Protein extraction for proteome analysis from cacao leaves and meristems, organs infected by Moniliophthora perniciosa, the causal agent of the witches' broom disease

Preparation of high-quality proteins from cacao vegetative organs is difficult due to very high endogenous levels of polysaccharides and polyphenols. In order to establish a routine procedure for the application of proteomic and biochemical analysis to cacao tissues, three new protocols were developed; one for apoplastic washing fluid (AWF) extraction, and two for protein extraction--under denaturing and nondenaturing conditions. The first described method allows a quick and easy collection of AWF--using infiltration-centrifugation procedure--that is representative of its composition in intact leaves according to the smaller symplastic contamination detected by the use of the hexose phosphate isomerase marker. Protein extraction under denaturing conditions for 2-DE was remarkably improved by the combination of chemically and physically modified processes including phenol, SDS dense buffer and sonication steps. With this protocol, high-quality proteins from cacao leaves and meristems were isolated, and for the first time well-resolved 1-DE and 2-DE protein patterns of cacao vegetative organs are shown. It also appears that sonication associated with polysaccharide precipitation using tert-butanol was a crucial step for the nondenaturing protein extraction and subsequent enzymatic activity detection. It is expected that the protocols described here could help to develop high-level proteomic and biochemical studies in cacao also being applicable to other recalcitrant plant tissues.     

A concise and efficient synthesis of vildagliptin

An original synthesis of vildagliptin ((S)-1-[2-(3-hydroxyadamantan-1-ylamino)acetyl]pyrrolidine-2-carbonitrile), a powerful DPP-4 inhibitor, was developed. Vildagliptin was assembled from 3-amino-1-adamantanol, glyoxylic acid and l-prolinamide in a 4-step reaction sequence with the isolation of only two intermediates. The procedure is competitive with existing protocols, leading to vildagliptin in 63% overall yield.     

In-tip nanoreactors for cancer cells proteome profiling

Mass spectrometry (MS)-based proteome profiling is essential for molecular diagnostics in modern biomedical study. To date, sample preparation including protein extraction and proteolysis is still very challenging and lack of efficiency. Recently tips-based sample preparation protocols exhibit strong potentials to achieve the goal of “a proteome in an hour”. However, in-tip proteolysis is still rarely reported and far from ideal for dealing with complex bio-samples. In this work, nanoreactors encapsulated micropipette tips were demonstrated as high performance devices for fast (∼minutes) and multiplexing proteolysis to assist the profiling of cancer cells proteome. Nanoporous silica materials with controlled pore size and surface chemistry were prepared as nanoreactors and encapsulated in micropipette tips for efficient in situ proteolysis. The as-constructed device showed desirable sensitivity (LOD of 0.204 ± 0.008 ng/μL and LOQ of 0.937 ± 0.055 ng/μL), selectivity, stability (two months under −20 °C), reusability (at least 10 times), and little memory effect in MS based bottom-up proteomic analysis. It was used for comprehensive protein mapping from cancer cell lines. The number of identified proteins was increased by 18%, 22%, 52%, and 52% dealing with HepG2, F56, MCF7, and HCCLM3 cancer cells, compared to traditional in-solution proteolysis based bottom-up proteomic strategy. With the enhanced performance, our work built a novel, efficient and miniaturized platform for facile proteomic sample preparation, which is promising for advanced biomarkers discovery in biomedical study.     

Characterization of quinoa seed proteome combining different protein precipitation techniques: Improvement of knowledge of nonmodel plant proteomics

A shotgun proteomics approach was used to characterize the quinoa seed proteome. To obtain comprehensive proteomic data from quinoa seeds three different precipitation procedures were employed: MeOH/CHCl₃/double‐distilled H₂O, acetone either alone or with trichloroacetic acid; the isolated proteins were then in‐solution digested and the resulting peptides were analyzed by nano‐liquid chromatography coupled to tandem mass spectrometry. However, since quinoa is a nonmodel plant species, only a few protein sequences are included in the most widely known protein sequence databases. To improve the data reliability a UniProt subdatabase, containing only proteins of Caryophillales order, was used. A total of 352 proteins were identified and evaluated both from a qualitative and quantitative point of view. This combined approach is certainly useful to increase the final number of identifications, but no particular class of proteins was extracted and identified in spite of the different chemistries and the different precipitation protocols. However, with respect to the other two procedures, from the relative quantitative analysis, based on the number of spectral counts, the trichloroacetic acid/acetone protocol was the best procedure for sample handling and quantitative protein extraction. This study could pave the way to further high‐throughput studies on Chenopodium Quinoa.     

In vitro methylation by methanol: Proteomic screening and prevalence investigation

It is assumed that much more functional importance for protein activity than expected may be granted by methylation that occurs at the side-chain of aspartate or glutamate residue. In vitro methylation mainly comes from the use of methanol in sample preparation prior to MS analysis. In this study, we first performed the methylation site-directed proteomic screening of bovine serum albumin, ovalbumin and 20S proteasome for gel staining using a meaningfully indicative MS-pattern of peak tag (termed as 4P tag) and manual inspection for mass spectral data. As a result, there were 17 proteolytic peptides with 20 modified sites confirmed to be in vitro methylated. Subsequently, the prevalence investigation was performed, focusing on the reaction kinetic behavior of in vitro methylation. This study provided a simple and robust approach for confirmation of in vitro methylation by methanol, as well as the precautious guide for the use of methanol in proteomic study.     

Protein extraction from Phoenix dactylifera L. leaves, a recalcitrant material, for two-dimensional electrophoresis

This work was aimed at optimizing a protein extraction procedure for date palm (Phoenix dactylifera L.) leaves, a highly recalcitrant plant tissue for 2-DE. Five protein extraction protocols based on different protein precipitation agents (TCA/acetone vs. phenol (Ph) methods) and protein resolubilization methods (physical treatments, e.g., sonication, shaking and/or heating) were tested. Ph/SDS extraction with methanol/ammonium acetate precipitation, followed by DOC preincubation and TCA/acetone precipitation and, finally, solubilization by shaking in rehydration solution was found to be the best protein extraction method. We conclude that DOC with TCA/acetone precipitation step eliminates interfering compounds, thus allowing efficient resolubilization of date palm leaf proteins. This method could be appropriate for proteomic studies such as date palm colonization by entomopathogenic fungi.     

Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis

Sample preparation is a fundamental step in proteomic methodologies. The quality of the results from a proteomic experiment is dependent on the nature of the sample and the properties of the proteins. In this study, various pre-treatment methods were compared by proteomic analysis; we analysed various rat brain structures after chloroform/methanol, acetone, TCA/acetone and TCA protein precipitation procedures. The protein content of the supernatant was also examined by 2-DE. We found that for four of the rat brain structures, precipitation with chloroform/methanol and acetone delivered the highest protein recovery for top-down proteomic analysis; however, TCA precipitation resulted in good protein separation and the highest number of protein spots in 2-DE. Moreover, TCA precipitation also gave high efficiency of protein recovery if prior sonication procedure was performed.     

Comparative evaluation of extraction methods for simultaneous mass-spectrometric analysis of complex lipids and primary metabolites from human blood plasma

Metabolomic results on human blood plasma largely depend on the sample preparation protocols employed for protein precipitation and metabolite extraction. Five different extraction methods were examined, which can be grouped into two categories, liquid-liquid extraction and protein precipitation methods, including long-standing protocols such as the Folch extraction and Bligh-Dyer extraction in comparison to modern methods such as the Matyash protocol and two global metabolite extraction methods. Extracts were subjected to analysis of blood plasma lipids and primary metabolites by using chip-based direct infusion nanoelectrospray tandem mass spectrometry and gas chromatography coupled to time-of-flight mass spectrometry, respectively. Optimal extraction schemes were evaluated based on the number of identified metabolites, extraction efficiency, compound diversity, reproducibility, and convenience for high-throughput sample preparations. Results showed that Folch and Matyash methods were equally valid and robust for lipidomic assessments while primary metabolites were better assessed by the protein precipitation methods with organic solvent mixtures. Graphical Abstract

Schematic workflow of five extraction methods and subsequent mass spectrometry analysis using GC-TOF MS and nanoelectrospray direct-infusion ion trap MS/MS?     

Comparative evaluation of five protocols for protein extraction from stony corals (Scleractinia) for proteomics

Corals especially the reef‐building species are very important to marine ecosystems. Proteomics has been used for researches on coral diseases, bleaching and responses to the environment change. A robust and versatile protein extraction protocol is required for coral proteomics. However, a comparative evaluation of different protein extraction protocols is still not available for proteomic analysis of stony corals. In the present study, five protocols were compared for protein extraction from stony corals. The five protocols were TRIzol, phenol‐based extraction (PBE), trichloroacetic acid (TCA)‐acetone, glass bead‐assisted extraction (GBAE) and a commercially available kit. PBE, TRIzol and the commercial kit were more robust for extracting proteins from stony corals. The protein extraction efficiency and repeatability, two dimensional electrophoresis (2‐DE) and matrix‐assisted laser desorption/ionization time of flight mass spectrometry (MALDI TOF MS) were employed to evaluate the protocols. The results indicated that PBE protocol had the better protein extraction efficiency than the others. Protein extraction coverage varied among the procedures. Each protocol favored for certain proteins. Therefore, it is very important for coral proteomic analysis to select a suitable protein protocol upon the experimental design. In general, PBE protocol can be the first choice for extracting proteins from stony corals.     

The α and β domains of human metallothionein-3 co-operatively protect against Aβ1-42-Cu2+ cytotoxicity

Cytotoxicity of A β with redox active metals in neuronal cells has been implicated in the progression of Alzheimer’s disease （AD）.Zn₇MT-3 protects cell against Aβ-Cu²⁺ toxicity.The roles of single domain proteins（α/β） andα-βdomain-domain interaction of Zn₇MT-3 in its anti-Aβ_1-42-Cu²⁺ toxicity activity were investigated herein.Aβ_1-42 and four mutants of human MT3 （α/βdomain,β（MT3）-α（MTl） and A31-34） were prepared and characterized.Aβ_1-42-Cu²⁺ induced hydroxyl radical and ROS production with/without Zn-MTs were measured by fluorescence spectroscopy and DCFH-DA in living cells,respectively.These results indicate that the two domains form a co-operative unit and each of them is indispensable in conducting its bioactivity.     

Evaluation of sample preparation protocols for proteomic analysis of sunflower leaves

Six protocols for extraction of proteins from sunflower (Helianthus annuus L.) leaves were evaluated for their abilities in both removing interferents and attaining the best resolution in two-dimensional gel electrophoresis. “Classical” phenol extraction followed by precipitation with ammonium acetate in methanol displayed the most efficient protocol, which allowed the detection of 244 protein spots with ca. 485 μg of protein in gel electrophoresis. Tandem mass spectrometry was performed to identify proteins in 61 spots, and cross species identification was used for this task. Proteins from twenty two spots were identified, and 12 of these proteins are up to now not included into the ExPASy sunflower protein databank.     

(Z,Z)-Selanediylbis(2-propenamides): Novel Class of Organoselenium Compounds with High Glutathione Peroxidase-Like Activity. Regio- and Stereoselective Reaction of Sodium Selenide with 3-Trimethylsilyl-2-propynamides

The efficient regio- and stereoselective synthesis of (Z,Z)-3,3′-selanediylbis(2-propenamides) in 76–93% yields was developed based on the reaction of sodium selenide with 3-trimethylsilyl-2-propynamides. (Z,Z)-3,3′-Selanediylbis(2-propenamides) are a novel class of organoselenium compounds. To date, not a single representative of 3,3′-selanediylbis(2-propenamides) has been described in the literature. Studying glutathione peroxidase-like properties by a model reaction showed that the activity of the obtained products significantly varies depending on the organic moieties in the amide group. Divinyl selenide, which contains two lipophilic cyclohexyl substituents in the amide group, exhibits very high glutathione peroxidase-like activity and this compound is considerably superior to other products in this respect.     

O-Alkylation of 3-hydroxyisoxazoles predominates under Mitsunobu conditions

Regiochemical control in the functionalization of ambident nucleophiles is of particular interest in organic chemistry. Herein, we demonstrate that O-alkylation of ambident 3-hydroxyisoxazoles, which are heterocyclic bioisosteres of carboxylic acids, predominates under Mitsunobu conditions. In several cases, excellent O-regioselectivity (?95%) was observed. It is noteworthy that reactions were complete within 15 min at room temperature. Furthermore, the conditions are compatible with a range of alcohols that cover all of the typical protecting groups for the 3-hydroxyisoxazole motif, providing milder, simpler and less hazardous protocols to those commonly followed in the literature.     

Proteomic and Bioinformatic Investigation of Altered Pathways in Neuroglobin-Deficient Breast Cancer Cells

Neuroglobin (NGB) is a myoglobin-like monomeric globin that is involved in several processes, displaying a pivotal redox-dependent protective role in neuronal and extra-neuronal cells. NGB remarkably exerts its function upon upregulation by NGB inducers, such as 17β-estradiol (E2) and H₂O₂. However, the molecular bases of NGB’s functions remain undefined, mainly in non-neuronal cancer cells. Human MCF-7 breast cancer cells with a knocked-out (KO) NGB gene obtained using CRISPR/Cas9 technology were analyzed using shotgun label-free quantitative proteomics in comparison with control cells. The differential proteomics experiments were also performed after treatment with E2, H₂O₂, and E2 + H₂O₂. All the runs acquired using liquid chromatography–tandem mass spectrometry were elaborated within the same MaxQuant analysis, leading to the quantification of 1872 proteins in the global proteomic dataset. Then, a differentially regulated protein dataset was obtained for each specific treatment. After the proteomic study, multiple bioinformatics analyses were performed to highlight unbalanced pathways and processes. Here, we report the proteomic and bioinformatic investigations concerning the effects on cellular processes of NGB deficiency and cell treatments. Globally, the main processes that were affected were related to the response to stress, cytoskeleton dynamics, apoptosis, and mitochondria-driven pathways.     

1,n′-Disubstituted ferrocenoyl amino acids and dipeptides: Conformational analysis by CD spectroscopy, X-ray crystallography, and DFT calculations

An experimental and computational study on the conformational preference of 1,n′-disubstituted ferrocenoyl amino acids and dipeptides is presented. Only l-amino acids were used for the synthesis of Fe[C₅H₄-CO-Met-Met-OMe]₂ (4), but according to the X-ray structure a 4:1 mixture of l,d,M,d,l and l,d,M,l,l isomers is obtained (l describes amino acid chirality and M the helical chirality of the ferrocene core). This result is in agreement with IR and CD solution phase data and can be explained with a racemization by 1 M NaOH during the synthesis. In order to determine the relative stabilities of the different conformations, DFT calculations on model compounds Fe[C₅H₄-CO-Gly-NH₂]₂ (5) and Fe[C₅H₄-CO-Ala-OMe]₂ (6) were performed using the B3LYP/LanL2DZ method with ECPs on the heavy atoms. Conformers 5A-5C with different hydrogen bond patterns have significantly different stabilities with a stabilization by about 30 kJ mol⁻¹ per hydrogen bond. The “Herrick conformation” 5A with two hydrogen bonds is the most stable in the gas phase, in accordance with the solution and solid phase data. In contrast, only small energetic differences (less than 10 kJ mol⁻¹) were calculated for conformers l,P,l-6A, l,P,d-6A and d,P,d-6A, which differ only in amino acid chirality.     

Activation of PPAR�� induces profound multilocularization of adipocytes in adult mouse white adipose tissues

We sought to determine the effects of activation of peroxisome proliferator-activated receptor-γ (PPAR-γ) on multilocularization of adipocytes in adult white adipose tissue (WAT). Male C57BL/6 normal, db/db, and ob/ob mice were treated with agonists of PPAR-γ, PPAR-α, or β₃-adrenoceptor for 3 weeks. To distinguish multilocular adipocytes from unilocular adipocytes, whole-mounted adipose tissues were co-immunostained for perilipin and collagen IV. PPAR-γ activation with rosiglitazone or pioglitazone induced a profound change of unilocular adipocytes into smaller, multilocular adipocytes in adult WAT in a time-dependent, dose-dependent, and reversible manner. PPAR-α activation with fenofibrate did not affect the number of locules or remodeling. db/db and ob/ob obese mice exhibited less multilocularization in response to PPAR-γ activation compared to normal mice. Nevertheless, all adipocytes activated by PPAR-γ contained a single nucleus regardless of locule number. Multilocular adipocytes induced by PPAR-γ activation contained substantially increased mitochondrial content and enhanced expression of uncoupling protein-1, PPAR-γ coactivator-1-α , and perilipin. Taken together, PPAR-γ activation induces profound multilocularization and enhanced mitochondrial biogenesis in the adipocytes of adult WAT. These changes may affect the overall function of WAT.     

Mass Spectrometric Identification of Antimicrobial Peptides from Medicinal Seeds

Traditional medicinal plants contain a variety of bioactive natural products including cysteine-rich (Cys-rich) antimicrobial peptides (AMPs). Cys-rich AMPs are often crosslinked by multiple disulfide bonds which increase their resistance to chemical and enzymatic degradation. However, this class of molecules is relatively underexplored. Herein, in silico analysis predicted 80–100 Cys-rich AMPs per species from three edible traditional medicinal plants: Linum usitatissimum (flax), Trifolium pratense (red clover), and Sesamum indicum (sesame). Bottom-up proteomic analysis of seed peptide extracts revealed direct evidence for the translation of 3–10 Cys-rich AMPs per species, including lipid transfer proteins, defensins, α-hairpinins, and snakins. Negative activity revealed by antibacterial screening highlights the importance of employing a multi-pronged approach for AMP discovery. Further, this study demonstrates that flax, red clover, and sesame are promising sources for further AMP discovery and characterization.     

Proteome investigation of the non-model plant pomegranate (Punica granatum L.)

A gel-free, shotgun proteomics approach was used to characterize pomegranate aril proteome by nanoliquid chromatography–high-resolution tandem mass spectrometry. To identify both high-abundance and low-abundance proteins, we applied two distinct sample preparation protocols, i.e., a classical one widely applied in literature and a second one able to reduce the dynamic range of protein concentration of the sample, based on combinatorial hexapeptide ligand library technology. However, the proteins identified with the latter protocol were only a small minority. Because pomegranate is a non-model plant species, i.e., information of its genome sequence are lacking, only a few protein sequences are included in the most widely known protein sequence databases. To improve both the number of identified proteins and data reliability, identification was performed integrating the results obtained with three distinct plant protein databases, since the majority of proteins could only be attributed by homology with other plant species. Nevertheless, many proteins had assigned only one unique peptide, because of the phylogenetic distance of pomegranate from the main model plants. After manual revision of the identified proteins to eliminate the redundant or ambiguous identifications, a list of 1,488 proteins was obtained, only six of which belonging to pomegranate species. To the author's best knowledge, this is the first work aimed at the proteomic characterization of Punica granatum.     

A concise synthesis of (3S,4S,5R)-1-(α-d-galactopyranosyl)-3-tetracosanoylamino-4,5-decanediol, a C-glycoside analogue of immunomodulating α-galactosylceramide OCH

A concise and convergent synthesis of the C-glycoside analogue 2b of immunomodulating α-galactosylceramide OCH 1b starting from readily available 2,3,4,6-tetra-O-benzyl-d-galactose 3 and l-arabinose 6 is described. The synthesis features the nucleophilic addition of an α-ethynyl sugar 5 to the phytosphingosine-precursor aldehyde 9 and would be applicable to a variety of C-glycoside analogues of interest.