Profiling of hydroxyurea-treated β-thalassemia/ serum proteome through nano-LC–ESI–MS/ MS in combination with microsol-isoelectric focusing

Advancements in proteomic tools offer a comprehensive solution to studying the complexity of diseases at molecular level. This study focusses on the clinical proteomic profiling of pre- and post-hydroxyurea (HU)-treated β-thalassemia patients in parallel with healthy individuals to better understand the role of HU in the treatment of β-thalassemia. The strategy encompasses sequential high-resolution protein fractionation using MicroSol-isoelectric focusing (ZOOM- IEF) followed by one-dimensional SDS-PAGE before nano-RP-LC–MS/ MS analysis of tryptic peptides. Protein identification was performed through Mascot search using NCBInr and SwissProt databases. Several different proteins were observed in pool serum samples of each of the three study groups. Approximately, 1250 proteins exclusive to each group were identified, and after removing the redundant and low sequence coverage proteins, the number was reduced to 576 (201 in healthy, 187 in HU-untreated and 188 in HU-treated group). Uniquely identified proteins in the HU-treated group regulate the focal adhesion, ECM-receptor interaction, PI3K-Akt signaling, Rap1 signaling, cAMP signaling, platelet activation, and Ca²⁺ signaling pathways in the HU-treated group. The proteomic profile presented here will add to the current state of understanding of molecular mechanisms involved in hydroxyurea treatment of β-thalassemia.     

Determination of Dothiepin in Human Plasma by LC–ESI–MS and its Application to Bioequivalence Studies

An LC–MS method for the determination of dothiepin in human plasma was developed and validated. Sample preparation involved extraction with n-hexane:2-propanol (95:5). Separation was on an Ultimate XB C18 column (2.1 × 150 mm, 5 μm). A single-quadrupole mass spectrometer with an electrospray interface was operated in the selected-ion monitoring mode to detect the [M+H]⁺ ions at m/z 296 for dothiepin and at m/z 278 for the internal standard (amitriptylene). The method demonstrated good linearity from 0.78 ng mL^?1 (the LOQ) to100 ng mL^?1. The mean extraction recovery was 82.4% for dothiepin and and 84.2% for the internal standard. The intra-day and inter-day precision ranged from 8.5 to 11.4% and 9.7 to 12.1% (RSD), respectively. The method was successfully applied to bioequivalence studies of dothiepin hydrochloride tablets to obtain the pharmacokinetic parameters.     

Development of a simple spectrophotometric method to estimate uranium concentration in LiCl–KCl matrix

“Off-the-shelf” clinical linear electron accelerators (LINAC) have been suggested as alternative to research accelerators once they are no longer suitable for the medical applications. We investigated feasibility of utilising a modified LINAC for instrumental photon activation analysis (IPAA) as a tool in environmental geochemistry studies. The IPAA results were compared with those obtained using a MT-25 research accelerator at Joint Institute for Nuclear Research in Dubna, Russia. To investigate soil pollution in Antalya, Turkey, 90 surface soil samples were analysed and significant enrichments of Ni, Cr and As were found.

     

Topologic Transformation of Inorganic Salt–Oxyethylated Surfactant–Water Phase Diagrams in Response to Changing Temperature

A general topologic transformation scheme of phase diagram is proposed for inorganic salt–oxyethylated surfactant–water systems that have a lower critical solution temperature (LCST) or where the surfactant–water binary subsystem is homogeneous over the entire range of liquid temperatures for the case where the salt has the salting-out, salting-in, or salting-in-and-salting-out effect. Examples are provided to illustrate the implementation of the suggested variants of the general scheme.     

Use of a porous silicon–gold plasmonic nanostructure to enhance serum peptide signals in MALDI-TOF analysis

Small peptides in serum are potential biomarkers for the diagnosis of cancer and other diseases. The identification of peptide biomarkers in human plasma/serum has become an area of high interest in medical research. However, the direct analysis of peptides in serum samples using mass spectrometry is challenging due to the low concentration of peptides and the high abundance of high-molecular-weight proteins in serum, the latter of which causes severe signal suppression. Herein, we reported that porous semiconductor-noble metal hybrid nanostructures can both eliminate the interference from large proteins in serum samples and significantly enhance the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) yields of peptides captured on the nanostructure. Serum peptide fingerprints with high fidelity can be acquired rapidly, and successful discrimination of colorectal cancer patients based on peptide fingerprints is demonstrated.     

Dispersive liquid–liquid microextraction applied to the simultaneous derivatization and concentration of triclosan and methyltriclosan in water samples

A fast and novel sample preparation procedure for the determination of triclosan (TCS) and methyltriclosan (MTCS) in water samples is presented. Dispersive liquid–liquid microextraction, using a ternary mixture consisting of a disperser, an extractant and N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide (MTBSTFA) as derivatization reagent, was used for the simultaneous derivatization, case of TCS, and concentration of both species in different water samples. Analytes were determined by gas chromatography with tandem mass spectrometry (GC–MS/MS). Influence of different factors on the performance of the sample preparation process is thoroughly discussed. Under final working conditions, a mixture of 1 mL of methanol, 40 μL of 1,1,1-trichloroethane and the same volume of MTBSTFA was added to 10 mL of water in a conical bottom glass tube. After centrifugation, the settled phase was injected directly in the chromatographic system. TCS was quantitatively extracted and converted into the corresponding tert-butyldimethylsilyl derivative, whereas for MTCS an extraction yield around 90% was attained. Limits of quantification between 2 and 5 ng L⁻¹ and reproducibility values below 10% were achieved; moreover, the performance of the extraction process was scarcely affected by the type of water sample. Globally, these values are comparable, or even better, to those reported for other approaches applied to the determination of same compounds, with the advantage of a shorter sample preparation step. Analysis of surface and wastewater samples confirmed the ubiquitous presence of TCS in the aquatic environment at levels from 20 to 700 ng L⁻¹.     

Dispersive liquid–liquid microextraction applied to isolation and concentration of alkylphenols and their short-chained ethoxylates in water samples

Dispersive liquid–liquid microextraction (DLLME) coupled with high-performance liquid chromatography with fluorescence detector was applied for the determination of alkylphenols and their short-chained ethoxylates in water samples. Development of DLLME procedure included optimisation of some important parameters such as kind and volume of extracting and dispersing solvents. Under optimised conditions 50 μL of trichloroethylene in 1.5 mL of acetone were rapidly injected into 5 mL of a water sample. After centrifuging the organic phase containing the analytes was taken for evaporation with a gentle nitrogen purge and reconstituted to 50 μL of acetonitrile. The aliquot of this solution was analysed with the use of HPLC. For octylphenol (OP) and octylphenol ethoxylates (OPEOs) linearity was satisfactory in the range 8–1000 μg L⁻¹ and for nonylphenol (NP) and nonylphenol ethoxylates (NPEOs) linearity was in the range from 50 to about 3000 μg L⁻¹. Limit of quantitation was 0.1 μg L⁻¹ for OP and OPEOs and 0.3 μg L⁻¹ for NP and NPEOs. Satisfactory recoveries between 66 and 79% were obtained for environmental samples. The results showed that DLLME is a simple, rapid and sensitive analytical method for the preconcentration of trace amounts of alkylphenols and their ethoxylates in environmental water samples.     

Differential Proteomic Analysis of Neonatal Cardiomyocytes in Response to β-Adrenergic Receptor Stimulation

Introduction Adrenoceptors(ARs),membersofthesuperfami lyofG proteincoupledreceptors,arethemostimpor tantreceptorsinvolvedincardiacregulation[1].ARsin cardiacmuscleincludebothαARsandβARssub types,whileinmostmammalianheart,βARsarethe predominantsubtypes.…     

The critical aggregation concentration of peptide surfactants is predictable from dynamic hydrophobic property

Peptide surfactants are a kind of newly emerged functional materials, which have a variety of applications such as building nanoarchitecture, stabilizing membrane proteins and controlling drug release. In the present study, we report the modelling and prediction of critical aggregation concentration (CAC), an important parameter that characterizes the self-assembling behaviour of peptide surfactants through the use of statistical modelling and quantitative structure–property relationship (QSPR) approaches. In order to accurately describe the structural and physicochemical properties of the highly flexible peptide molecules, a new method called molecular dynamics-based hydrophobic cross-field (MD-HCF) is proposed to capture both the hydrophobic profile and dynamic feature of 32 surface-activity, structure-known peptides. A number of statistical models are then developed using partial least squares (PLS) regression with or without improvement by genetic algorithm (GA). We demonstrate that MD-HCF performs much better than the widely used CODESSA method in both its predictability and interpretability. We also highlight the importance of dynamic hydrophobic property in accurate prediction and reasonable explanation of peptide self-assembling behaviour in solution, albeit which is exhaustive to compute compared with those derived directly from peptide static structure. To the best of our knowledge, this study is the first to computationally model and predict the self-assembling behaviour of peptide surfactants.     

Investigation of the interaction between HIV-1 DNA and cyclic peptides by electrospray ionization mass spectrometry

The interaction between HIV-I DNA and five cyclic peptides (CPI-CP5) was investigated using electrospray ionization mass spectrometry (ESI-MS). It revealed that CPI [c(Ala-Tyr-Leu-Ala-Gly)] and CP4 [c(Pro-D-Tyr-Leu-D-Ala-Gly)] have the higher binding affinity with the duplex DNA among the five cyclic peptides.     

A simple sheathless CE-MS interface with a sub-micrometer electrical contact fracture for sensitive analysis of peptide and protein samples

Online coupling of capillary electrophoresis (CE) to electrospray ionization mass spectrometry (MS) has shown considerable potential, however, technical challenges have limited its use. In this study, we have developed a simple and sensitive sheathless CE-MS interface based on the novel concept of forming a sub-micrometer fracture directly in the capillary. The simple interface design allowed the generation of a stable ESI spray capable of ionization at low nanoliter flow-rates (45–90 nL/min) for high sensitivity MS analysis of challenging samples like those containing proteins and peptides. By analysis of a model peptide (leucine enkephalin), a limit of detection (LOD) of 0.045 pmol/μL (corresponding to 67 attomol in a sample volume of ∼15 nL) was obtained. The merit of the CE-MS approach was demonstrated by analysis of bovine serum albumin (BSA) tryptic peptides. A well-resolved separation profile was achieved and comparable sequence coverage was obtained by the CE-MS method (73%) compared to a representative UPLC-MS method (77%). The CE-MS interface was subsequently used to analyse a more complex sample of pharmaceutically relevant human proteins including insulin, tissue factor and α-synuclein. Efficient separation and protein ESI mass spectra of adequate quality could be achieved using only a small amount of sample (30 fmol). In addition, analysis of ubiquitin samples under both native and denatured conditions, indicate that the CE-MS setup can facilitate native MS applications to probe the conformational properties of proteins. Thus, the described CE-MS setup should be useful for a wide range of high-sensitivity applications in protein research.     

多肽新药研发策略研究进展

多肽药物具有生物活性高、药用剂量小、产业化开发优势明显等诸多优点,已成为全球关注的创新药物研发热点之一.但是其代谢不稳定、半衰期短及较难通透组织屏障等缺点严重阻碍了多肽新药在临床治疗中的广泛应用.为了解决这些限制多肽药物的瓶颈,本课题组发展了一系列的改造策略.通过这些策略的应用,以期加快多肽药物临床应用的步伐.本文主要结合本课题组的工作对多肽新药创制过程中所遇到的关键问题及解决思路进行综述.     

Efficient peptide mapping and its application to identify embryo proteins in rice proteome analysis

Using direct N-terminal analysis, only 31 N-terminally unblocked proteins out of 100 rice embryo proteins could be identified. To obtain protein sequence information for the remaining 69 blocked proteins, we developed a simple, efficient and rapid method. Using this method, we determined the peptide maps of 20 proteins per day in 10 pmol amounts. Applying this method to rice proteome analysis, we determined the internal sequences of all 69 blocked proteins. A total of 28 proteins out of 100 analyzed showed sequence similarity to the proteins with known functions in the SWISS-PROT and NCBI databases. Alternatively, we also used peptide mass fingerprinting determined by matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) to identify the rice proteins separated by two-dimensional electrophoresis (2-DE). Although peptide-mass fingerprinting is a high-throughput method, we could not easily identify all the rice proteins or genes by this method, because the complete database information on rice, is not yet available and many proteins are post-translationally modified. Therefore, at present, the improved peptide mapping method as we report here is considered to be very useful in rice proteome analysis, especially for blocked proteins.     

Direct ampholyte-free liquid-phase isoelectric peptide focusing: application to the human serum proteome

In this study, we utilized a multidimensional peptide separation strategy combined with tandem mass spectrometry (MS/MS) for the identification of proteins in human serum. After enzymatically digesting serum with trypsin, the peptides were fractionated using liquid-phase isoelectric focusing (IEF) in a novel ampholyte-free format. Twenty IEF fractions were collected and analyzed by reversed-phase microcapillary liquid chromatography (microLC)-MS/MS. Bioinformatic analysis of the raw MS/MS spectra resulted in the identification of 844 unique peptides, corresponding to 437 proteins. This study demonstrates the efficacy of ampholyte-free peptide autofocusing, which alleviates peptide losses in ampholyte removal strategies. The results show that the separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures.     

Recent developments in peptide macrocyclization

Cyclic peptides have been widely applied in fields ranging from drug discovery to nanomaterials. After years of development, the preparation of peptide macrocycles, especially late-stage macrocyclization of peptides, remains challenging using traditional synthetic methods. This digest highlights recent developments in the synthesis of cyclic peptides.     

Determination of the critical premicelle concentration, first critical micelle concentration and second critical micelle concentration of surfactants by resonance Rayleigh scattering method without any probe

The purpose of this work is to determine the values of critical premicelle concentration (CPMC), first critical micelle concentration (FCMC) and second critical micelle concentration (SCMC) of surfactants using a common spectrofluorophotometer by recording resonance Rayleigh scattering (RRS) signal without any probe. The plot of the RRS intensities at the maximum scattering wavelength (I(RRS)(max)) versus surfactant concentrations (c) was constructed to obtain the I(RRS)(max)-c curve. From the inflexions in I(RRS)(max)-c curve, the CPMC, FCMC and SCMC values of a surfactant can be obtained sensitively. The FCMC of some anionic, cationic and nonionic surfactants such as sodium dodecyl sulfate (SDS), sodium dodecyl benzene sulfonate (SDBS), cetyltrimethylammonium bromide (CTAB), cetylpyridinium chloride (CPC), Tween-20, and Tween-80 were determined by RRS method and the values are in good agreement with those obtained from conductivity and surface tension measurements and literature values. The CPMC and SCMC of SDS and CTAB were also determined by RRS method respectively and the values conform to literature values too. Furthermore, RRS method can also be used to determine the FCMC of an amphiphilic macromolecule-hemoglobin, whose structure resembles a surfactant. From the experimental results, it is concluded that RRS method can be applied to the simultaneous determination of the CPMC, FCMC and SCMC values in a sensitive, accurate and no probe way.     

Investigating the scope of pseudoproline assisted peptide cyclization

The cyclization of linear peptides from six to nine amino acids in length and containing between two and four pseudoproline turn inducers derived from serine or threonine was investigated to determine the effect of peptide length, amino acid composition and spacing between the pseudoproline residues on macrocyclization yield.