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1.
Anal Chem ; 93(32): 11081-11088, 2021 08 17.
Artigo em Inglês | MEDLINE | ID: mdl-34355885

RESUMO

The debate of whether a glass substrate can be used in Fourier transform infrared spectroscopy is strongly linked to its potential clinical application. Histopathology glass slides of 1 mm thickness absorb the mid-IR spectrum in the rich fingerprint spectral region. Thus, it is important to assess whether emerging IR techniques can be employed to study biological samples placed on glass substrates. For this purpose, we used optical photothermal infrared (O-PTIR) spectroscopy to study for the first time malignant and non-malignant lung cells with the purpose of identifying IR spectral differences between these cells placed on standard pathology glass slides. The data in this feasibility study showed that O-PTIR can be used to obtain good-quality IR spectra from cells from both the lipid region (3000-2700 cm-1) and the fingerprint region between 1770 and 950 cm-1 but with glass contributions from 1350 to 950 cm-1. A new single-unit dual-range (C-H/FP) quantum cascade laser (QCL) IR pump source was applied for the first time, delivering a clear synergistic benefit to the classification results. Furthermore, O-PTIR is able to distinguish between lung cancer cells and non-malignant lung cells both in the lipid and fingerprint regions. However, when these two spectral ranges are combined, classification accuracies are enhanced with Random Forest modeling classification accuracy results ranging from 96 to 99% across all three studied cell lines. The methodology described here for the first time with a single-unit dual-range QCL for O-PTIR on glass is another step toward its clinical application in pathology.


Assuntos
Vidro , Lasers Semicondutores , Pulmão , Espectrofotometria Infravermelho , Espectroscopia de Infravermelho com Transformada de Fourier
2.
J Chem Phys ; 155(4): 040903, 2021 Jul 28.
Artigo em Inglês | MEDLINE | ID: mdl-34340394

RESUMO

Proteins are complex, heterogeneous macromolecules that exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires experimental tools to characterize them with high spatial and temporal precision. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution. Two-dimensional (2D) IR methods that provide richer information are becoming more routine but remain challenging to apply to proteins. Spectral congestion typically prevents selective investigation of native vibrations; however, the problem can be overcome by site-specific introduction of amino acid side chains that have vibrational groups with frequencies in the "transparent window" of protein spectra. This Perspective provides an overview of the history and recent progress in the development of transparent window 2D IR of proteins.


Assuntos
Proteínas/química , Espectrofotometria Infravermelho/métodos , Monóxido de Carbono/química , Cianetos/química , Ligantes , Metais/química , Simulação de Dinâmica Molecular , Conformação Proteica
3.
J Phys Chem Lett ; 12(32): 7777-7782, 2021 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-34374547

RESUMO

Enzyme catalysis achieves tremendous rate accelerations. Enzyme reaction centers provide a constraint geometry that preferentially binds an activated form of the substrate and thus lowers the energy barrier. However, this transition state picture neglects the flexibility of proteins and its role in enzymatic catalysis. Especially for proton transfer reactions, it has been suggested that motions of the protein modulate the donor-acceptor distance and prepare a tunneling-ready state. We report the detection of frequency fluctuations of an azide anion (N3-) bound in the active site of the protein carbonic anhydrase II, where a low-frequency mode of the protein has been proposed to facilitate proton transfer over two water molecules during the catalyzed reaction. 2D-IR spectroscopy resolves an underdamped low-frequency mode at about 1 THz (30 cm-1). We find its frequency to be viscosity- and temperature-dependent and to decrease by 6 cm-1 between 230 and 320 K, reporting the softening of the mode's potential.


Assuntos
Anidrase Carbônica II/química , Animais , Azidas/química , Domínio Catalítico , Bovinos , Prótons , Espectrofotometria Infravermelho/métodos , Temperatura , Vibração , Viscosidade , Água/química
4.
Spectrochim Acta A Mol Biomol Spectrosc ; 263: 120217, 2021 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-34343843

RESUMO

Photoinduced NO-linkage isomers were investigated in the solid state of labelled trans-[Ru(14/15NO)(py4)F](ClO4)2 complex by combined IR-spectroscopy and DFT calculations. Based on the experimental data and the DFT calculations of this isotopically labelled 14/15NO nitrosyl compound, we present a complete assignment of the vibrational bands of three nitrosyl linkage isomers in a range from 4000 to 200 cm-1. The calculated IR-spectra match well with the experimental data allowing reliable assignment of the vibrational bands. The structural change from the Ru-NO (GS) to the Ru-ON (MS1) and Ru-η2-(NO) (MS2) linkage configuration leads to the downshift of the ν(NO) and ν(Ru-(NO)) bands, and a corresponding increase of the energy of the ν(Ru-F) band. The shift of the bands corresponds to the change of the Ru-(NO) and Ru-F bond lengths: increase of the Ru-(NO) bond length leads to the decrease of the energy of the ν(Ru-(NO)) band; decrease of the Ru-F bond length leads to the increase of the energy of the ν(Ru-F) band. These observations can be extrapolated to the family of related nitrosyl complexes and therefore be used for the qualitative prediction of the Ru-(NO) and Ru-Ltrans-to-NO bond lengths of different linkage isomers in the framework of one complex. While the formation of linkage isomers is a reversible process, long-time irradiation sometimes induces irreversible reactions such as the release of NO. Here, we show that the photolysis of trans-[Ru(14/15NO)(py4)F](ClO4)2 in KBr pellets may lead to the release of nitrous oxide N2O, conceivably through the formation of a {Ru-(κ2-ONNO)} intermediate.


Assuntos
Rutênio , Cristalografia por Raios X , Óxido Nítrico , Espectrofotometria Infravermelho , Vibração
5.
ACS Sens ; 6(8): 2875-2882, 2021 08 27.
Artigo em Inglês | MEDLINE | ID: mdl-34347437

RESUMO

Surface-enhanced infrared absorption spectroscopy (SEIRAS) is a powerful tool that allows studying the reactivity of protein monolayers at very low concentrations and independent from the protein size. In this study, we probe the surface's morphology of electroless gold deposition for optimum enhancement using two different types of immobilization adapted to two proteins. Independently from the mode of measurement (i.e., transmission or reflection) or type of protein immobilization (i.e., through electrostatic interactions or nickel-HisTag), the enhancement and reproducibility of protein signals in the infrared spectra critically depended on the gold nanostructured surface morphology deposited on silicon. Just a few seconds deviation from the optimum time in the nanoparticle deposition led to a significantly weaker enhancement. Scanning electron microscopy and atomic force microscopy measurements revealed the evolution of the nanostructured surface when comparing different deposition times. The optimal deposition time led to isolated gold nanostructures on the silicon crystal. Importantly, in the case of the immobilization using nickel-HisTag, the surface morphology is rearranged upon immobilization of linker and the protein. A complex three-dimensional (3D) network of nanoparticles decorated with the protein could be observed leading to the optimal enhancement. The electroless deposition of gold is a simple technique, which can be adapted to flow cells and used in analytical approaches.


Assuntos
Ouro , Nanoestruturas , Proteínas de Membrana , Reprodutibilidade dos Testes , Espectrofotometria Infravermelho , Propriedades de Superfície
6.
Talanta ; 234: 122653, 2021 Nov 01.
Artigo em Inglês | MEDLINE | ID: mdl-34364462

RESUMO

Deoxynivalenol (DON) contamination in wheat flour induces a number of adverse health effects to consumers and livestock, even at very low concentrations. Direct detection methods for massive screening of DON in wheat flour is still lacking. A new methodology integrating multi-molecular infrared spectroscopy (MM-IR) with two-trace two-dimensional correlation spectroscopy (2T-2DCOS) was developed for in-situ qualitative and quantitative determination of DON in wheat flour as a whole. Typical spectral variation of wheat flour samples with diverse concentration of DON were stepwise characterized by MM-IR and tiny spectral profile differences resulting from concentration variation of DON were visually disclosed by 2T-2DCOS. Based on the obtained key spectral features of DON, 180 of wheat flour samples with DON higher and lower than 1.00 mg/kg were undoubtedly classified by Principal Component Analysis (PCA) and Support Vector Machines (SVM) with an accuracy rate up to 100% (for Second derivative spectra consisted of selected bands, SD-SS). Furthermore, a robust quantitative prediction model was established based on partial least squares (PLS) of SD-SS (Rc: 0.998, RMSEC: 0.135; Rp: 0.968, RMSEP: 0.421), and its excellent predictive capacity of model was validated by both residual prediction deviation (RPD) value of 3.2 and t-test. It was demonstrated that the developed methodology was applicable for screening and quantitative detection of DON in wheat flour based on the novel correlation analysis methods (SD-2DCOS-IR and 2T-2DCOS-IR) with chemometrics tools, which could be utilized both at laboratory and industrial level for quality control purposes of a large wheat flour sample set.


Assuntos
Farinha , Triticum , Farinha/análise , Contaminação de Alimentos/análise , Humanos , Análise dos Mínimos Quadrados , Espectrofotometria Infravermelho
7.
J Phys Chem A ; 125(29): 6348-6355, 2021 Jul 29.
Artigo em Inglês | MEDLINE | ID: mdl-34270243

RESUMO

Sodiated complexes of the aliphatic amino acids, Gly, Ala, Val, Leu, and Ile, were examined with infrared multiple-photon dissociation action spectroscopy utilizing light from a free-electron laser. To identify structures, the experimental spectra were compared to linear spectra calculated at the B3LYP/6-311+G(d,p) level of theory. Relative energetics of all complexes were calculated at B3LYP, B3P86, MP2(full), B3LYP-GD3BJ, and M06-2X levels using a 6-311+G(2d,2p) basis set. Spectral comparison for all complexes indicates that the dominant conformation, [N, CO], binds to the amino nitrogen and carbonyl oxygen. For all complexes except Gly, contributions are observed from [CO2-] structures, where the sodium cation binds to both oxygens of the carboxylate group in the zwitterionic form of the amino acid. The semiquantitative distribution between these two structures appears to be best-predicted by the B3LYP and MP2(full) levels of theory, with predictions from the other three levels inconsistent with the experiment.


Assuntos
Aminoácidos/metabolismo , Sódio/metabolismo , Aminoácidos/química , Modelos Químicos , Conformação Molecular , Sódio/química , Espectrofotometria Infravermelho/métodos , Termodinâmica
8.
Spectrochim Acta A Mol Biomol Spectrosc ; 263: 120162, 2021 Dec 15.
Artigo em Inglês | MEDLINE | ID: mdl-34280799

RESUMO

The EU goal to reduce marine plastic litter by ca. 30% by 2020 stressed the need to deploy analytical methods to ascertain the polymeric nature of a residue. Furthermore, as plastics age under natural conditions and usual databases do not include their weathered spectra, (micro)plastics in environmental samples may be unidentified. In this paper, polyamide (nylon) microplastics weathering was monitored because of its ubiquity in household commodities, clothes, fishery items and industry, whose residues end up frequently in the environment. Infrared spectra (ATR and microreflectance) and Scanning Electron Microscopy (SEM) images were collected periodically while exposing nylon to controlled weathering. It was seen that ATR was more sensitive than microreflectance to monitor the structural evolution of polyamide and that the spectra and the surface of weathered microplastics showed remarkable differences with the pristine material, which stresses the need for considering its evolution when identifying microplastics in environmental studies. The evolution of six band ratios related to the chemical evolution of this polymer are presented. SEM images revealed the formation of secondary microplastics at the most advanced weathering stages of polyamide.


Assuntos
Microplásticos , Poluentes Químicos da Água , Monitoramento Ambiental , Nylons , Plásticos , Espectrofotometria Infravermelho , Poluentes Químicos da Água/análise
9.
J Chem Theory Comput ; 17(8): 5007-5020, 2021 Aug 10.
Artigo em Inglês | MEDLINE | ID: mdl-34296615

RESUMO

An efficient anharmonic vibrational method is developed exploiting the locality of molecular vibration. Vibrational coordinates localized to a group of atoms are employed to divide the potential energy surface (PES) of a system into intra- and inter-group contributions. Then, the vibrational Schrödinger equation is solved based on a PES, in which the inter-group coupling is truncated at the harmonic level while accounting for the intra-group anharmonicity. The method is applied to a pentagonal hydrogen bond network (HBN) composed of internal water molecules and charged residues in a membrane protein, bacteriorhodopsin. The PES is calculated by the quantum mechanics/molecular mechanics (QM/MM) calculation at the level of B3LYP-D3/aug-cc-pVDZ. The infrared (IR) spectrum is computed using a set of coordinates localized to each water molecule and amino acid residue by second-order vibrational quasi-degenerate perturbation theory (VQDPT2). Benchmark calculations show that the proposed method yields the N-D/O-D stretching frequencies with an error of 7 cm-1 at the cost reduced by more than five times. In contrast, the harmonic approximation results in a severe error of 150 cm-1. Furthermore, the size of QM regions is carefully assessed to find that the QM regions should include not only the pentagonal HBN itself but also its HB partners. VQDPT2 calculations starting from transient structures obtained by molecular dynamics simulations have shown that the structural sampling has a significant impact on the calculated IR spectrum. The incorporation of anharmonicity, sufficiently large QM regions, and structural samplings are of essential importance to reproduce the experimental IR spectrum. The computational spectrum paves the way for decoding the IR signal of strong HBNs and helps elucidate their functional roles in biomolecules.


Assuntos
Bacteriorodopsinas/química , Água/química , Simulação de Dinâmica Molecular , Espectrofotometria Infravermelho , Vibração
10.
Spectrochim Acta A Mol Biomol Spectrosc ; 262: 120107, 2021 Dec 05.
Artigo em Inglês | MEDLINE | ID: mdl-34245968

RESUMO

An approach for measuring water concentration in oil, based on the use of CuSO4 particles and infrared spectroscopy, is described. The particles interact with both dissolved water and water droplets to form the monohydrate, CuSO4·H2O. These particles are collected on an infrared transparent membrane and then an infrared spectrum in transmission mode is recorded. Strong interaction of the water with the CuSO4 shifts and intensifies the water bending mode to produce a unique band at 1743 cm-1. The method provided values which are equivalent to those measured by Karl Fischer titration over the range of 10 to 3500 mg L-1 with a linearity R2 value of > 0.99 and an average %RSD for all measurements was 6%. No matrix specific calibrations are required.


Assuntos
Sulfato de Cobre , Água , Calibragem , Pós , Espectrofotometria Infravermelho
11.
Molecules ; 26(11)2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34200454

RESUMO

The current understanding of deviations of human microbiota caused by antibiotic treatment is poor. In an attempt to improve it, a proof-of-principle spectroscopic study of the breath of one volunteer affected by a course of antibiotics for Helicobacter pylori eradication was performed. Fourier transform spectroscopy enabled searching for the absorption spectral structures sensitive to the treatment in the entire mid-infrared region. Two spectral ranges were found where the corresponding structures strongly correlated with the beginning and end of the treatment. The structures were identified as methyl ester of butyric acid and ethyl ester of pyruvic acid. Both acids generated by bacteria in the gut are involved in fundamental processes of human metabolism. Being confirmed by other studies, measurement of the methyl butyrate deviation could be a promising way for monitoring acute gastritis and anti-Helicobacter pylori antibiotic treatment.


Assuntos
Antibacterianos/uso terapêutico , Infecções por Helicobacter/tratamento farmacológico , Helicobacter pylori/efeitos dos fármacos , Antibacterianos/química , Ácido Butírico/química , Ésteres/química , Gastrite/tratamento farmacológico , Microbioma Gastrointestinal/efeitos dos fármacos , Humanos , Masculino , Pessoa de Meia-Idade , Ácido Pirúvico/química , Espectrofotometria Infravermelho/métodos
12.
Molecules ; 26(12)2021 Jun 17.
Artigo em Inglês | MEDLINE | ID: mdl-34204550

RESUMO

Recently, considerable attention has been paid to Bombyx mori silk fibroin by a range of scientists from polymer chemists to biomaterial researchers because it has excellent physical properties, such as strength, toughness, and biocompatibility. These appealing physical properties originate from the silk fibroin structure, and therefore, structural determinations of silk fibroin before (silk I) and after (silk II) spinning are a key to make wider applications of silk. There are discrepancies about the silk I structural model, i.e., one is type II ß-turn structure determined using many solid-state and solution NMR spectroscopies together with selectively stable isotope-labeled model peptides, but another is α-helix or partially α-helix structure speculated using IR and Raman methods. In this review, firstly, the process that led to type II ß-turn structure by the authors was introduced in detail. Then the problems in speculating silk I structure by IR and Raman methods were pointed out together with the problem in the assignment of the amide I band in the spectra. It has been emphasized that the conformational analyses of proteins and peptides from IR and Raman studies are not straightforward and should be very careful when the proteins contain ß-turn structure using many experimental data by Vass et al. In conclusion, the author emphasized here that silk I structure should be type II ß-turn, not α-helix.


Assuntos
Fibroínas/química , Fibroínas/metabolismo , Seda/química , Animais , Bombyx/química , Proteínas de Insetos/química , Espectroscopia de Ressonância Magnética/métodos , Peptídeos/química , Conformação Proteica , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Seda/metabolismo , Espectrofotometria Infravermelho/métodos , Análise Espectral Raman/métodos
13.
Int J Mol Sci ; 22(14)2021 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-34298985

RESUMO

In this study, the temperature-dependent solubility of nicotinamide (niacin) was measured in six neat solvents and five aqueous-organic binary mixtures (methanol, 1,4-dioxane, acetonitrile, DMSO and DMF). It was discovered that the selected set of organic solvents offer all sorts of solvent effects, including co-solvent, synergistic, and anti-solvent features, enabling flexible tuning of niacin solubility. In addition, differential scanning calorimetry was used to characterize the fusion thermodynamics of nicotinamide. In particular, the heat capacity change upon melting was measured. The experimental data were interpreted by means of COSMO-RS-DARE (conductor-like screening model for realistic solvation-dimerization, aggregation, and reaction extension) for concentration dependent reactions. The solute-solute and solute-solvent intermolecular interactions were found to be significant in all of the studied systems, which was proven by the computed mutual affinity of the components at the saturated conditions. The values of the Gibbs free energies of pair formation were derived at an advanced level of theory (MP2), including corrections for electron correlation and zero point vibrational energy (ZPE). In all of the studied systems the self-association of nicotinamide was found to be a predominant intermolecular complex, irrespective of the temperature and composition of the binary system. The application of the COSMO-RS-DARE approach led to a perfect match between the computed and measured solubility data, by optimizing the parameter of intermolecular interactions.


Assuntos
Niacinamida/química , Termodinâmica , Acetonitrilas , Varredura Diferencial de Calorimetria , Cristalografia por Raios X , Dimerização , Dimetil Sulfóxido , Dimetilformamida , Dioxanos , Metanol , Modelos Químicos , Concentração Osmolar , Solubilidade , Soluções , Solventes , Espectrofotometria Infravermelho , Temperatura , Vibração , Água
14.
Int J Mol Sci ; 22(11)2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34200392

RESUMO

Knowledge of all the intermolecular forces occurring in ionic liquids (ILs) is essential to master their properties. Aiming at investigating the weaker hydrogen bonding in aprotic liquids, the present work combined computational study and far-infrared spectroscopy on four imidazolium-based ILs with different anions. The DFT calculations of the ionic couples, using the ωB97X-D functional and considering both the empirical dispersion corrections and the presence of a polar solvent, show that, for all samples, the lowest energy configurations of the ion pair present H atoms, directly bound to C atoms of the cation and close to O atoms of the anion, capable of creating moderate to weak hydrogen bonding with anions. For the liquids containing anions of higher bonding ability, the absorption curves generated from the calculated vibrational frequencies and intensities show absorption bands between 100 and 125 cm-1 corresponding to the stretching of the hydrogen bond. These indications are in complete agreement with the presently reported temperature dependence of the far-infrared spectrum, where the stretching modes of the hydrogen bonding are detected only for samples presenting a moderate interaction and become particularly prominent at low temperatures. Moreover, from the analysis of the infrared spectra, the occurrence of various phase transitions as a function of temperature was detected, and the difference in the average energy between the H-bonded and the dispersion-governed molecular configurations was evaluated.


Assuntos
Simulação por Computador , Teoria da Densidade Funcional , Imidazóis/química , Líquidos Iônicos/química , Espectrofotometria Infravermelho/métodos , Ligação de Hidrogênio , Modelos Químicos
15.
Analyst ; 146(15): 4822-4834, 2021 Aug 07.
Artigo em Inglês | MEDLINE | ID: mdl-34198314

RESUMO

Mid-infrared Spectroscopic Imaging (MIRSI) provides spatially-resolved molecular specificity by measuring wavelength-dependent mid-infrared absorbance. Infrared microscopes use large numerical aperture objectives to obtain high-resolution images of heterogeneous samples. However, the optical resolution is fundamentally diffraction-limited, and therefore wavelength-dependent. This significantly limits resolution in infrared microscopy, which relies on long wavelengths (2.5 µm to 12.5 µm) for molecular specificity. The resolution is particularly restrictive in biomedical and materials applications, where molecular information is encoded in the fingerprint region (6 µm to 12 µm), limiting the maximum resolving power to between 3 µm and 6 µm. We present an unsupervised curvelet-based image fusion method that overcomes limitations in spatial resolution by augmenting infrared images with label-free visible microscopy. We demonstrate the effectiveness of this approach by fusing images of breast and ovarian tumor biopsies acquired using both infrared and dark-field microscopy. The proposed fusion algorithm generates a hyperspectral dataset that has both high spatial resolution and good molecular contrast. We validate this technique using multiple standard approaches and through comparisons to super-resolved experimentally measured photothermal spectroscopic images. We also propose a novel comparison method based on tissue classification accuracy.


Assuntos
Algoritmos , Microscopia , Análise de Fourier , Espectrofotometria Infravermelho , Espectroscopia de Infravermelho com Transformada de Fourier
16.
Phys Chem Chem Phys ; 23(28): 15352-15363, 2021 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-34254612

RESUMO

Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.


Assuntos
DNA/química , Sítio Alostérico , Pareamento de Bases , Sequência de Bases , Bisbenzimidazol/química , Cinética , Ligantes , Modelos Moleculares , Conformação de Ácido Nucleico , Espectrofotometria Infravermelho , Temperatura
17.
J Phys Chem Lett ; 12(25): 5951-5956, 2021 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-34157231

RESUMO

We demonstrate a method to address the problem of spectral overlap in multidimensional vibrational spectroscopy and use it to investigate supercooled aqueous sorbitol solutions. The absence of crystallization in these solutions has been attributed to "soft" confinement of water in subnanometer voids in the sorbitol matrix, but the details of the hydrogen-bond structure are still largely unknown. 2D-IR spectroscopy of the OH-stretch mode is an excellent tool to investigate hydrogen bonding, but in this case it seems difficult because of the overlapping water and sorbitol contributions to the 2D-IR spectrum. Using the difference in OH-stretch lifetimes of water and sorbitol we can cleanly separate these contributions. Surprisingly, the separated 2D-IR spectra show that the hydrogen-bond disorder of soft-confined water is independent of temperature and decoupled from its orientational order. We believe the approach we use to separate overlapping 2D-IR spectra will enhance the applicability of 2D-IR spectroscopy to study multicomponent systems.


Assuntos
Espectrofotometria Infravermelho , Temperatura , Água/química , Ligação de Hidrogênio
18.
J Med Chem ; 64(12): 8410-8422, 2021 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-34110823

RESUMO

The article describes the application of the alanine-scanning technique used in combination with Raman, surface-enhanced Raman, attenuated total reflection Fourier transform infrared, and surface-enhanced infrared absorption (SEIRA) spectroscopies, which allowed defining the role of individual amino acid residues in the C-terminal 6-14 fragment of the bombesin chain (BN6-14) on the path of its adsorption on the surface of Ag (AgNPs) and Au nanoparticles (AuNPs). A reliable analysis of the SEIRA spectra of these peptides was possible, thanks to a curve fitting of these spectra. By combining alanine-scanning with biological activity studies using cell lines overexpressing bombesin receptors and the intracellular inositol monophosphate assay, it was possible to determine which peptide side chains play a significant role in binding a peptide to membrane-bound G protein-coupled receptors (GPCRs). Based on the analysis of spectral profiles and bioactivity results, conclusions for the specific peptide-metal and peptide-GPCR interactions were drawn and compared.


Assuntos
Bombesina/química , Bombesina/metabolismo , Nanopartículas Metálicas/química , Fragmentos de Peptídeos/química , Fragmentos de Peptídeos/metabolismo , Receptores da Bombesina/metabolismo , Adsorção , Bombesina/genética , Ouro/química , Células HEK293 , Humanos , Mutagênese , Mutação , Fragmentos de Peptídeos/genética , Ligação Proteica , Prata/química , Espectrofotometria Infravermelho , Análise Espectral Raman
19.
Colloids Surf B Biointerfaces ; 206: 111939, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34186307

RESUMO

Infrared (IR) spectroscopy is a unique and powerful method in the identification, characterization, and classification of chemical and biological molecules. However, the low absorbance of biological molecules has arisen as a major bottleneck and inhibits the application of IR in practical applications. To overcome this limitation, in the last four decades, surface-enhanced IR absorption (SEIRA) spectroscopy has been proposed and has become the focus of interest in various applications. In this study, for the first time, we proposed the employment of 3D anisotropic gold nanorod arrays (GNAs) as a highly active SEIRA platform in bacterial detection. For this, GNA platforms were fabricated through an oblique angle deposition (OAD) approach by using a physical vapor deposition (PVD) system. OAD of gold at proper deposition angle (10°) created closely-packed and columnar gold nanorod structures onto the glass slides in a well-controlled manner. GNA platform was tested as a SEIRA system in three different species of bacteria (Escherichia coli, Staphylococcus aureus, and Bacillus subtilis) by collecting IR spectra of each bacteria from different parts of GNA. The employment of GNA provided robust IR spectra with high reproducibility and signal-to-noise ratio. For the comparison, IR spectra of each bacteria were collected from aluminum foil and a smooth gold surface (SGS). No or very low IR spectra were observed in comparison to the GNA platform for these substrates. Unsupervised (PCA, HCA) and supervised (SIMCA, LDA, and SVM classification) machine learning analysis of bacteria spectra obtained from GNA substrate indicated that all bacteria samples can be detected and identified without using a label-containing biosensor, in a fast and simple manner.


Assuntos
Nanopartículas Metálicas , Nanotubos , Bactérias , Ouro , Reprodutibilidade dos Testes , Espectrofotometria Infravermelho , Análise Espectral Raman , Propriedades de Superfície
20.
Proc Natl Acad Sci U S A ; 118(26)2021 06 29.
Artigo em Inglês | MEDLINE | ID: mdl-34185681

RESUMO

The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), invades a human cell via human angiotensin-converting enzyme 2 (hACE2) as the entry, causing the severe coronavirus disease (COVID-19). The interactions between hACE2 and the spike glycoprotein (S protein) of SARS-CoV-2 hold the key to understanding the molecular mechanism to develop treatment and vaccines, yet the dynamic nature of these interactions in fluctuating surroundings is very challenging to probe by those structure determination techniques requiring the structures of samples to be fixed. Here we demonstrate, by a proof-of-concept simulation of infrared (IR) spectra of S protein and hACE2, that time-resolved spectroscopy may monitor the real-time structural information of the protein-protein complexes of interest, with the help of machine learning. Our machine learning protocol is able to identify fine changes in IR spectra associated with variation of the secondary structures of S protein of the coronavirus. Further, it is three to four orders of magnitude faster than conventional quantum chemistry calculations. We expect our machine learning protocol would accelerate the development of real-time spectroscopy study of protein dynamics.


Assuntos
Enzima de Conversão de Angiotensina 2/metabolismo , Aprendizado de Máquina , SARS-CoV-2/metabolismo , Glicoproteína da Espícula de Coronavírus/metabolismo , Enzima de Conversão de Angiotensina 2/química , Humanos , Cinética , Ligação Proteica , Estrutura Secundária de Proteína , Espectrofotometria Infravermelho , Glicoproteína da Espícula de Coronavírus/química
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