Characterization and Techno-Functional Properties of High Protein Walnut Flour from an Oil by-Product.

A high protein walnut flour (HPWF) was obtained by defatting walnut flour (WF), which is a by-product of the oil industry. The objective of this study was the chemical and techno-functional characterization of HPWF. Composition, amino acid content, protein secondary structure, protein solubility and thermal transitions were measured. Besides, the techno-functional properties, emulsion activity and stability, and water holding and oil absorption capacities, of HPWF were evaluated. Also, the molecular mass of proteins under denaturing conditions and the microstructure of HPWF were evaluated by electrophoresis and confocal scanning laser microscopy, respectively. HPWF had 55.4% protein content and 21.5% total dietary fibre. In terms of HPWF amino acid composition, the limiting amino acids were the sulphurated cysteine and methionine. By FTIR analysis, the main secondary structures were ß-sheet (49%) followed by α-helix (24%); both structures are considered to be ordered. Likewise, HPWF soluble proteins increased at basic pH and HPWF proteins were separated in 11 bands with molecular masses ranging from 97 kDa to 18 kDa by electrophoresis. With respect to techno-functional properties, HPWF presented good emulsion activity (51%) and high thermal emulsion stability (46%). In addition, HPWF retained 571% and 242% of water and oil by weight, respectively. Finally, the micrograph showed the predominance of protein structures and fibre fragments, and the presence of few lipids mostly trapped. These results showed that HPWF is an interesting source of plant-based proteins and walnut flour can be used to obtain high protein ingredients from non-traditional sources.

Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to ß-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases.

In small clinical studies, the application of transcranial photobiomodulation (PBM), which typically delivers low-intensity near-infrared (NIR) to treat the brain, has led to some remarkable results in the treatment of dementia and several neurodegenerative diseases. However, despite the extensive literature detailing the mechanisms of action underlying PBM outcomes, the specific mechanisms affecting neurodegenerative diseases are not entirely clear. While large clinical trials are warranted to validate these findings, evidence of the mechanisms can explain and thus provide credible support for PBM as a potential treatment for these diseases. Tubulin and its polymerized state of microtubules have been known to play important roles in the pathology of Alzheimer's and other neurodegenerative diseases. Thus, we investigated the effects of PBM on these cellular structures in the quest for insights into the underlying therapeutic mechanisms. In this study, we employed a Raman spectroscopic analysis of the amide I band of polymerized samples of tubulin exposed to pulsed low-intensity NIR radiation (810 nm, 10 Hz, 22.5 J/cm2 dose). Peaks in the Raman fingerprint region (300-1900 cm-1)-in particular, in the amide I band (1600-1700 cm-1)-were used to quantify the percentage of protein secondary structures. Under this band, hidden signals of C=O stretching, belonging to different structures, are superimposed, producing a complex signal as a result. An accurate decomposition of the amide I band is therefore required for the reliable analysis of the conformation of proteins, which we achieved through a straightforward method employing a Voigt profile. This approach was validated through secondary structure analyses of unexposed control samples, for which comparisons with other values available in the literature could be conducted. Subsequently, using this validated method, we present novel findings of statistically significant alterations in the secondary structures of polymerized NIR-exposed tubulin, characterized by a notable decrease in α-helix content and a concurrent increase in ß-sheets compared to the control samples. This PBM-induced α-helix to ß-sheet transition connects to reduced microtubule stability and the introduction of dynamism to allow for the remodeling and, consequently, refreshing of microtubule structures. This newly discovered mechanism could have implications for reducing the risks associated with brain aging, including neurodegenerative diseases like Alzheimer's disease, through the introduction of an intervention following this transition.

The effect of different conditioning agents on dentin roughness and collagen structure.

OBJECTIVES: To assess the impact of various organic and inorganic acids on the roughness, demineralization, and collagen secondary structures of human dentin and to compare these effects with those of traditional agents, specifically phosphoric acid (PA) and ethylenediaminetetraacetic acid (EDTA). METHODS: Coronal dentin discs (n = 10) were examined by optical profilometry (roughness) and ATR-FTIR before and after conditioning with 32 % PA, 3 % nitric acid (NA), 20 % citric acid (CA), 20 % phytic acid (IP6) or 17 % EDTA. Spectra data were processed to quantify dentin demineralization (DM%) and percentage area of amide I curve-fitted components of ß-turns, 310-helix, α-helix, random coils, ß-sheets, and collagen maturation index. Statistical analysis was performed by one-way ANOVA or Kruskal-Wallis for DM% and roughness parameters, and paired t-test/Wilcoxon test for amide I components at significance level set at α = 0.05. RESULTS: All treatments resulted in increased roughness parameters, with the most significant changes occurring primarily with PA, while EDTA exhibited the least changes. DM% was NA>PA>IP6>CA>EDTA in a descending order. Regarding amide I components, NA demonstrated a significant reduction in ß-turns, 310-helices, and α-helices and it increased ß-sheets and random coils. PA resulted in reduction in ß-turns and α-helices while it increased ß-sheets. CA and EDTA did not cause significant changes. The collagen maturation index significantly increased only after IP6 treatment. CONCLUSIONS: The effect on dentin roughness parameters, demineralization, and collagen secondary structures varied based on the type of dentin surface treatment. CLINICAL SIGNIFICANCE: Understanding the impact of acids on the intrinsic properties of dentin is clinically essential for gaining insights into how these effects influence adhesion to dentin, the long-term stability of resin-based restorations, and the success of remineralization therapies.

Characterization of Polyphenol Composition and Starch and Protein Structure in Brown Rice Flour, Black Rice Flour and Their Mixtures.

The study investigates the structural and chemical properties of brown rice flour (WRF), black rice flour (BRF) and their mixtures in ratios of 25%, 50% and 75% to provide reference information for the gluten-free bakery industry. BRF contains higher concentrations of proteins, lipids, total minerals, crude fiber, total polyphenols, proanthocyanidins and flavonoids than WRF. A higher amylose content in BRF than in WRF resulted in flour mixtures with slower starch digestion and a lower glycemic response depending on the BRF ratio added. Differences in the chemical composition of WRF and BRF led to improved composition of the flour mixtures depending on the BRF ratio. The presence of anthocyanidins and phenolic acids in higher concentrations in the BRF resulted in a red-blue color shift within the flour mixtures. The deconvoluted FTIR spectra showed a higher proportion of α-helixes in the amide I band of BRF proteins, indicating their tighter folding. An analysis of the FTIR spectra revealed a more compact starch structure in BRF than in WRF. By processing reflection spectra, nine optically active compound groups were distinguished in rice flour, the proportion in BRF being 83.02% higher than in WRF. Due to co-pigmentation, the bathochromic shift to higher wavelengths was expressed by the proanthocyanins and phenolic acids associated with the wavelengths 380 nm to 590 nm and at 695 nm. Anthocyanins, protein-tannin complexes, methylated anthocyanins and acylated anthocyanins, associated with wavelengths 619, 644 and 668 nm, exhibited a hypsochromic effect by shifting the wavelengths to lower values. This research represents a first step in the development of rice-based products with increased nutritional value and a lower glycemic index.

Unpolarized laser method for infrared spectrum calculation of amide I CO bonds in proteins using molecular dynamics simulation.

The investigation of the strong infrared (IR)-active amide I modes of peptides and proteins has received considerable attention because a wealth of detailed information on hydrogen bonding, dipole-dipole interactions, and the conformations of the peptide backbone can be derived from the amide I bands. The interpretation of experimental spectra typically requires substantial theoretical support, such as direct ab-initio molecular dynamics simulation or mixed quantum-classical description. However, considering the difficulties associated with these theoretical methods and their applications are limited in small peptides, it is highly desirable to develop a simple yet efficient approach for simulating the amide I modes of any large proteins in solution. In this work, we proposed a comprehensive computational method that extends the well-established molecular dynamics (MD) simulation method to include an unpolarized IR laser for exciting the CO bonds of proteins. We showed the amide I frequency corresponding to the frequency of the laser pulse which resonated with the CO bond vibration. At this frequency, the protein energy and the CO bond length fluctuation were maximized. Overall, the amide I bands of various single proteins and amyloids agreed well with experimental data. The method has been implemented into the AMBER simulation package, making it widely available to the scientific community. Additionally, the application of the method to simulate the transient amide I bands of amyloid fibrils during the IR laser-induced disassembly process was discussed in details.

Disassembly of Amyloid Fibril with Infrared Free Electron Laser.

Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid ß-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated through a linear accelerator, and the oscillation wavelengths are tunable from 3 µm to 100 µm. Many biological and organic compounds can be structurally altered by the mode-selective vibrational excitations due to the wavelength variability and the high-power oscillation energy (10-50 mJ/cm2). We have found that several different kinds of amyloid fibrils in amino acid sequences were commonly disassembled by the irradiation tuned to amide I (6.1-6.2 µm) where the abundance of ß-sheet decreased while that of α-helix increased by the vibrational excitation of amide bonds. In this review, we would like to introduce the IR-FEL oscillation system briefly and describe combination studies of experiments and molecular dynamics simulations on disassembling amyloid fibrils of a short peptide (GNNQQNY) from yeast prion and 11-residue peptide (NFLNCYVSGFH) from ß2-microglobulin as representative models. Finally, possible applications of IR-FEL for amyloid research can be proposed as a future outlook.

Dissecting amide-I vibrations in histidine dipeptide.

The amide-I vibrational characteristics and conformational preferences of the model compound - histidine dipeptide (Ac-His-NHCH3, HISD) in gas phase and solution have been revealed with the help of ab initio calculations and wavefunction analyses. The Gibbs free energy surfaces (FESs) of solvated HISD were smoothed by solvent effect to exhibit different structural populations concerning various external environments. It was shown that the most stable conformations of HISD in CHCl3 and gas phase are C7eq, while those in DMSO and water are ß and PPII, respectively. Compared with ALAD, the number of accessible conformational states on these FESs was predicted to be reduced due to the steric effect of imidazole group. The two amide-I normal modes of HISD were found to have intrinsically secondary structural dependencies, and be sensitive to surrounding environments. The average amide-Ia frequencies of HISD isomers in these environments were predicted to be almost the same as those of ALAD, while the amide-Ib mean frequencies were estimated to be lower than ALAD due to the intramolecular interactions between the imidazole group and amino-terminal amide unit. The good linear correlations between amide-I frequencies and the atomic electrostatic potentials (ESPs) of amide groups were also found to interpret the solvent-induced amide-I frequency shifts of HISD at the electronic structure level. These results allow us to gain a deep understanding of amide-I vibrations of HISD, and would be helpful for the site-specific conformational monitoring and spectral interpretation of solvated polypeptides.

Selective IR super-resolution imaging of ß-keratins at the bulk or interface in feather detected by using a nonlinear optical process.

We developed the new IR super-resolution microscope by using a 4-wave mixing (4-wave), which is a third-order nonlinear optical process, and carried out the IR super-resolution imaging of the cross section of the rachis of an avian feather. We clearly observed strong signals in the entire region of the rachis at the amide I vibration of ß-keratin in both of the XXYY and YYXX polarization combination. These results are different from images detected by using the vibrational sum-frequency generation (VSFG) method. While the VSFG imaging detects molecules only from the interface, the 4-wave method enables us to observe the signal from the bulk area. We concluded that the four repeating units of ß-keratins in the bulk area which are suggested by X-ray diffraction studies are visualized in the 4-wave detected method. We also applied two IR super-resolution microscopies for the barb and discuss the site dependence of the orientation, distribution and concentration of ß-keratin.

µ-FTIR, µ-Raman, and SERS Analysis of Amide I Spectral Region in Oral Biofluid Samples during Orthodontic Treatment.

Gingival crevicular fluid (GCF) is a site-specific exudate deriving from the epithelium lining of the gingival sulcus. GCF analysis provides a simple and noninvasive diagnostic procedure to follow-up periodontal and bone remodeling in response to diseases or mechanical stimuli such as orthodontic tooth movement (OTM). In recent years, the use of vibrational spectroscopies such as Fourier Transform Infrared and Raman microspectroscopy and Surface-Enhanced Raman spectroscopy contributed to characterizing changes in GCF during fixed orthodontic treatment. Amide I band plays a relevant role in the analysis of these changes. The aim of this study was to investigate the spectroscopy response of Amide I depending on the OTM process duration. A model based on Gaussian-Lorentzian curves was used to analyze the infrared spectra, while only Lorentzian functions were used for Raman and SERS spectra. Changes induced by the OTM process in subcomponents of the Amide I band were determined and ascribed to secondary structure modification occurring in proteins. The vibrational spectroscopies allow us to efficiently monitor the effects of the orthodontic force application, thus gaining increasing attention as tools for individual patient personalization in clinical practice.

Does Nitrogen Fertilization Affect the Secondary Structures of Gliadin Proteins in Hypoallergenic Wheat?

One of the macronutrients indispensable for plant growth and development is nitrogen (N). It is responsible for starch and storage protein (gliadins and glutenins) biosynthesis and, in consequence, influences kernels' quality and yields. However, applying N-fertilizers increases gluten content in wheat, and it may intensify the risk of developing allergy symptoms in gluten-sensitive individuals. The purpose of our research was to analyse whether and how the elimination of N-fertilizers during the cultivation of wasko.gl- wheat (modified genotype lacking ω-gliadins) changes the secondary structures of gliadin proteins. To this aim, using the FT-Raman technique, we examined flour and gliadin protein extracts obtained from kernels of two winter wheat lines: wasko.gl+ (with a full set of gliadin proteins) and wasko.gl- (without ω-gliadin fraction) cultivated on two different N-fertilization levels-0 and 120 kg N·ha-1. On the basis of the obtained results, we proved that nitrogen fertilization does not have a major impact on the stability of the secondary structures of gliadin proteins for wasko.gl- wheat line with reduced allergenic properties. Furthermore, the results presented herein suggest the possibility of increasing the stability of glutenin structures as a result of the N-fertilization of wasko.gl- wheat line, which gives hope for its use in the production of wheat articles devoted to people suffering from diseases related to gluten sensitivity.

Determine both the conformation and orientation of a specific residue in α-synuclein(61-95) even in monolayer by 13C isotopic label and p-polarized multiple-angle incidence resolution spectrometry (pMAIRS).

Protein's magic function stems from its structure and various analytical techniques have been developed for it. Among proteins, membrane proteins are encoded 20-30% of genomes, whereas cause challenges for many analytical techniques. For example, lots of membrane proteins cannot form single crystal structure required by X-ray crystallography. As for NMR, the measurements were hindered by the low tumbling rates of membrane (i.e., phospholipid bilayers) where membrane proteins exist. In addition, membrane proteins usually lay parallel to the surface of phospholipid bilayers or form transmembrane structure. No matter parallel or perpendicular to phospholipid bilayers surface, membrane proteins form monolayer structure which is also difficult for X-ray and NMR to provide high-resolution results. Because NMR and X-ray crystallography are the two major analytical techniques to address protein's structure, membrane proteins only contribute 2.4% to the solved protein databank. Surface FT-IR techniques can evaluate the conformation and orientation of membrane proteins by amide I band. Specifically for α-helical peptides/proteins, the orientation of the axis is critical to decide whether proteins form transmembrane structure. Notice that the traditional FT-IR can only provide "low-resolution" results. Here, 13C isotope was introduced into the nonamyloid component (NAC), which spans residues 61-95 of α-synuclein (α-syn). Then, p-polarized multiple-angle incidence resolution spectrometry (pMAIRS) was used to determine the orientation of a specific residue of α-helical NAC in monolayer. In general, pMAIRS is a novel technique to work complementary with X-ray and NMR to address membrane peptides/proteins structure with high resolution even in monolayer.

Raman Spectroscopy Study of Skin Biopsies from Patients with Parkinson's Disease: Trends in Alpha-Synuclein Aggregation from the Amide I Region.

Parkinson's disease (PD) is one of the most common neurological pathologies with a high prevalence worldwide. PD is characterized by Lewy bodies, whose major component is the aggregates of α-synuclein (αSyn) protein. Interestingly, recent works have demonstrated that skin biopsy studies are a promising diagnostic tool for evaluating α-synucleinopathies. In this sense, this work focuses on the detection of αSyn in skin biopsies employing Raman spectroscopy, using three different approaches: (i) the in vitro Raman spectrum of α-synuclein, (ii) the ex vivo Raman spectra of human skin biopsies from healthy and Parkinson's disease patients, and (iii) theoretical calculations of the Raman spectra obtained from different model αSyn fragments using density functional theory (DFT). Significant differences in the intensity and location of Raman active frequencies in the amide I region were found when comparing healthy and PD subjects related to α-synuclein conformational changes and variations in their aggregation behavior. In samples from healthy patients, we identified well-known Raman peaks at 1655, 1664, and 1680 cm-1 associated with the normal state of the protein. In PD subjects, shifted Raman bands and intensity variations were found at 1650, 1670, and 1687 cm-1 associated with aggregated forms of the protein. DFT calculations reveal that the shape of the amide I Raman peak in model αSyn fragments strongly depends on the degree of aggregation. Sizable frequency shifts and intensity variations are found within the highly relevant 1600-1700 cm-1 domain, revealing the sensitivity of the amide I Raman band to the changes in the local atomic environment. Interestingly, we obtain that the presence of surrounding waters also affects the structure of the amide I band, leading to the appearance of new peaks on the low-frequency side and a notable broadening of the Raman spectra. These results strongly suggest that, through Raman spectroscopy, it is possible to infer the presence of aggregated forms of αSyn in skin biopsies, a result that could have important implications for understanding α-synuclein related diseases.

Vibrational and fluorescence spectroscopy to study gluten and zein interactions in complex dough systems.

The volume-spanning network formed by gluten during breadmaking is crucial in the production of high-quality bakery products. Zein proteins are also capable of forming a protein network under specific conditions. Vibrational (Fourier transform infrared spectroscopy (FTIR) and Raman scattering) and fluorescence spectroscopy are powerful, non-invasive techniques capable of assessing protein structures and interactions. The main objective of this project was to explore the suitability of these techniques to study zein and gluten structures and interactions in complex dough systems. The dough samples were prepared by mixing 20 w/w% of protein (with different proportions of zein and gluten) and 80 w/w% of corn starch. The tyrosine (Tyr) fluorescence emission peak (λexc = 280 nm) was still present even in those zein-gluten samples containing the highest gluten concentration and lowest zein concentration. This suggests that the Tyr moieties (stemming from zein) are not in close proximity to tryptophan (Trp) of gluten and their fluorescence is not quenched efficiently. Raman scattering results also showed the presence of different Tyr residues, exposed and buried, as well as different conformations of disulfide bridges, in zein and gluten samples. Based on the results from spectroscopic measurements and scanning electron microscopy (SEM), two distinct network structures composed of gluten and zein were identified in the mixed dough systems. The present work illustrates how complementary vibrational (Raman scattering and FTIR) and fluorescence spectroscopy methods can be combined to non-invasively assess protein structure and interactions in a complex food matrix.

Modeling amide-I vibrations of alanine dipeptide in solution by using neural network protocol.

Infrared spectroscopy is a powerful tool for the understanding of molecular structure and function of polypeptides. Theoretical interpretation of IR spectra relies on ab initio calculations may be very costly in computational resources. Herein, we developed a neural network (NN) modeling protocol to evaluate a model dipeptide's backbone amide-I spectra. DFT calculations were performed for the amide-I vibrational motions and structural parameters of alanine dipeptide (ALAD) conformers in different micro-environments ranging from polar to non-polar ones. The obtained backbone dihedrals, C = O bond lengths and amide-I frequencies of ALAD were gather together for NN architecture. The applications of built NN protocols for the prediction of amide-I frequencies of ALAD in other solvation conditions are quite satisfactory with much less computational cost comparing with electronic structure calculations. The results show that this cost-effective way enables us to decipher the polypeptide's dynamic secondary structures and biological functions with their backbone vibrational probes.

Multi-Probe Equilibrium Analysis of Gradual (Un)Folding Processes.

Studies of small proteins that exhibit noncooperative, gradual (un)folding can offer unique insights into the rarely accessible intermediate stages of the protein folding processes. Detailed experimental characterization of these intermediate states requires approaches that utilize multiple site-specific probes of the local structure. Isotopically edited infrared (IR) spectroscopy has emerged as a powerful methodology capable of providing such high-resolution structural information. Labeling of selected amide carbonyls with 13C results in detectable side-bands of amide I' vibrations, which are sensitive to local conformation and/or solvent exposure without introducing any significant structural perturbation to the protein. Incorporation of isotopically labeled amino acids at specific positions can be achieved by the chemical synthesis of the studied proteins. We describe the basic procedures for synthesis of 13C isotopically edited protein samples, experimental IR spectroscopic measurements and analysis of the site-specific equilibrium thermal unfolding of a small protein from the temperature-dependent IR data.

FT-Raman Spectroscopy as a Tool to Study the Secondary Structures of Wheat Gliadin Proteins.

Raman spectroscopy is a useful method in biological, biomedical, food, and agricultural studies, allowing the simultaneous examination of various chemical compounds and evaluation of molecular changes occurring in tested objects. The purpose of our research was to explain how the elimination of ω-fractions from the wheat gliadin complex influences the secondary structures of the remaining αßγ-gliadins. To this aim, we analyzed the endosperm of wheat kernels as well as gliadin proteins extracted from two winter wheat genotypes: wasko.gl+ (control genotype containing the full set of gliadins) and wasko.gl- (modified genotype lacking all ω-gliadins). Based on the decomposition of the amide I band, we observed a moderate increase in ß-forms (sheets and turns) at the expense of α-helical and random coil structures for gliadins isolated from the flour of the wasko.gl- line. Since ω-gliadins contain no cysteine residues, they do not participate in the formation of the disulfide bridges that stabilize the protein structure. However, they can interact with other proteins via weak, low-energetic hydrogen bonds. We conclude that the elimination of ω-fractions from the gliadin complex causes minor modifications in secondary structures of the remaining gliadin proteins. In our opinion, these small, structural changes of proteins may lead to alterations in gliadin allergenicity.

Normal mode calculation and infrared spectroscopy of proteins in water solution: Relationship between amide I transition dipole strength and secondary structure.

Dipole Strength (DS) of the amides has gained a renewed interest in chemical physics since it provides an important tool to disclose the on-site vibrational energy distributions. Apart from earlier experimental efforts on polypeptides, little is still known about DS in complex proteins. We accurately measured the Fourier Transform Infrared absorption spectra of nine proteins in water solution obtaining their Molar Extinction Coefficient in the amide I and II spectral region. Our results show that the amide I DS value depends on the protein secondary structure, being that of the α-rich and unstructured proteins lower by a factor of 2 than that of the ß-rich proteins. The average DS for amino acids in α and ß secondary structures confirms this finding. Normal Mode calculation and Molecular Dynamics were performed and used as tools for data analysis and interpretation. The present outcomes corroborate the hypothesis that antiparallel ß-sheet environment is more prone to delocalize the on-site CO stretching vibration through coupling mechanisms between carbonyl groups, whereas α-helix structures are energetically less stable to permit vibrational mode delocalization.

The effect of universal adhesives on dentine collagen.

OBJECTIVES: The purpose of the study was to evaluate the integrity of dentine type I collagen after self-etching (SE) treatments with strong and mild universal adhesives. METHODS: Coronal dentine specimens (n=10/product) were imaged by optical microscopy and analyzed by ATR-FTIR spectroscopy before and after treatment with 32% phosphoric acid gel (PA-negative control), 17% neutral EDTA (ED-positive control) conditioners and Adhese Universal (AD), Clearfil Universal Bond Quick (CQ), G-Premio Bond (GP), Prelude One (PR) and Scotchbond Universal (SB) adhesives. From the spectroscopic analysis the following parameters were determined: a) Extent of dentine demineralization (DM%) and b) percentage area of the Amide I curve-fitted components of ß-turns, 310-helix/ß-turns, α-helix, random coils, ß-sheets and collagen maturation (R) index. Statistical analysis was performed by one-way ANOVA (DM%), paired t-test/Wilcoxon test (Amide I components) and Spearman correlation coefficient (DM% vs Amide I components) at an a=0.05 level. RESULTS: PA, ED and GP removed the smear-layer and opened tubule orifices, whereas all other treatments removed only the intratubular smear-layer fraction. The ranking of the statistically significant differences in DM% was PA>GP>ED>AD, SB, CQ, PR, with AD being significantly different from PR. Regarding the Amide I components, PA demonstrated a significant reduction in ß-turns, α-helices and an increase in ß-sheets, GP a reduction in ß-turns, AD an increase in ß-turns and random coils, and CQ an increase in ß-turns. PR, SB and ED showed insignificant differences in all the Amide I components. Significant correlations were found between DM%-random coils and DM%-R. SIGNIFICANCE: The universal adhesives used in the SE mode induced none to minimal changes in dentine collagen structure, without evidence of the destabilization pattern observed after conventional phosphoric acid treatments.

Deciphering the structural preference encoded in amide-I vibrations of lysine dipeptide in gas phase and in aqueous solution.

Protein's biological function is critically associated with its structural feature, which is encoded in its amino acid sequence. For evaluation of conformational fluctuation and folding mechanism, DFT calculations were performed on the model compound - lysine dipeptide (LYSD) in gas phase to demonstrate the correlation between amide-I vibrations and secondary structure. Molecular dynamics simulations were carried out for the structural dynamics of LYSD in aqueous solution. The results show that LYSD tends form C7eq, C5, ß, PPII and α conformations in the gas phase and primarily presented PPII and α conformations in aqueous solution. The obtained amide-I vibrational frequencies of LYSD conformers were assigned, thus build the correlations between amide-I probes and secondary structure of LYSD. These results provide theoretical insights into the structural feature of LYSD through amide-I vibrations, and would shed light on site specific structural prediction of polypeptides.

Adsorption of dipeptide L-alanyl-L-tryptophan on gold colloidal nanoparticles studied by surface-enhanced Raman spectroscopy.

Surface adsorption of a dipeptide L-alanyl-L-tryptophan (Ala-Trp) on gold nanoparticles reduced by citrate (CT) and borohydride (BH) ions was investigated by a surface-enhanced Raman scattering (SERS) technique. Two distinct SERS spectra of Ala-Trp depending on the types of gold nanoparticles were observed, and the vibrational assignments were based on the density functional theory simulations and the previous SERS results of Trp. Ala-Trp mainly adsorbs through the amine group on CT gold nanoparticles with a perpendicular orientation of the indole ring to the surface. In contrast, the adsorption occurs via the π electrons of the indole ring on the BH gold surfaces while maintaining a flat geometry of the indole ring to the surface. The amide I band of Ala-Trp was observed only with the CT gold colloids in acidic and neutral conditions where partial surface adsorption via the amide group is expected.