylic acid)—PAA—for targeted delivery of radioactive isotopes. These nanocarriers are internally crosslinked hydrophilic macromolecules—nanogels—bearing carboxylic groups to facilitate functionalization. PAA nanogels were conjugated with an engineered bombesin-derivative—oligopeptide combined with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate chelating moiety, aimed to provide selective radioligand transport. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) toluene-4-sulfonate was used as the coupling agent. After tests on a model amine—p-toluidine—both commercial and home-synthesized DOTA-bombesin were successfully coupled to the nanogels and the obtained products were characterized. The radiolabeling efficiency of nanocarriers with ¹⁷⁷Lu, was chromatographically tested. The results provide a proof of concept for the synthesis of radiation-synthesized nanogel-based radioisotope nanocarriers for theranostic applications.

Molecular excited states through a machine learning lens

Theoretical simulations of electronic excitations and associated processes in molecules are indispensable for fundamental research and technological innovations. However, such simulations are notoriously challenging to perform with quantum mechanical methods. Advances in machine learning open many new avenues for assisting molecular excited-state simulations. In this Review, we track such progress, assess the current state of the art and highlight the critical issues to solve in the future. We overview a broad range of machine learning applications in excited-state research, which include the prediction of molecular properties, improvements of quantum mechanical methods for the calculations of excited-state properties and the search for new materials. Machine learning approaches can help us understand hidden factors that influence photo-processes, leading to a better control of such processes and new rules for the design of materials for optoelectronic applications.

The Role of Surface Properties on Protein Aggregation Behavior in Aqueous Solution of Different pH Values

This study aimed to investigate the effect of pH-mediated surface properties of bovine serum albumin (BSA) on protein aggregation and the changes of protein structure and colloidal stability at different solution pH levels. The hydrophobicity of BSA surface was characterized by endogenous fluorescence spectroscopy, fluorescence quenching of acrylamide, and fluorescence probe. The results showed that the hydrophobicity of BSA surface was similar at pH 5, 6, 7.4, followed by pH 4, 8, 9, 10, and finally by pH 3 and 11 with strong acidity and alkalinity. The positive charge on the BSA surface was increased gradually with the decrease of solution pH, while the negative charge on protein surface was increased gradually with the increase of solution pH. The degree of protein aggregation was examined by turbidimetry, flow cytometry, and SDS-PAGE. The results showed that the oscillating aggregation of BSA did not change with the solution pH, but was partially dependent on the relative contribution of electrostatic and hydrophobic interactions between the protein molecules. In addition, the secondary structure, conformational stability, unfolding degree, and colloidal stability of proteins were investigated by circular dichroism, fluorescence spectroscopy, protein pulse hydrolysis, and dynamic light scattering, respectively. The results suggested that the solution pH could change the structure and stability of the protein at different levels. Solution pH has distinct effects on the structural stability of protein at different levels. The change of protein surface properties mediated by solution pH is related to protein aggregation.

Crowder-Induced Conformational Ensemble Shift in Escherichia coli Prolyl-tRNA Synthetase

The effect of molecular crowding on the structure and function of Escherichia coli prolyl-transfer RNA synthetase (Ec ProRS), a member of the aminoacyl-transfer RNA synthetase family, has been investigated using a combined experimental and theoretical method. Ec ProRS is a multidomain enzyme; coupled-domain dynamics are essential for efficient catalysis. To gain insight into the mechanistic detail of the crowding effect, kinetic studies were conducted with varying concentrations and sizes of crowders. In parallel, spectroscopic and quantum chemical studies were employed to probe the "soft interactions" between crowders and protein side chains. Finally, the dynamics of the dimeric protein was examined in the presence of crowders using a long-duration (70 ns) classical molecular dynamic simulations. The results of the simulations revealed a shift in the conformational ensemble, which is consistent with the preferential exclusion of cosolutes. The "soft interactions" model of the crowding effect also explained the alteration in kinetic parameters. In summary, the study found that the effects of molecular crowding on both conformational dynamics and catalytic function are correlated in the multidomain Ec ProRS, an enzyme that is central to protein synthesis in all living cells. This study affirmed that large and small cosolutes have considerable impacts on the structure, dynamics, and function of modular proteins and therefore must be considered for stabilizing protein-based pharmaceuticals and industrial enzymes.

Probing conformational changes of monomeric transthyretin with second derivative fluorescence

We have studied the intrinsic fluorescence spectra of a monomeric variant of human transthyretin (M-TTR), a protein involved in the transport of the thyroid hormone and retinol and associated with various forms of amyloidosis, extending our analysis to the second order derivative of the spectra. This procedure allowed to identify three peaks readily assigned to Trp41, as the three peaks were also visible in a mutant lacking the other tryptophan (Trp79) and had similar FRET efficiency values with an acceptor molecule positioned at position 10. The wavelength values of the three peaks and their susceptibility to acrylamide quenching revealed that the three corresponding conformers experience different solvent-exposure, polarity of the environment and flexibility. We could monitor the three peaks individually in urea-unfolding and pH-unfolding curves. This revealed changes in the distribution of the corresponding conformers, indicating conformational changes and alterations of the dynamics of the microenvironment that surrounds the associated tryptophan residue in such transitions, but also native-like conformers of such residues in unfolded states. We also found that the amyloidogenic state adopted by M-TTR at mildly low pH has a structural and dynamical microenvironment surrounding Trp41 indistinguishable from that of the fully folded and soluble state at neutral pH.

Structural stability of human butyrylcholinesterase under high hydrostatic pressure

Human butyrylcholinesterase is a nonspecific enzyme of clinical, pharmacological and toxicological significance. Although the enzyme is relatively stable, its activity is affected by numerous factors, including pressure. In this work, hydrostatic pressure dependence of the intrinsic tryptophan fluorescence in native and salted human butyrylcholinesterase was studied up to the maximum pressure at ambient temperature of about 1200 MPa. A correlated large shift toward long wavelengths and broadening observed at pressures between 200 and 700 MPa was interpreted as due to high pressure-induced denaturation of the protein, leading to an enhanced exposure of tryptophan residues into polar solvent environment. This transient process in native butyrylcholinesterase presumably involves conformational changes of the enzyme at both tertiary and secondary structure levels. Pressure-induced mixing of emitting local indole electronic transitions with quenching charge transfer states likely describes the accompanying fluorescence quenching that reveals different course from spectral changes. All the pressure-induced changes turned irreversible after passing a mid-point pressure of about 400 ± 50 MPa. Addition of either 0.1 M ammonium sulphate (a kosmotropic salt) or 0.1 M lithium thiocyanate (a chaotropic salt) to native enzyme similarly destabilized its structure.

The impact of length variations in the L2 loop on the structure and thermal stability of non-specific porins: The case of OmpCs from the Yersinia pseudotuberculosis complex

Porins are integral proteins of the outer membranes of gram-negative bacteria. In membranes, they exist as homotrimers and the L2 loops contribute to their stability. Comparison of OmpC porins of the Yersinia pseudotuberculosis complex with other enterobacterial porins demonstrated L2 loop length diversity, which is caused by varying numbers of dipeptide/tripeptide repeats. The OmpC porins are highly homologous to each other, and they can be subdivided into five isoforms based on their L2 loop structure. Optical spectroscopy and SDS-PAGE experiments revealed that particularities of the L2 loops affected the structure and thermal stability of the porins. Thermal denaturation studies showed that porins with shorter loops, compared to porins with longer loops, had more stable tertiary and less stable secondary and quaternary structures. According to our comparative modeling results, the L2 loops differ in their structure by adopting different spatial positions and forming different polar bonds with a neighbor monomer. The replacement of asparagine with arginine at the C-terminus of the L2 loop shifts the loop upwards and causes the loss of contacts with the arginine clusters within the pores. The increase in the length of these loops ensures that they shift down toward the pore and restore their contacts with arginines on the channel wall, as is the case in classical nonspecific porins. Despite the fact that the surface charge density varies considerably among the OmpC porins, the L2 loops form a typical negatively charged region in the center of the trimer.

Assessment of organic pollution of an industrial river by synchronous fluorescence and UV-vis spectroscopy: the Fensch River (NE France)

To rapidly monitor the surface water quality in terms of organic pollution of an industrial river undergoing restoration, optical methods (UV-visible spectrometry and fluorescence) were applied in parallel to classical physical-chemical analyses. UV-visible spectra were analyzed using the maximum of the second derivative at 225 nm (related to nitrates), specific absorbance at 254 nm (SUVA₂₅₄), and the spectral slope between 275 and 295 nm (S _275-295) (related to the aromaticity and molecular weight of dissolved organic carbon). The synchronous fluorescence spectra (wavelength difference = 50 nm) exhibited a high variability in the composition of dissolved organic material between the upstream and downstream sections and also versus time. The principal components analysis of the entire set of synchronous fluorescence spectra helped to define three river sections with different pollution characteristics. Spectral decomposition was applied to the two most upstream sections: five fluorophores, classical in rivers impacted by domestic sewage and related to protein-like (λ _ex = 280 nm) and humic-like fluorescence (M-type with λ _ex ≈ 305-310 nm and C-type with λ _ex ≥ 335 nm), were identified. The irregular shape of the synchronous fluorescence spectra in the most downstream section is likely due to organic pollutants of industrial origin; however, their variability and the complexity of the spectra did not allow the further elucidation of their nature.

The Signaling State of Orange Carotenoid Protein

Orange carotenoid protein (OCP) is the photoactive protein that is responsible for high light tolerance in cyanobacteria. We studied the kinetics of the OCP photocycle by monitoring changes in its absorption spectrum, intrinsic fluorescence, and fluorescence of the Nile red dye bound to OCP. It was demonstrated that all of these three methods provide the same kinetic parameters of the photocycle, namely, the kinetics of OCP relaxation in darkness was biexponential with a ratio of two components equal to 2:1 independently of temperature. Whereas the changes of the absorption spectrum of OCP characterize the geometry and environment of its chromophore, the intrinsic fluorescence of OCP reveals changes in its tertiary structure, and the fluorescence properties of Nile red indicate the exposure of hydrophobic surface areas of OCP to the solvent following the photocycle. The results of molecular-dynamics studies indicated the presence of two metastable conformations of 3'-hydroxyechinenone, which is consistent with characteristic changes in the Raman spectra. We conclude that rotation of the β-ionylidene ring in the C-terminal domain of OCP could be one of the first conformational rearrangements that occur during photoactivation. The obtained results suggest that the photoactivated form of OCP represents a molten globule-like state that is characterized by increased mobility of tertiary structure elements and solvent accessibility.

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.

Spectrophotometric characterization of dissolved organic matter in a rural watershed: the Madon River (N-E France)

In the last 20 years, increasing dissolved organic carbon (DOC) concentrations have been observed in several rivers and lakes in Europe. This increase has reduced the quality of the aquatic environment. In this study, UV-vis spectroscopy and synchronous fluorescence spectroscopy with a difference of 50 nm between the excitation and emission (SF50) were used to characterize the DOC in a rural river (Madon River). The specific absorbance index at 254 nm (SUVA254) which is related to the aromaticity of DOC was extracted from UV-vis spectra, whose maximum of the second derivative (occurring near 225 nm) is related to nitrates. SF50 spectra which are characterized by well-defined peaks indicated large spatial and temporal variations. Two methods were used to analyze and compare these spectra. The first method was based on the decomposition of the SF50 spectra into four Gauss functions: B1 (related to tryptophan-like fluorescence), B2 and B3 (related to humic substances), and B4 (related to chlorophyll-like substances). The second method was principal components analysis (PCA), which results yielded three principal components that accounted for 95% of the variance. Although PCA enables the consideration of the spectra without making assumptions regarding the number of fluorophores, the results from the decomposition in Gauss function were easier to interpret.

Human mitochondrial NDUFS3 protein bearing Leigh syndrome mutation is more prone to aggregation than its wild-type

NDUFS3 is an integral subunit of the Q module of the mitochondrial respiratory Complex-I. The combined mutation (T145I + R199W) in the subunit is reported to cause optic atrophy and Leigh syndrome accompanied by severe Complex-I deficiency. In the present study, we have cloned and overexpressed the human NDUFS3 subunit and its double mutant in a soluble form in Escherichia coli. The wild-type (w-t) and mutant proteins were purified to homogeneity through a serial two-step chromatographic purification procedure of anion exchange followed by size exclusion chromatography. The integrity and purity of the purified proteins was confirmed by Western blot analysis and MALDI-TOF/TOF. The conformational transitions of the purified subunits were studied through steady state as well as time resolved fluorescence and CD spectroscopy under various denaturing conditions. The mutant protein showed altered polarity around tryptophan residues, changed quenching parameters and also noticeably altered secondary and tertiary structure compared to the w-t protein. Mutant also exhibited a higher tendency than the w-t protein for aggregation which was examined using fluorescent (Thioflavin-T) and spectroscopic (Congo red) dye binding techniques. The pH stability of the w-t and mutant proteins varied at extreme acidic pH and the molten globule like structure of w-t at pH1 was absent in case of the mutant protein. Both the w-t and mutant proteins showed multi-step thermal and Gdn-HCl induced unfolding. Thus, the results provide insight into the alterations of NDUFS3 protein structure caused by the mutations, affecting the overall integrity of the protein and finally leading to disruption of Complex-I assembly.