Experimental monitoring and data analysis tools for protein folding

Comparison of multivariate curve resolution strategies in quantitative LCxLC: Application to the quantification of furanocoumarins in apiaceous vegetables

Comprehensive two-dimensional liquid chromatography (LC × LC) has been gaining popularity for the analysis of complex samples in a wide range of fields including metabolomics, environmental analysis, and food analysis. While LC × LC can provide greater chromatographic resolution than one-dimensional LC (1D-LC), overlapping peaks are often still present in separations of complex samples, a problem that can be alleviated by chemometric curve resolution techniques such as multivariate curve resolution-alternating least squares (MCR-ALS). MCR-ALS has also been previously shown to assist in the quantitative analysis of LC x LC data by isolating pure analyte signals from background signals which are often present at higher levels in LC x LC compared to 1D-LC. In this work we present the analysis of a dataset from the LC × LC analyses of parsley, parsnip and celery samples for the presence and concentrations of 14 furanocoumarins. Several MCR-ALS implementations are compared for the analysis of LC × LC data. These implementations include analyzing the LC x LC chromatogram alone, analyzing the one-dimensional chromatogram alone, as well as two hybrid approaches that make use of both the first and second dimension chromatograms. Furthermore, we compared manual integration of resolved chromatograms versus a simple summation approach, using the resolved chromatographic peaks in both cases. It is found that manual integration of the resolved LC × LC chromatograms provides the best quantification as measured by the consistency between replicate injections. If the summation approach is desired for automation, the choice of MCR-ALS implementation has a large effect on the precision of the analysis. Based on these results, the concentrations of the 14 furanocoumarins are determined in the three apiaceous vegetable types by analyzing the LC × LC chromatograms with MCR-ALS and manual integration for peak area determination. The concentrations of the analytes are found to vary greatly between samples, even within a single vegetable type.

New insight into protein-nanomaterial interactions with UV-visible spectroscopy and chemometrics: human serum albumin and silver nanoparticles

In recent years, great efforts have focused on the exploration and fabrication of protein nanoconjugates due to potential applications in many fields including bioanalytical science, biosensors, biocatalysis, biofuel cells and bio-based nanodevices. An important aspect of our understanding of protein nanoconjugates is to quantitatively understand how proteins interact with nanomaterials. In this report, human serum albumin (HSA) and citrate-coated silver nanoparticles (AgNPs) are selected as a case study of protein-nanomaterial interactions. UV-visible spectroscopy together with multivariate curve resolution by alternating least squares (MCR-ALS) algorithm is first exploited for the detailed study of AgNPs-HSA interactions. Introduction of the chemometrics tool allows extracting the kinetic profiles, spectra and distribution diagrams of two major absorbing pure species (AgNPs and AgNPs-HSA conjugate). These resolved profiles are then analysed to give the thermodynamic, kinetic and structural information of HSA binding to AgNPs. Transmission electron microscopy, circular dichroism spectroscopy and Fourier transform infrared spectroscopy are used to further characterize the complex system. Moreover, a sensitive spectroscopic biosensor for HSA is fabricated with the MCR-ALS resolved concentration of absorbing pure species. It is found that the linear range for the HSA nanosensor was from 1.9 nM to 45.0 nM with a detection limit of 0.9 nM. It is believed that the proposed method will play an important role in the fabrication and optimization of a robust nanobiosensor or cross-reactive sensors array for the detection and identification of biocomponents.

Competitive interactions of anti-carcinogens with serum albumin: a spectroscopic study of bendamustine and dexamethasone with the aid of chemometrics

Interactions between the anti-carcinogens, bendamustine (BDM) and dexamethasone (DXM), with bovine serum albumin (BSA) were investigated with the use of fluorescence and UV-vis spectroscopies under pseudo-physiological conditions (Tris-HCl buffer, pH 7.4). The static mechanism was responsible for the fluorescence quenching during the interactions; the binding formation constant of the BSA-BDM complex and the binding number were 5.14×10(5)Lmol(-1) and 1.0, respectively. Spectroscopic studies for the formation of BDM-BSA complex were interpreted with the use of multivariate curve resolution - alternating least squares (MCR-ALS), which supported the complex formation. The BSA samples treated with site markers (warfarin - site I and ibuprofen - site II) were reacted separately with BDM and DXM; while both anti-carcinogens bound to site I, the binding constants suggested that DXM formed a more stable complex. Relative concentration profiles and the fluorescence spectra associated with BDM, DXM and BSA, were recovered simultaneously from the full fluorescence excitation-emission data with the use of the parallel factor analysis (PARAFAC) method. The results confirmed that on addition of DXM to the BDM-BSA complex, the BDM was replaced and the DXM-BSA complex formed; free BDM was released. This finding may have consequences for the transport of these drugs during any anti-cancer treatment.

Exploring in vivo violacein biosynthesis by application of multivariate curve resolution on fused UV-VIS absorption, fluorescence, and liquid chromatography-mass spectrometry data

In this work, the application of multivariate curve resolution-alternating least squares (MCR-ALS) is proposed for extracting information from multitechnique fused multivariate data (UV-VIS absorption, fluorescence, and liquid chromatography-mass spectrometry) gathered during the biosynthesis of violacein pigment. Experimental data sets were pretreated and arranged in a row-wise augmented data matrix before their chemometric investigation. Five different chemical components were resolved. Kinetic and spectral information about these components were obtained and their relationship with violacein biosynthesis was established. Three new chemical compounds with molar masses of 453, 465, and 479 u, until now not reported in the literature, were identified and proposed as intermediates in the biosynthesis of other indolocarbazoles. The precursor (tryptophan), one intermediate (deoxyviolacein), and the final product (violacein) of violacein biosynthesis were identified and characterized using the proposed approach. The chemometric procedure based on the MCR-ALS method has proved to be a powerful tool to investigate violacein biosynthesis and its application can be easily extended to the study of other bioprocesses.