Probing the effect of the molecular interface of gold nanoparticles on the disassembly of insulin amyloid fibrils

Aberrant protein aggregation into amyloid fibrils underlies the onset of several degenerative pathologies, requiring increasing efforts to identify ever newer approaches to prevent their formation and to disassemble toxic amyloid structures. In this context, gold nanoparticles (AuNPs) show great promise, thanks to their ability to chemically interact with proteins while simultaneously serving as local spectroscopic probes due to their peculiar optical properties. Here, we investigate the role of the surface chemistry of AuNPs in the disassembly of insulin amyloid fibrils. By taking advantage of the remarkable sensitivity and spatial resolution of surface enhanced Raman spectroscopy, we elucidate the molecular mechanisms driving fibril-AuNP interaction at the nanoscale, identifying the amino acids directly involved. The obtained results will serve as a benchmark for developing novel diagnostic and therapeutic strategies employing AuNPs for the treatment of amyloid-related diseases.

Raman Optical Activity Enhanced via Supramolecular Aggregation and Other Intermolecular Interactions-A Review

In this review, we show that Raman optical activity (ROA) combined with electronic circular dichroism (ECD) are effective tools for detecting supramolecular chirality and related processes such as chiral signal amplification and chirality transfer (also called induction) between chiral and achiral solutes. Research on spontaneous self-organization has led to significant discoveries in vibrational optical activity (VOA) over the past decade. As a leading topic, we discuss different aggregation pathways of carotenoids, which contributed to the definition of new phenomena in the field of ROA, i.e., aggregation-induced resonance Raman optical activity (AIRROA), and the first chirality induction observed in nature. We present the chirality of carotenoids as i) amplification via supramolecular assembly, ii) induction by a small number of chiral monomers, and iii) transfer from the local environment. We also report here other complex systems that are relevant to the VOA community in the context of chiroptical analysis. These include ROA signal enhancement, e.g., recorded for amyloid fibrils or achiral linker aggregates attached to silver colloid (plasmonic effects). Finally, we highlight the challenges faced by ROA studies of supramolecular aggregates of strongly absorbing compounds, where chirality transfer may be misinterpreted as artifacts due to the ECD-Raman effect.

Characterization of structural changes occurring in insulin at different time intervals at room temperature by surface-enhanced Raman spectroscopy

BACKGROUND

Insulin storage above the temperature recommended by food and drug administration (FDA) causes decrease in its functional efficacy due to degradation and aggregation of its protein based active pharmaceutical ingredient (API) that results poor glycemic control in diabetic patients. The aggregation of protein causes serious neurodegenerative diseases such as type-2 diabetes, Huntington disease, Parkinson's disease, and Alzheimer's disease. Surface-enhanced Raman spectroscopy (SERS) has been employed for the denaturation study of many proteins at the temperature above the recommendations of food and drug administration (FDA) (above 30 °C) which indicates potential of technique for such studies.

OBJECTIVE

SERS along with multivariate discriminating analysis techniques-based analysis of degradation of liquid pharmaceutical insulin protein after regular intervals of time at room temperature to analyze the structural changes in this protein during the storage of insulin pharmaceutical at room temperature.

METHODS

Silver nanoparticles (Ag-NPs) prepared by chemical reduction method are used as SERS active substrate for the surface enhancement of the insulin spectral signal. SERS spectral measurements of insulin were collected from eight different samples of insulin in the time range of 7 pm to 7 am first at fridge temperature (5 °C), second after half hour and next six with the time difference of 2 h each time at room temperature. The acquired SERS spectral data was preprocessed and analyzed. SERS structural transformations detection and discrimination potential in insulin was further confirmed by applying multivariate discriminating analysis techniques including principal component analysis (PCA) and Partial least square regression analysis (PLSR).

RESULTS

SERS significantly detects the structural changes produced in insulin even after 2 h of insulin placement at room temperature. PCA successfully differentiates the insulin spectral data obtained after regular intervals of time according to PC-1 (77 %) explained variance. Application of PLSR model provides quantitative confirmation of SERS efficiency, by providing insulin data regression coefficients plot, efficient prediction of time with calibration data set having 0.77 mean square absolute error of calibration (RMSAEC), validation data set with 0.80 mean square absolute error of prediction (RMSAEP) and 0.98 coefficient of determination (R2) for both calibration and validation data set.

CONCLUSION

SERS is proved as a highly sensitive and discriminating technique to detect and discriminate insulin structural changes after regular intervals of time at room temperature.

Molecular dynamics and Raman optical activity spectra reveal nucleotide conformation ratios in solution

Nucleotide conformational flexibility affects their biological functions. Although the spectroscopy of Raman optical activity (ROA) is well suited to structural analyses in aqueous solutions, the link between the spectral shape and the nucleotide geometry is not fully understood. We recorded the Raman and ROA spectra of model nucleotides (rAMP, rGMP, rCMP, and dTMP) and interpreted them on the basis of molecular dynamics (MD) combined with density functional theory (DFT). The relation between the sugar puckering, base conformation and spectral intensities is discussed. Hydrogen bonds between the sugar's C3' hydroxyl and the phosphate groups were found to be important for the sugar puckering. The simulated spectra correlated well with the experimental data and provided an understanding of the dependence of the spectral shapes on conformational dynamics. Most of the strongest spectral bands could be assigned to vibrational molecular motions. Decomposition of the experimental spectra into calculated subspectra based on arbitrary maps of free energies provided experimental conformer populations, which could be used to verify and improve the MD predictions. The analyses indicate some flaws of common MD force fields, such as being unable to describe the fine conformer distribution. Also the accuracy of conformer populations obtained from the spectroscopic data depends on the simulations, improvement of which is desirable for gaining a more detailed insight in the future. Improvement of the spectroscopic and computational methodology for nucleotides also provides opportunities for its application to larger nucleic acids.

A Novel Method for Carbon Nanotube Functionalization Using Immobilized Candida antarctica Lipase

Carbon nanotubes (CNTs) have been proposed as nanovehicles for drug or antigen delivery since they can be functionalized with different biomolecules. For this purpose, different types of molecules have been chemically bonded to CNTs; however, this method has low efficiency and generates solvent waste. Candida antarctica lipase is an enzyme that, in an organic solvent, can bind a carboxylic to a hydroxyl group by esterase activity. The objective of this work was to functionalize purified CNTs with insulin as a protein model using an immobilized lipase of Candida antarctica to develop a sustainable functionalization method with high protein attachment. The functionalized CNTs were characterized by scanning electron microscope (SEM), Raman spectroscopy, Fourier-transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The enzymatic functionalization of insulin on the surface of the CNTs was found to have an efficiency of 21%, which is higher in conversion and greener than previously reported by the diimide-activated amidation method. These results suggest that enzymatic esterification is a convenient and efficient method for CNT functionalization with proteins. Moreover, this functionalization method can be used to enhance the cellular-specific release of proteins by lysosomal esterases.

Probing the solvation of the α-helix with extended amide III bands in Raman optical activity

Experimental and theoretical Raman optical activity (ROA) study of α-helical peptides and proteins has suggested that the relative intensity of two extended amide III ROA bands at ∼1340 cm^-1 (I band) and ∼1300 cm^-1 (II band) can be used to monitor the permittivity of the surrounding medium of the α-helix. So far, the ROA intensity ratio, I_I/I_II, has been interpreted from two different viewpoints. The first one is in terms of a direct effect of permittivity around the α-helix. The second one is based on a structural equilibrium of two types of α-helical structures, "hydrated" and "unhydrated" ones. In the present study, temperature- and solvent-dependences of I_I/I_II are measured for highly-α-helical peptides and compared to the theoretical spectra while varying the permittivity or the type of α-helical structure. A fragment method with partial optimization in the normal modes is adopted in density functional theory calculations. The main features of the experimental spectra and a trend of the observed I_I/I_II are well reproduced by the simulations, which leads us to a conclusion that the I_I/I_II is dominantly governed by a direct influence of the permittivity of the environment and just accessorily by the equilibrium of the two types of α-helices. The simulations also opposed the conventional assignments of the I and II bands to "hydrated" and "unhydrated" α-helical structures, respectively. In the case of α-helical proteins, solvent exposure of the α-helix may be monitored by the ROA ratio.

Advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase

The purpose of this review is to demonstrate advances, challenges and perspectives of quantum chemical approaches in molecular spectroscopy of the condensed phase. Molecular spectroscopy, particularly vibrational spectroscopy and electronic spectroscopy, has been used extensively for a wide range of areas of chemical sciences and materials science as well as nano- and biosciences because it provides valuable information about structure, functions, and reactions of molecules. In the meantime, quantum chemical approaches play crucial roles in the spectral analysis. They also yield important knowledge about molecular and electronic structures as well as electronic transitions. The combination of spectroscopic approaches and quantum chemical calculations is a powerful tool for science, in general. Thus, our article, which treats various spectroscopy and quantum chemical approaches, should have strong implications in the wider scientific community. This review covers a wide area of molecular spectroscopy from far-ultraviolet (FUV, 120-200 nm) to far-infrared (FIR, 400-10 cm-1)/terahertz and Raman spectroscopy. As quantum chemical approaches, we introduce several anharmonic approaches such as vibrational self-consistent field (VSCF) and the combination of periodic harmonic calculations with anharmonic corrections based on finite models, grid-based techniques like the Numerov approach, the Cartesian coordinate tensor transfer (CCT) method, Symmetry-Adapted Cluster Configuration-Interaction (SAC-CI), and the ZINDO (Semi-empirical calculations at Zerner's Intermediate Neglect of Differential Overlap). One can use anharmonic approaches and grid-based approaches for both infrared (IR) and near-infrared (NIR) spectroscopy, while CCT methods are employed for Raman, Raman optical activity (ROA), FIR/terahertz and low-frequency Raman spectroscopy. Therefore, this review overviews cross relations between molecular spectroscopy and quantum chemical approaches, and provides various kinds of close-reality advanced spectral simulation for condensed phases.

Toward Label-Free SERS Detection of Proteins through Their Disulfide Bond Structure

The molecular structure of many proteins contains disulfide bonds between their cysteine residues. In this work we demonstrate the utilization of the disulfide bond structure of proteins for their label-free determination by surface-enhanced Raman spectroscopy (SERS). The new approach for label-free SERS detection of proteins is demonstrated for human insulin. The protein was selectively extracted from spiked plasma samples using target-specific functionalized nanomaterial. Enzyme-linked immune assay (ELISA) was used to detect insulin in the blood plasma and cross-validate the SERS method. The disulfide bonds in the molecular structure of the protein were chemically reduced and used for their chemisorption onto the gold-coated copper oxide substrate in a unified orientation at a very short distance from the hotspots. The oriented chemisorption of the protein caused significant enhancement to the signal intensity of its Raman vibration modes. This is attributed to the strong short-range electromagnetic and chemical enhancement effects that are experienced by the immobilized protein. Using this approach, label-free and reproducible SERS detection of insulin, down to 10 zM (relative standard deviation [RSD] = 5.52%), was achieved. Sixty-five percent of proteins contain disulfide bonds in their molecular structure. Therefore, the new label-free SERS detection method has strong potential for the determination of ultralow concentrations of proteins at pathology labs and in biology research.

Conformational Disorder and Dynamics of Proteins Sensed by Raman Optical Activity

Raman optical activity (ROA) spectra of proteins hold a lot of information about their structure in solution. To create a better understanding of the ROA spectra of, among others, the intrinsically disordered proteins (IDPs), involved in neurodegenerative diseases, the effect of conformational disorder and dynamics on the ROA spectra was studied. Density functional theory (DFT) calculations of small ensembles of model peptides with increasing disorder show that the ROA patterns of α-helical and polyproline II (PPII) structure reflect the average backbone angles in the ensemble. The amide III region in the ROA spectra of the α-helical peptides is shown to retain its typical -/+/+ pattern, while the amide III region of PPII secondary structure diminishes in intensity with increasing structural disorder. The results show that the ROA spectra of IDPs hence more likely stem from short stretches of well-defined PPII helices rather than a very flexible chain. Further DFT calculations support that mixing of PPII with helical secondary structure is consistent with experimental spectra of IDPs, while mixing with β-strand results in spectral patterns that are not observed experimentally. The detailed information obtained from these results contributes to a better understanding of the spectrum-structure relation.